1R3D | pdb_00001r3d

Crystal structure of protein VC1974 from Vibrio cholerae, Pfam abhydrolase

• PDB DOI: https://doi.org/10.2210/pdb1R3D/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2003-10-01 Released: 2004-11-30 
• Deposition Author(s): Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.216 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Structural Genomics target NYSGRC-T920 related to A/B hydrolase fold.

Gorman, J., Shapiro, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.26 kDa 
• Atom Count: 2,149 
• Modeled Residue Count: 257 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
conserved hypothetical protein VC1974	A	264	Vibrio cholerae	Mutation(s): 4  Gene Names: VC1974 EC: 4.2.99.20
UniProt
Find proteins for Q9KQM4 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQM4  Go to UniProtKB:  Q9KQM4

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: 1.90 Å
• R-Value Free:  0.216 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.47	α = 90
b = 99.47	β = 90
c = 53.492	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-30 
Deposition Author(s): Gorman, J., Shapiro, L., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-11-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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: 2024-10-30
  Changes: Data collection, Database references, Structure summary