4I2N | pdb_00004i2n

Crystal structure of 31kD Heat Shock Protein, VcHsp31 from Vibrio cholerae

PDB DOI: https://doi.org/10.2210/pdb4I2N/pdb

Classification: HYDROLASE
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-11-22 Released: 2013-11-27
Deposition Author(s): Das, S., Sen, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.223 (Depositor)
R-Value Work:
0.187 (Depositor), 0.193 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Temperature dependent structural flexibility and functional activation of 31kD Heat Shock Protein, VcHsp31 from Vibrio cholerae

Das, S., Sen, U.

To be published.

Macromolecule Content

Total Structure Weight: 189.04 kDa
Atom Count: 14,800
Modeled Residue Count: 1,686
Deposited Residue Count: 1,716
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intracellular protease/amidase	A, B, C, D, E A, B, C, D, E, F	286	Vibrio cholerae O395	Mutation(s): 0 Gene Names: A5F0Q0, VC0395_0351, VC395_A0912
UniProt
Find proteins for A0A0H3AFW5 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AFW5 Go to UniProtKB: A0A0H3AFW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3AFW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth D] SDF format, chain N [auth E] SDF format, chain P [auth F] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] MOL2 format, chain P [auth F] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E] mmCIF format, chain P [auth F] mmCIF format, chain I [auth B]	G [auth A], I [auth B], L [auth D], N [auth E], P [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth D] Focus chain N [auth E] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth D] Focus chain N [auth E] Focus chain P [auth F]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] SDF format, chain K [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain K [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain K [auth C]	H [auth A] J [auth B] K [auth C] M [auth D] O [auth E] H [auth A], J [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.223 (Depositor)
R-Value Work: 0.187 (Depositor), 0.193 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.514	α = 90
b = 79.094	β = 95.22
c = 133.132	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
AUTOMAR	data reduction
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-11-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-27
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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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.