4JQO

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with citrulline and inorganic phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal structures and kinetic properties of anabolic ornithine carbamoyltransferase from human pathogens Vibrio vulnificus and Bacillus anthracis

Shabalin, I.G.Winsor, J.Grimshaw, S.Minor, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine carbamoyltransferase
A, B, C
358Vibrio vulnificus CMCP6Mutation(s): 0 
Gene Names: argFVV1_1466
EC: 2.1.3.3
UniProt
Find proteins for Q8DCF5 (Vibrio vulnificus (strain CMCP6))
Explore Q8DCF5 
Go to UniProtKB:  Q8DCF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DCF5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIR
Query on CIR

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C]
CITRULLINE
C6 H13 N3 O3
RHGKLRLOHDJJDR-BYPYZUCNSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
M [auth B]
N [auth B]
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B],
O [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
Q [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.418α = 90
b = 82.597β = 90
c = 171.968γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
CCP4phasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.2: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection