3CQB | pdb_00003cqb

Crystal structure of heat shock protein HtpX domain from Vibrio parahaemolyticus RIMD 2210633

• PDB DOI: https://doi.org/10.2210/pdb3CQB/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-02 Released: 2008-05-27 
• Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

The crystal structure of heat shock protein HtpX domain from Vibrio parahaemolyticus RIMD 2210633.

Wu, R., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.81 kDa 
• Atom Count: 1,772 
• Modeled Residue Count: 204 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable protease htpX homolog	A, B	107	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: htpX, VP1118 EC: 3.4.24
UniProt
Find proteins for Q87QN1 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87QN1  Go to UniProtKB:  Q87QN1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.873	α = 90
b = 75.873	β = 90
c = 65.471	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary