4H31 | pdb_00004h31

Crystal structure of anabolic ornithine carbamoyltransferase from Vibrio vulnificus in complex with carbamoyl phosphate and L-norvaline

• PDB DOI: https://doi.org/10.2210/pdb4H31/pdb

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


• Deposited: 2012-09-13 Released: 2012-09-26 
• Deposition Author(s): Shabalin, I.G., Winsor, J., Grimshaw, S., Osinski, T., 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: 1.70 Å
• R-Value Free: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Structural studies of ornithine carbamoyltransferase from various pathogens

Shabalin, I.G., Winsor, J., Grimshaw, S., Osinski, T., Chordia, M.D., Anderson, W.F., 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: 123.02 kDa 
• Atom Count: 8,512 
• Modeled Residue Count: 1,002 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE5	EA [auth C], F [auth A], Z [auth B]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
CP	DA [auth C], E [auth A], R [auth B]	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H4 N O5 P FFQKYPRQEYGKAF-UHFFFAOYSA-N
NVA	BA [auth C], D [auth A], Q [auth B]	NORVALINE C5 H11 N O2 SNDPXSYFESPGGJ-BYPYZUCNSA-N
PEG	AA [auth B], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], JA [auth C], K [auth A], L [auth A], M [auth A], O [auth A], P [auth A], S [auth B], U [auth B], W [auth B], X [auth B], Y [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	CA [auth C], IA [auth C], J [auth A], N [auth A], T [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m3rg6v

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.262	α = 90
b = 80.911	β = 90
c = 152.733	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Shabalin, I.G., Winsor, J., Grimshaw, S., Osinski, T., Chordia, M.D., Shuvalova, L., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-09-26
  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