2R39 | pdb_00002r39

Crystal structure of FixG-related protein from Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb2R39/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-08-29 Released: 2007-09-11 
• Deposition Author(s): Chang, C., Bigelow, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.238 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure of FixG-related protein from Vibrio parahaemolyticus.

Chang, C., Bigelow, L., Abdullah, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 13.28 kDa 
• Atom Count: 909 
• Modeled Residue Count: 109 
• Deposited Residue Count: 118 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FixG-related protein	A	118	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VP3052
UniProt
Find proteins for Q87KC5 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87KC5  Go to UniProtKB:  Q87KC5

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.238 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.567	α = 90
b = 74.567	β = 90
c = 49.36	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Chang, C., Bigelow, L., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary