1XEA | pdb_00001xea

Crystal structure of a Gfo/Idh/MocA family oxidoreductase from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb1XEA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-09-09 Released: 2004-09-28 
• Deposition Author(s): R Rajashankar, K., Reynes, J.A., Kniewel, R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.271 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a Gfo/Idh/MocA family oxidoreductase from Vibrio cholerae

R Rajashankar, K., Reynes, J.A., Kniewel, R., Lima, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 147.87 kDa 
• Atom Count: 10,198 
• Modeled Residue Count: 1,244 
• Deposited Residue Count: 1,292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, Gfo/Idh/MocA family	A, B, C, D	323	Vibrio cholerae	Mutation(s): 7  Gene Names: VCA1048
UniProt
Find proteins for Q9KKQ4 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KKQ4  Go to UniProtKB:  Q9KKQ4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	E [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.271 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.529	α = 90
b = 112.835	β = 90
c = 177.214	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): R Rajashankar, K., Reynes, J.A., Kniewel, R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary