Earlier news is available and is archived in the
Best wishes for a happy holiday season and a wonderful new year! 2008 highlights have included the release of the
structure in the archive and the 100th
Molecule of the Month; the educational Looking
at Structures feature; resources for deposition, such SF-Tool for structure factor
files; website tools like the enhanced RSS
feed and a browser compatability check; and the wwPDB's publication of the
Comprehensive Format Guide Version 3.2.
For even more developments, check out the 2008 RCSB PDB Annual Report
Where are all the hydrogen atoms in this file? Should I care about the R-factor? Why are there 20 overlapped structures in my file?
These questions and many others are explored in the RCSB PDB's new
Using text, images, and interactive Jmols,
Structures intends to help researchers and educators get the most out of the PDB archive. Broad topics include how to
understand PDB data, how to visualize structures, how to read coordinate files, and potential challenges in exploring the archive.
A Table of Contents appears on the right side of every page so at any time users can access the individual pages:
Dealing with Coordinates,
Methods for Determining Structure,
Missing Coordinates and Biological Units,
Molecular Graphics Programs,
R-value and R-free.
Structures is available from the General Education section of the left-hand menu.
The RCSB PDB is currently looking for new people to join our team.
Available positions include a Java Developer, a Scientific Software
Developer and a System Administrator.
For more details, please see the RCSB PDB Job Listings page.
The 2008 Annual Report
(PDF) highlights current progress and accomplishments, and explores the RCSB PDB's
different activities in data deposition, query, and education. This publication is currently being
distributed to the diverse community of PDB users in academia, industry, and education. If you would
also like a printed copy, please send your postal address to email@example.com.
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A new standardized version of the PDB archive will be available from
ftp://ftp.wwpdb.org in early 2009.
All entries released prior to December 2, 2008 will be re-released as PDB Format
Version 3.15 files. This release will overwrite all existing files.
A snapshot of the archive before this release will be available from
For documentation, please see www.wwpdb.org/docs.html
Questions may be sent to firstname.lastname@example.org.
Beginning December 2, 2008, all newly-released PDB entries will follow PDB File Format Contents Guide Version
HTML). This format includes site and assembly annotation, and supports the nomenclature introduced
in 2007 in the Chemical Component Dictionary. The Version 3.20 Changes Guide highlights the lists changes in
format from 3.1.
Please send any questions to email@example.com.
Sequence Details pages for all protein structures now include a Jmol view of the structure that
can display domain annotations from SCOP,
To activate this view from a structure summary page, first select the Sequence Details tab. The
default view displays a 2D graphical representation of the UniProt,
PDB-ATOM and PDB-SEQRES sequences. Users can also select third-party domain annotations from this 2D
image to appear to the corresponding structure in a Jmol
To view these annotations mapped onto the 3D structure, select [show 3D in Jmol] from the top of the page.
Then, click on any of the domains on the sequence view. The corresponding colors for that domain will appear
in the 3D Jmol viewer. The annotations shown in Jmol can change by clicking on an annotation shown in the 2D
By default, the Jmol window stays positioned on the top of the page. Select [dynamic Jmol position]
to have the Jmol viewer adjust so that it is always to the top right of the page as you scroll down.
Interested in an older Education Corner from the Newsletter? Want to know what papers have been published that discuss
the project? Looking for a flyer to guide you through the deposition process? The
News and Publications
page offers access to all RCSB PDB publications. Located in the General Information section of the
left-hand menu, this page archives our Annual Reports that describe the history, mission, and accomplishments of the
project; Publications in peer-reviewed journals; weekly News about new features and events; the quarterly Newsletter;
To request printed versions of any of these documents, please send your mailing address to
When depositing many structures that are related to one another, there are a few ways of making
the ADIT/ADIT-NMR deposition process simpler:
pdb_extract takes information about data collection, phasing, density modification, and the final structure
refinement from the output files and log files produced by the various applications used for structure
determination. The collected information is organized into a file ready for deposition using ADIT/ADIT-NMR.
The "author information form"
contains author names, citation information, protein names and source--the types of information that are
repeated in multiple related entries. This form can be filled out once and used with pdb_extract to prepare
several structures for deposition.
The Fall edition of the RCSB PDB Newsletter (HTML |
PDF) describes how Ligand Expo can be used to
deposit structures, and announces the Comprehensive Format Guide for the PDB File Format (Version 3.2).
Other highlights include the enhanced RSS feed for PDB structures and searches based on PubMed abstracts
at the RCSB PDB website.
