2Z6B | pdb_00002z6b

Crystal Structure Analysis of (gp27-gp5)3 conjugated with Fe(III) protoporphyrin

PDB DOI: https://doi.org/10.2210/pdb2Z6B/pdb

Classification: HYDROLASE/STRUCTURAL PROTEIN
Organism(s): Tequatrovirus T4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-07-28 Released: 2008-04-15
Deposition Author(s): Koshiyama, T., Yokoi, N., Ueno, T., Kanamaru, S., Nagano, S., Shiro, Y., Arisaka, F., Watanabe, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free:
0.315 (Depositor), 0.298 (DCC)
R-Value Work:
0.243 (Depositor), 0.230 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2Z6B

This is version 1.4 of the entry. See complete history.

Literature

Molecular design of heteroprotein assemblies providing a bionanocup as a chemical reactor.

Koshiyama, T., Yokoi, N., Ueno, T., Kanamaru, S., Nagano, S., Shiro, Y., Arisaka, F., Watanabe, Y.

(2008) Small 4: 50-54

PubMed: 18098245 Search on PubMed
DOI: https://doi.org/10.1002/smll.200700855
Primary Citation Related Structures:
2Z6B

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.

Macromolecule Content

Total Structure Weight: 108.89 kDa
Atom Count: 7,389
Modeled Residue Count: 941
Deposited Residue Count: 975
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail-associated lysozyme	A	584	Tequatrovirus T4	Mutation(s): 2 Gene Names: 5 EC: 3.2.1.17
UniProt
Find proteins for P16009 (Enterobacteria phage T4) Explore P16009 Go to UniProtKB: P16009
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16009
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate structural protein Gp27	B [auth D]	391	Tequatrovirus T4	Mutation(s): 0 Gene Names: 27
UniProt
Find proteins for P17172 (Enterobacteria phage T4) Explore P17172 Go to UniProtKB: P17172
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17172
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NEN Query on NEN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1-ETHYL-PYRROLIDINE-2,5-DIONE C₆ H₉ N O₂ GHAZCVNUKKZTLG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.315 (Depositor), 0.298 (DCC)
R-Value Work: 0.243 (Depositor), 0.230 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.536	α = 90
b = 138.536	β = 90
c = 389.121	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-04-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.