4JHX | pdb_00004jhx

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoylphosphate and arginine

• PDB DOI: https://doi.org/10.2210/pdb4JHX/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio vulnificus CMCP6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-05 Released: 2013-03-20 
• Deposition Author(s): Shabalin, I.G., Bacal, P., Winsor, J., Grimshaw, S., Grabowski, M., Chordia, M.D., Shuvalova, L., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.190 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.154 (Depositor) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 119.63 kDa 
• Atom Count: 8,271 
• Modeled Residue Count: 985 
• Deposited Residue Count: 1,074 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A, B, C	358	Vibrio vulnificus CMCP6	Mutation(s): 0  Gene Names: argF, VV1_1466 EC: 2.1.3.3
UniProt
Find proteins for Q8DCF5 (Vibrio vulnificus (strain CMCP6)) Explore Q8DCF5  Go to UniProtKB:  Q8DCF5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	F [auth A]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
CP	D [auth A], K [auth C]	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H4 N O5 P FFQKYPRQEYGKAF-UHFFFAOYSA-N
PEG	I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	E [auth A], G [auth B], H [auth B], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.190 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.154 (Depositor) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m3388n

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.029	α = 90
b = 79.387	β = 90
c = 147.169	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Shabalin, I.G., Bacal, P., Winsor, J., Grimshaw, S., Grabowski, M., Chordia, M.D., Shuvalova, L., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-03-20
  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