The origin and applications of the iPhone program Molecules is described in this quarter's
Education Corner by Brad Larson (Sunset Lake Software).
In the Community Focus, Paul D. Adams (Lawrence Berkeley Laboratory) discusses PHENIX, the Technology
Port of the PSI Structural Genomics Knowledgebase, and his work at the Joint BioEnergy Institute.
If you would like to receive a printed version of the RCSB PDB quarterly newsletter, please send your
postal address to firstname.lastname@example.org.
Subscription information for the plain text electronic version is also available.
The RCSB PDB offers an RSS (Really Simple Syndication) feed that provides users with a list
of newly updated structures as soon as they are released. Based upon user feedback, this weekly
feed now includes each PDB ID and structure title. Subscribers to this feed can quickly scan the
list for structures of interest.
To start, select an RSS reader. Many RSS feed readers are already packaged with web browsers and
email programs, while others are available as dedicated programs or websites.
To incorporate the RCSB PDB feed, either drag or select the orange RSS icon from the top of the
RCSB PDB home page (located just next to the latest release date) and add the URL for new structures
to your reader.
Congratulations to the awardees of the
2008 Nobel Prize in Chemistry
for the discovery and development of the green fluorescent protein (GFP)--Osamu Shimomura (Marine Biological Laboratory,
Woods Hole, MA and Boston University Medical School), Martin Chalfie (Columbia University), and Roger Y. Tsien (University
of California, San Diego).
To learn more about GFP from a molecular point of view, the
June 2003 Molecule
of the Month feature discusses its structure and function.
Bioinformatics of Green Fluorescent Protein is a tutorial that uses visualization tools from the RCSB PDB
website to examine this protein.
The RCSB PDB Poster Prize
for best student poster related to macromolecular
crystallography at the XXI Congress & General Assembly of the International
Union of Crystallography (IUCr; August 23 - 31 in Osaka, Japan) was awarded for
"Structural insights into the mitochondrial import complex, TIM9.10"
by Chaille T. Webb,1,2 Michael Baker,1 Michael T. Ryan,1
Peter M. Colman,1 and Jacqueline M. Gulbis1
and Eliza Hall Institute of Medical Research and 2The University of Melbourne,
Webb will receive a subscription to Science and a copy of the International Tables for Crystallography.
Thanks to all of the participating students and the judging committee.
PubMed abstracts for the primary citations of PDB entries are integrated with the RCSB PDB website.
For query results of multiple structures, the Citations Tab provides a PubMed-like list of the corresponding primary citations.
This list can be downloaded in Medline format for use with bibliographic programs such as Endnote and RefWorks by selecting
the "Medline Format" option from the lefthand menu. The Citations Tab also links to all structures that share a primary
citation, and to related articles in PubMed.
For each PDB structure, the "Abstract" link on a Structure Summary page provides
information downloaded from PubMed about the citation. The keywords, title, and abstract
on this page can be used to query the PDB for other entries that have the same words in
their abstracts. The citation information can be downloaded in Medline format by
selecting the "Medline Format" option from the lefthand menu.
Selecting the PubMed icon takes users to the abstract in PubMed.
Using the Advanced Search, PubMed keyword searches can be combined with any other query option.
archives chemical and structural information about
all residue and small molecule components found in PDB entries.
is a new
tool that can access, visualize, and build reports about these data. It
can also be used to prepare a file for deposition:
Ligand Expo capabilities have been described
and in a
flyer available for download.
During the past year, the wwPDB annotators have collaborated on a
project to clarify the details and procedures related to data
processing and annotation. The result is a PDB Contents Guide Version
3.2 that more fully describes the
file format. This document is available as a
and is accompanied by
document highlighting these clarifications.
In the coming months, all files released by the wwPDB will follow the
format as described in this document. Details will be made available on
this website and at
The wwPDB and related resources will be discussed at several meetings
in September. In addition to the wwPDB Advisory Committee meeting to be
held on September 29, the following presentations will be made:
Detailed information about the wwPDB is also available at
PDB Poster Prize for best student poster related to structure and
function prediction at the
16th Annual International
Conference on Intelligent Systems for Molecular Biology (July 19-23,
2008; Toronto, Canada) went to Dariya Glazer for "Clustering Across
Space and Time" (Dariya Glazer, Randy Radmer, Russ Altman, Stanford
Glazer will receive a subscription to Science and a reference book.
Thanks to everyone who participated, especially our judges: Marco Punta
(Committee Chair), Yana Bromberg, Columbia; Matteo Dal Peraro, Ecole
Polytechnique Federale de Lausanne; Claudia Dall'Armi, Columbia; Marco
DeVivo, Rib-X Pharmaceuticals, Inc.; Zsuzsanna Dosztanyi, Markus
Fischer, Laszlo Kajan, Andrew Kernytsky, Rajesh Nair, Avner
Schlessinger, Ta-tsen Soong, Columbia University; and the International
Society for Computational Biology, particularly Steven Leard.
The PDB contains biomolecular polymers including polypeptides, polynucleotides, polysaccharides, and their complexes.
Polypeptide structures containing 24 or more residues can be deposited
to the PDB. Smaller peptides that are complexed with a larger polymer
(greater than the minimum length defined above) may be deposited to the
PDB. Crystal structures of peptides with fewer than 24 residues, such
as antibiotics, should be sent to the
Data Centre (CCDC).
Polynucleotide structures with 4 or more residues are accepted at the
PDB. Smaller oligonucleotides (dinucleotides and trinucleotides) can be
deposited at the
Nucleic Acid Database
Coordinates for the repeating unit of fibrous polymers and
polysaccharide structures with 4 or more sugar residues may be
deposited at the PDB archive. Molecules that do not conform to these
guidelines but have been previously deposited in the archive will not
Structures may be deposited to the archive via the
worldwide Protein Data Bank.
Downloads from the PDB archive are one of the primary means of accessing scientific structure results.
While there are cross-links between the corresponding scientific publication and the PDB entry,
in many cases it is the structure file that is accessed and downloaded more frequently.
The wwPDB website has recently added
statistics for FTP and HTTP (web) downloads and views for each PDB structure.
The high volume of data downloaded around the world underscores the importance of including informative,
accurate, and annotated PDB data in the archive. Data are available by month, starting from August 2007,
for each wwPDB site. These statistics can be accessed a number of ways:
All download statistics are updated monthly, and collected on an aggregate, rather than individual, basis.
The wwPDB does not share server log information with third parties for marketing or other purposes.
To access these features, select Statistics>Downloads from the top menu bar at
www.wwpdb.org. The wwPDB website also offers
links to member sites, documentation, news, and deposition and processing statistics.
Questions may be sent to email@example.com.
The wwPDB partners will be exhibiting at the
XXI Congress & General
Assembly of the International Union of Crystallography (IUCr; August
23 - 31 in Osaka, Japan) at booth #14. Please stop by for website
demonstrations and to meet with wwPDB members from around the globe.
RCSB PDB Director Helen M. Berman will present a keynote lecture
entitled "What the Protein Data Bank tells us about the past,
present, and future of structural biology" on Sunday August 24.
On Saturday, August 30, John Westbrook will present "Data Quality in
the PDB Archive".
The RCSB PDB Poster Prize
will be awarded to the best student poster at the meeting and announced at the awards ceremony.
To participate, please place the RCSB PDB sticker available at the meeting onto your poster.
PDB structures can be cited using their PDB ID and the related published citation.
Structures may also be referenced using their Digital Object Identifier (DOI).
These DOIs are formatted as 10.2210/pdbXXXX/pdb - where XXXX is the PDB ID.
For example, the DOI for entry 4HHB is "10.2210/pdb4hhb/pdb".
This DOI can be used in a URL
or entered in a DOI resolver (such as
to automatically link to pdb4hhb.ent.Z in the main PDB FTP archive.
DOIs are also available for each RCSB PDB Molecule of the Month feature with the format:
10.2210/rcsb_pdb/mom_YYYY_MM (where YYYY is the year, and MM the number of the month, one or two digits).
For example, the DOI for the May 2003 feature on hemoglobin by Shuchismita Dutta and David S. Goodsell is
An RCSB PDB Molecule of the Month feature may be referenced using the DOI and the author/s of the article.
A page describing
policies & references
for using and citing PDB data and RCSB PDB resources is available.
A structure can be deposited over a period of time by using ADIT's
"Session Restart ID" feature. This identifier appears in red
in the center of the browser window when ADIT's "deposit"
step is first started. It is also seen in the title of the browser
throughout the deposition session.
The case-sensitive restart ID should be entered in the space provided
on the ADIT home page to return to the deposition session. Any data
entered in a category are stored every time the user selects the SAVE
button. All entered data associated with a particular entry can be
accessed using the restart ID until the "DEPOSIT NOW" button
is selected, for up to six months after the session has been last
ADIT is available at the
ADIT-NMR can be used to deposit data to both the
PDB and BMRB.
A tutorial guide to using ADIT is available in
Japanese. Example "in progress"
deposition sessions are available to practice learning how to use ADIT
The Summer edition of the RCSB PDB Newsletter
new deposition tools, such as SF-Tool and Ligand Expo, and explores
usage statistics for PDB data. The New Jersey and National Protein
Modeling events at the Science Olympiad are described, along with
recent presentations and publications.
In this quarter's Education Corner, Judy Voet (Swarthmore) and Donald
Voet (University of Pennsylvania) discuss Biochemistry and Molecular
Biology Education (BAMBED), a Journal for University, College, and High
John Norvell (NIGMS) discusses his career, NIGMS, and the Protein
If you would like to receive a printed version of the RCSB PDB
quarterly newsletter, please send your postal address to
information for the plain text electronic version is also available.
The 2007 release of remediated data improved the representation of
deposited and experimental coordinate frames, symmetry, and frame
transformations in the archive. A paper describing the scheme used by
the wwPDB to represent viruses and other biological assemblies with
regular noncrystallographic symmetry has been published:
Acta Cryst. (2008). D64, 874-882 [
Representation of viruses in the remediated PDB archive
C. L. Lawson, S. Dutta, J. D. Westbrook, K. Henrick and H. M. Berman
Stop by exhibit booth #19 at the 16th Annual International Conference
for Intelligent Systems for Molecular Biology
(ISMB) to visit with the
RCSB PDB (July 19-23; Toronto, Canada). Also at this meeting, the
PDB Poster Prize will be awarded for the outstanding student poster in
the "structure and function prediction" category. Associate Director
Phil Bourne will be involved with presentations and discussions,
including a 3DSig Keynote Lecture at the Structural Bioinformatics and
Computational Biophysics satellite meeting.
At the 22nd Annual Symposium of
Protein Society (July 19-23; San Diego, CA), Peter Rose will present
the poster "Effective Mining of the Protein Data Bank".
Other upcoming meetings include presentations and a wwPDB exhibit booth
at the XXI Congress and General Assembly of the
International Union of
Crystallography (August 23-31; Osaka, Japan).
The San Diego Supercomputer Center (SDSC) hosts servers used by the
RCSB PDB. On July 8-9, 2008, SDSC will perform necessary repairs
and maintenance on an electrical transformer.
We anticipate providing uninterrupted service during this time through
off-site failover servers located at the Skaggs School of Pharmacy and
Rutgers University for the following resources:
RCSB PDB deposition services will not be affected. The update to the
website and FTP site will proceed as scheduled.
The following services will NOT be available during this time:
Email sent to
RCSB PDB members with an sdsc.edu address will be queued and delivered
after the maintenance has been completed.
The Chemical Component Dictionary archives chemical and structural
information about all of the small molecules found within PDB structure
entries. Ligand Expo
is a new tool that can access, visualize, and build reports about these
With Ligand Expo, users can also
Ligand Expo is an update of the Ligand Depot resource.
PDB Poster Prize for best student poster related to macromolecular
crystallography at the American Crystallographic Association's Annual
Meeting (May 31 - June 5, 2008; Knoxville, TN) went to Wei Yong for
"X-ray crystallographic studies of pig sarcosine dehydrogenase" (Wei
Yong, Ila Misra, Jung-Ja Kim, Medical College of Wisconsin).
Yong will receive a subscription to
Science and an
International Tables of Crystallography volume of his choosing.
Thanks to everyone who participated, especially our judges: Robert Rose
(Chair; North Carolina State University); Gloria E.O. Borgstahl (Eppley
Institute for Cancer Research and Allied Diseases); Antonella Longo
(North Carolina State University); Robert McKenna (University of
Florida); Joseph E Wedekind (University of Rochester).
The RCSB PDB Poster Prize will also be awarded this year at the 16th
Annual International Conference on Intellligent Systems for Molecular
Biology (July 19-23, 2007; Toronto, Canada) and the Congress and
General Assembly of the International Union of Crystallography (August
23-31, 2008; Osaka, Japan).
A meeting of the wwPDB X-ray Validation Task Force was held to collect
recommendations and develop consensus on additional validation that
should be performed on PDB entries, and to identify software
applications to perform validation tasks.
The workshop was organized by Randy Read (Cambridge University), and
sponsored by the RCSB PDB & PDBe. Detailed information about the
workshop is available at
A plain text file containing sequence and secondary structure
information in FASTA format for all structures is available from
A separate file,
includes disordered regions in addition to the secondary structure.
These files, which replace analogous ones previously found in the FTP tree, are updated weekly.
Exhibit booth #500 at the 2008 Meeting of the American Crystallographic
Association will be the place to find out about the latest RCSB PDB
developments. Please stop by to see demonstrations of
a new tool for exploring the small molecules found in PDB entries,
a resource for validating and translating crystallographic
Approximately 140,000 unique visitors explore the RCSB PDB website at
www.pdb.org each month (as identified by a unique IP address). During
this period, these users download more than 500 GB (GigaBytes) of data.
At the same time, about 7,000 unique visitors download more than 10
million files from the FTP site at ftp://ftp.wwpdb.org, for a total of
about 2 TB (TeraBytes) of data. The PDB archive is also accessed
through FTP sites supported by
wwPDB members MSD-EBI and PDBj.
There were more than 100 million FTP file downloads, with peak rates of
more than 10 files per second, during the six-month period that
followed the August 2007 release of the archive of remediated data. In
comparison, less than 10 million files were downloaded in all of the
Visitors from 150 countries visit the RCSB PDB FTP and website.
Approximately one third of all visitors are from the United States,
another third from Europe, and a third from the rest of the world.
Since users are accessing data from around the globe, traffic is evenly
distributed over the course of 24 hours. On an average day, download
rates never drop below 50% of peak daytime values.
Standard server log information, such as IP address, time spent on the
site, browser type, etc., is collected and assessed on an aggregate,
rather than individual, basis in order to track site statistics, data
that are most popular to our visitors, performance monitoring, and
troubleshooting. Studying access statistics and usage patterns helps to
project future hardware needs, and aids in the design of new
functionality. We also use this information for site and system
security. We do not share server log information with third parties for
marketing or other purposes.
A streamlined, web-based tool is available for validating
crystallographic experimental data.
can be used to:
for this program is available. Questions, comments, and suggestions
should be sent to
The Spring edition of the RCSB PDB Newsletter has been published in
PDF formats. This issue
highlights deposition tools, including a tool for converting structure
factor files between a variety of formats, and two sites for depositing
electron microscopy map data. The different types of statistics about
data in the PDB archive are described, and recent outreach activities
In this quarter's Education Corner, Jeramia Ory (Kings College)
describes how he uses Chimera to create molecular multimedia in his
Christine Orengo (University College London) is the subject of this
quarter's Community Focus. In this feature, Dr. Orengo discusses CATH,
her research, and the development of
The Protein Chart, a "periodic table" of proteins.
The girls at Princeton High School held on to their
by coming in first place at the
2008 Protein Modeling
event at the Science Olympiad State Finals in New Jersey for the second year in a
Teams from all over the Garden State presented their hand-built 3D
models of a calmodulin protein, along with an abstract, to be judged by
staff from the RCSB PDB. At the competition, teams built a model of a
selected region of the structure using Jmol and took a written exam
about the structure.
Teams used the
Molecule of the Month, among other RCSB PDB resources, to help
prepare for this event.
The highest ranking teams were Princeton High School (First Place),
Livingston High School (Second), and West Windsor-Plainsboro High
School North (Third).
Congratulations to all participating teams--there were many great
models, abstracts, and responses to the written exam. Pictures of the
event and rubrics used in judging are available at
Questions about the NJ Science Olympiad Protein Modeling trial event
should be sent to
Special thanks to our judges from the RCSB PDB (Andrei Kouranov,
Chenghua Shao, Irina Persikova, Jasmine Young, Jing Zhou, and Christine
Zardecki (Event Supervisor)), the
NJ Science Olympiad
organizers, and to the
MSOE Center for BioMolecular
Modeling for the design of this event.
"National DNA Day" is April 25. Commemorating the completion of the
Human Genome Project in 2003 and the discovery of DNA's double helix,
DNA Day encourages teachers and students to celebrate these historic
achievements. Online resources relating to DNA Day include:
Two wwPDB papers describing deposition have been recently published.
With this week's update, the PDB archive reached a significant
milestone in its 37-year history: The holdings now contain more
than 50,000 current experimental structures.
The worldwide Protein Data Bank
(wwPDB) has seen the archive
double in size since 2004. The PDB was founded in 1971 with seven
structures at Brookhaven National Laboratory. Today, the wwPDB receives
approximately 25 new experimentally-determined structures from
scientists each day for inclusion in the archive. More than 5 million
files are downloaded
from the PDB archive every month. Users
include structural biologists, computational biologists, biochemists,
and molecular biologists in academia, government, and industry as well
as educators and students.
