1XVS | pdb_00001xvs

Crystal structure of apaG Protein from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb1XVS/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-28 Released: 2004-12-14 
• Deposition Author(s): Chang, C., Joachimiak, A., Li, H., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of apaG from Vibrio cholerae

Chang, C., Joachimiak, A., Li, H., Moy, S., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 29.04 kDa 
• Atom Count: 2,226 
• Modeled Residue Count: 248 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein apaG	A, B	126	Vibrio cholerae	Mutation(s): 4  Gene Names: apaG
UniProt
Find proteins for Q9KUS3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KUS3  Go to UniProtKB:  Q9KUS3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.01 Å
• R-Value Free:  0.266 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.138	α = 90
b = 67.998	β = 131.43
c = 64.002	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-14 
Deposition Author(s): Chang, C., Joachimiak, A., Li, H., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-12-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-09
  Changes: Structure summary