Macromolecule Content

Total Structure Weight: 123.02 kDa
Atom Count: 8,512
Modelled Residue Count: 1,002
Deposited Residue Count: 1,074
Unique protein chains: 1

4H31

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

PDB DOI: 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.167
R-Value Work: 0.135
R-Value Observed: 0.137

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DCF5
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE5 Query on PE5 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain Z [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain Z [auth B]	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		Ligand Interaction
CP Query on CP Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain DA [auth C] SDF format, chain E [auth A] MOL2 format, chain R [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A]	DA [auth C], E [auth A], R [auth B]	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H₄ N O₅ P FFQKYPRQEYGKAF-UHFFFAOYSA-N		Ligand Interaction
NVA Query on NVA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain D [auth A] SDF format, chain Q [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth B]	BA [auth C], D [auth A], Q [auth B]	NORVALINE C₅ H₁₁ N O₂ SNDPXSYFESPGGJ-BYPYZUCNSA-N		Ligand Interaction
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain I [auth A] SDF format, chain O [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain AA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain X [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B]	AA [auth B], FA [auth C], G [auth A], GA [auth C], H [auth A], 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		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain N [auth A] SDF format, chain T [auth B] SDF format, chain V [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B]	CA [auth C], IA [auth C], J [auth A], N [auth A], T [auth B], CA [auth C], IA [auth C], J [auth A], N [auth A], T [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.167
R-Value Work: 0.135
R-Value Observed: 0.137
Space Group: P 2₁ 2₁ 2₁
Diffraction Data DOI: 10.18430/M3RG6V

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2022-04-13
Changes: Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.