It is estimated that the size of the PDB archive will triple to 150,000 structures by the year 2014.
The 50,000 structure mark was reached after another milestone
event--the publication of the 100th edition of the Molecule of the
Proteins, one of the main building blocks for living organisms, come in
a variety of shapes, with the form of a protein corresponding to its
function. The structures housed in the PDB demonstrate great diversity
in size, complexity, and function, including:
This month's feature on
receptors is the 100th installment of
Molecule of the Month. Since January 2000, this series has
explored the structure and function of proteins and nucleic acids found
in the PDB archive such as
resistance transporters. To commemorate this event, the RCSB PDB will
be offering temporary tattoos of an adrenergic receptor at upcoming
meetings. The feature is also available in a specially formatted
available for download.
Written and illustrated by David S. Goodsell (The Scripps Research
Molecule of the Month provides an easy introduction to the RCSB
PDB for teachers and students. It is used in many classrooms to
introduce structures to students, and is an integral part of the
protein modeling event at the
The text and images are related to the featured molecule;
the RCSB PDB pages link to examples of the molecule. In
response to requests, a view of the highlighted structure in
is included in new features to provide an interactive view of the
Molecule of the Month features are made available from the RCSB
PDB home page with the first update of each month. Alphabetical
chronological listings of past issues are provided. PDBj has recently
started to translate the
Molecule of the Month into Japanese.
Links to the series are also available from RCSB PDB's Structure
Explorer pages. Selecting "Learn more: [M]" takes the reader to
any Molecule of the Month feature related to that particular entry.
For a description of how the series is created, please see the RCSB PDB
Newsletter's PDB Focus on David Goodsell.
PDB entries are processed by three members of the wwPDB (RCSB PDB,
MSD-EBI, and PDBj) and are released immediately (REL), when the
corresponding paper is published (HPUB), or on a particular date
(HOLD). There is also a one-year limit on both HPUB and HOLD status
after which a structure with no major issues can be released even if
there is no corresponding publication.
Each week, all files scheduled for release or modification are checked
and validated one final time. Authors may be contacted to resolve any
issues that may arise while preparing the entries for release.
When the release of HPUB structures is requested, the wwPDB routinely
confirms the primary citation. If this is not accomplished within that
release cycle, the entry may be scheduled to be released in a later
To be included in the next weekly update, any required author
correspondence should be sent to the appropriate wwPDB member by the
All entries due for release are transferred to the RCSB PDB for final
packaging into the master PDB ftp archive. These files are then
released by 4:00 EST each Wednesday.
Requests received after these cutoff times will be processed during the
next update cycle.
PubMed abstracts are accessible from a published entry's Structure
Summary page. The "Abstract" link returns a page with the article
title, abstract, keywords, authors, organizational affiliation,
journal, and PubMed identifier. The
PubMed abstract at
can also be viewed by clicking on the icon next to "Abstract".
The text box at the bottom of the Abstract page can be used to search
for related structures in the PDB using any word in the abstract or
keyword fields. Terms can be entered into the text box either by typing
the word manually or by clicking the mouse over any word in the
abstract or the keyword fields.
Positions with the RCSB PDB include openings at the University of
California, San Diego for a Scientific Software
Developer and for a Lead Web Architect.
A chapter describing the various options and procedures for querying,
downloading and validating 3D structures from the RCSB PDB website was
published in Current Protocols in Bioinformatics in December
2007. This is an update of the chapter with the same title that was
published in 2005.
S. Dutta, H.M. Berman and W.F. Bluhm: Using the Tools and Resources of the RCSB Protein Data Bank
Current Protocols in Bioinformatics (December 2007) 1.9.1-1.9.24.
(journal subscription required for full text)
The RCSB PDB will be exhibiting at a
& Learning Celebration on March 7-8 in New York City. Thousands of
educators and policy makers from the Tri-State are expected to attend.
It's still not too late for educators to take our online
survey. Do you use the Molecule of the Month?
Teach classes? Use the RCSB PDB when working with students? Then we
want to hear from you! The RCSB PDB is looking for feedback about the
educational resources available from our website, and in particular,
the types of educational activities and resources that are of interest
to our users.
