3EY8 | pdb_00003ey8

Structure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1

• PDB DOI: https://doi.org/10.2210/pdb3EY8/pdb

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


• Deposited: 2008-10-20 Released: 2009-01-13 
• Deposition Author(s): Harrop, S.J., Deshpande, C.N., Sureshan, V., Boucher, Y., Xu, X., Cui, H., Chang, C., Edwards, A., Joachimiak, A., Savchenko, A., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.187 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Structure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1

Harrop, S.J., Deshpande, C.N., Sureshan, V., Boucher, Y., Xu, X., Cui, H., Chang, C., Edwards, A., Joachimiak, A., Savchenko, A., Curmi, P.M.G., Mabbutt, B.C.

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: 30.12 kDa 
• Atom Count: 2,400 
• Modeled Residue Count: 260 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biphenyl-2,3-diol 1,2-dioxygenase III-related protein	A, B	133	Vibrio cholerae	Mutation(s): 9  Gene Names: VC_A0328, VC_A0341, VC_A0463
UniProt
Find proteins for Q9K3D3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9K3D3  Go to UniProtKB:  Q9K3D3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 1.60 Å
• R-Value Free:  0.187 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.851	α = 90
b = 62.087	β = 90
c = 98.055	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-13 
Deposition Author(s): Harrop, S.J., Deshpande, C.N., Sureshan, V., Boucher, Y., Xu, X., Cui, H., Chang, C., Edwards, A., Joachimiak, A., Savchenko, A., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-30
  Changes: Structure summary