3DW1 | pdb_00003dw1

Proteinase K by LB nanotemplate method after the third step high X-Ray dose on ESRF ID14-2 beamline

PDB DOI: https://doi.org/10.2210/pdb3DW1/pdb

Classification: HYDROLASE
Organism(s): Parengyodontium album
Mutation(s): No

Deposited: 2008-07-21 Released: 2009-07-07
Deposition Author(s): Pechkova, E., Tripathi, S.K., Nicolini, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.211 (Depositor), 0.211 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Radiation damage in protein structural characterization by Synchrotron Radiation: State of the art and Nanotechnology-based perspective

Pechkova, E., Tripathi, S.K., Nicolini, C.

To be published.

Macromolecule Content

Total Structure Weight: 28.97 kDa
Atom Count: 2,220
Modeled Residue Count: 279
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase K	A [auth X]	279	Parengyodontium album	Mutation(s): 0 EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album) Explore P06873 Go to UniProtKB: P06873
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06873
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.211 (Depositor), 0.211 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.012	α = 90
b = 68.012	β = 90
c = 102.311	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary

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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.