We greatly appreciate your participation in this survey. As a token of
appreciation, we will send temporary tattoos of tRNA to survey
respondents who send their postal address to
Which journal has published the most structures? What structures have
been solved by more than one experimental method? Answers to these
questions can be found by exploring the various statistics about the
data in the PDB archive available by clicking the "PDB Statistics" link
at the top of every page on the RCSB PDB website.
Charts, graphs, and tables related to content distribution include
The growth of structures released in the PDB archive can be viewed per
year, by experimental method, and by molecule type. Other graphs show
the growth of unique protein classifications as defined by SCOP and
Positions with the RCSB PDB include openings at the University of
California, San Diego for a Senior Scientist/Scientific Software
Developer and for a Lead Web Architect.
Sculptures and photographs by
Voss-Andreae are currently on display at Rutgers Student Center (New
Brunswick, NJ) until February 22, 2008.
Voss-Andreae's unique sculptures are designed to tell stories
about hemoglobin, collagen, and other structures essential to life.
Julian Voss-Andreae is a German-born sculptor based in Portland, He
graduated from the Pacific Northwest College of Art (PNCA) in 2004 with
a BFA in sculpture. While still at PNCA, Voss-Andreae developed a novel
kind of sculpture based on the structure of proteins, the building
blocks of life. Voss-Andreae's work has been commissioned
internationally and has been highlighted in journals such as Leonardo
Photographs of Voss-Andreae's sculptures are part of the RCSB PDB's Art
of Science traveling exhibit, which also features images available from
the RCSB PDB website and the Molecule of the Month. For more
information on hosting this exhibit, please contact firstname.lastname@example.org.
With a sleek new format, the latest RCSB PDB Newsletter has been
formats. This issue describes a new version of ADIT that was developed
to improve data accuracy and consistency, new outreach programs, and
the publication of the 2007 Annual Report.
In this quarter's
Corner, Teresa MacDonald (The University of Kansas Natural History
Museum) describes edible protein models.
Focus looks at this year's New Jersey Science Olympiad competition.
Subscription information for the plain text electronic version is
Electron microscopy map data can now be deposited to the EMDB using the
improved web-based tool EmDep2. EmDep2 is available from the
existing deposition site at the EBI in Europe and at a new deposition
site at the RCSB PDB in the USA.
The Electron Microscopy Data Bank (EMDB) contains experimentally
determined three-dimensional maps and associated experimental data and
This improvement to EMDB services is the first product of a
collaboration beween the European Network of Excellence 3D-EM
and the recently NIH-funded partnership for
a Unified Data Resource for CryoEM
European Bioinformatics Institute, the Research Collaboratory for
Structural Bioinformatics at Rutgers, and the National Center for
Macromolecular Imaging at Baylor College of Medicine.
EmDep2 (EBI): http://www.ebi.ac.uk/msd-srv/emdep/
EmDep2 (RCSB PDB): http://emdb.rutgers.edu/emdep/
The PDB archive has grown from its early beginnings in 1971 as a
handwritten petition signed by crystallographers to its current status
as an online biological database and resource used by a diverse
community of teachers, students, and researchers in academia and
This history is described in an article published in an issue of
Acta Crystallographica that commemorates
milestones in the crystallographic community. Intended for a broad
in this issue describe powerful and diverse uses of crystallography,
along with a look at the
of publishing by the International Union of Crystallography.
Protein Data Bank: a historical perspective (2008) Acta Cryst. A64:
88-95. doi: 10.1107/S0108767307035623
Many models of the structure calmodulin were built by high school
students for the RCSB PDB-sponsored Protein Modeling event at the
Northern and Central New Jersey Science Olympiad.
This year's protein modeling competition has three components. Students
first build a model of the full calmodulin structure
and bring it to be impounded in the morning for judging. In this model,
teams are encouraged to include additions and an abstract that help to
illustrate the function of the structure.
At the event itself, teams build a portion of PDB entry 1cll with a
(from www.3dmoleculardesigns.com). They also answer
questions about the structure, function, importance, and history of the
modeled protein. For all sections of the event, students use the
Molecule of the Month,
the PDB file, Jmol
and the Structure Explorer page for 1cll.
Detailed information about this event is available at
At the Central New Jersey Regional held at Princeton University,
Bridgewater-Raritan High School came in first; South Brunswick High
School, second; and West Windsor-Plainsboro High School North, third.
At the Northern New Jersey Regional held at New Jersey Institute of
Technology, Livingston High School came in first; Westfield High
School, second; and Bergen County Academies, third.
The state finals will take place March 11, 2008 at Middlesex County
College in Edison, NJ.
