4JQO

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

PDB DOI: https://doi.org/10.2210/pdb4JQO/pdb

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

Deposited: 2013-03-20 Released: 2013-04-17
Deposition Author(s): Shabalin, I.G., Winsor, J., Grimshaw, S., Domagalski, M.J., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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
View more details

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.

Macromolecule Content

Total Structure Weight: 120.59 kDa
Atom Count: 8,297
Modelled Residue Count: 1,012
Deposited Residue Count: 1,074
Unique protein chains: 1

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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIR Query on CIR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C]	E [auth A], K [auth B], P [auth C]	CITRULLINE C₆ H₁₃ N₃ O₃ RHGKLRLOHDJJDR-BYPYZUCNSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	D [auth A], J [auth B], O [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain O [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C]	F [auth A], L [auth B], Q [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.189
R-Value Work: 0.162
R-Value Observed: 0.163
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m3d59s

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.418	α = 90
b = 82.597	β = 90
c = 171.968	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
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

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