Special thanks to our judges from the RCSB PDB (Shuchismita Dutta,
Sutapa Ghosh, Andrei Kouranov, Irina Persikova, Monica Sekharan,
Chengua Shao, Huangwang Yang, Jasmine Young, Christine Zardecki, and
Jing Zhou), the NJ Science Olympiad organizers, and to the
MSOE Center for BioMolecular Modeling
for the design of this event. We look forward to seeing everyone at the
state competition on March!
Remediation of the Protein Data Bank archive has
been published in
Nucleic Acids Research's 2008 Database Issue.
K. Henrick; Z. Feng; W. F. Bluhm; D. Dimitropoulos; J. F. Doreleijers;
S. Dutta; J. L. Flippen-Anderson; J. Ionides; C. Kamada; E. Krissinel;
C. L. Lawson; J. L. Markley; H. Nakamura; R. Newman; Y. Shimizu; J.
Swaminathan; S. Velankar; J. Ory; E. L. Ulrich; W. Vranken; J.
Westbrook; R. Yamashita; H. Yang; J. Young; M. Yousufuddin; H. M.
Nucleic Acids Research (2008) 36: D426-D433. doi:
All data in the PDB archive reflects the features incorporated as part
of this wwPDB project, including standardized IUPAC nomenclature for
chemical components, updated sequence database references and
taxonomies, improved representations of viruses, and more.
These data are available through the FTP archive and wwPDB member
Documentation about the Remediation Project is available at
A time-stamped snapshot of the PDB archive
(ftp.wwpdb.org) as of
January 7, 2008 has been added to
Snapshots of the PDB have been archived annually since 2004. It is
hoped that these snapshots will provide readily identifiable data sets
for research on the PDB archive.
The script at
may be used to make a local copy of a snapshot or sections of the
The directory 20080107 includes the 48,161 experimentally-determined
coordinate files that were current as of January 7, 2008. Coordinate
data are available in PDB, mmCIF, and XML formats. The date and time
stamp of each file indicates the last time the file was modified.
Data in the PDB archive currently follow either PDB File Format Version
3.0 or 3.1. This is indicated in REMARK 4 of the file.
Version 3.0 is the format used for files released as a result of the
Since August 1, 2007, all files processed and released into the archive
follow Version 3.1. When modifications are made to files released prior
to that date, they are then re-released in Version 3.1.
Version 3.1 differs in descriptions of the biological unit (REMARK
300/350), geometry (REMARK 500), atom/residues modeled as zero
occupancy (REMARK 475/480), non-polymer residues with missing atoms
(REMARK 610), and metal coordination (REMARK 620). Documentation
describing the differences between these versions is available at
Beginning March 4, 2008, it will be indicated in the REVDAT record with
the name "VERSN" when a Version 3.0 file is re-released as Version 3.1.
For example, if the journal record is updated in an entry that still
follows Version 3.0, the REVDAT would appear as:
REVDAT 1 04-MAR-08 1ABC 1 JRNL VERSN
REVDAT 1 13-FEB-07 1ABC 0
There is no change to how depositors submit their files. Any required
changes in nomenclature can be made automatically by the wwPDB during
the annotation process.
Documentation about file formats and the Remediation Project is
The command-line program sf-convert can easily translate data in
various formats to the mmCIF format for use with ADIT validation and
deposition software. sf_convert can also translate structure factors
already released in the PDB from mmCIF to different formats.
This tool can input files from the following programs and formats:
mmCIF, CIF, MTZ, CNS, Xplor, HKL2000, Scalepack, Dtrek, TNT, SHELX,
SAINT, EPMR, XSCALE, XPREP, XTALVIEW, X-GEN, XENGEN, MULTAN, MAIN, and
OTHER (an ASCII file with H, K, L, F, and SigmaF separated by a space).
sf-convert can then output the data formatted as mmCIF, MTZ, CNS, TNT,
SHELX, EPMR, XTALVIEW, HKL2000, Dtrek, XSCALE, MULTAN, MAIN, or OTHER.
Beginning February 1, 2008, structure factor files will be required
when depositing crystal structures to the PDB.
sf-convert is available for download from
The RCSB PDB's
Annual Report is currently being distributed. This snapshot provides
an introduction to the resource and to recent accomplishments in data
deposition, data access, and education. The 2007 report also describes
the highlights of the wwPDB's Remediation Project.
The report is available as a
If you would like a printed copy of the report, please send mail to
showcasing PDB structures is now available
Printed copies are also available via
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