6OVW | pdb_00006ovw

Crystal structure of ornithine carbamoyltransferase from Salmonella enterica

PDB DOI: https://doi.org/10.2210/pdb6OVW/pdb

Classification: ISOMERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-05-08 Released: 2019-05-22
Deposition Author(s): Chang, C., Mesa, N., Skarina, T., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.186 (Depositor), 0.187 (DCC)
R-Value Work:
0.167 (Depositor), 0.168 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6OVW

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

Literature

Crystal structure of ornithine carbamoyltransferase from Salmonella enterica

Chang, C., Mesa, N., Skarina, T., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 37.16 kDa
Atom Count: 2,868
Modeled Residue Count: 334
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A	334	Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344	Mutation(s): 0 Gene Names: argI, SL1344_4399 EC: 2.1.3.3
UniProt
Find proteins for A0A0H3NPU3 (Salmonella typhimurium (strain SL1344)) Explore A0A0H3NPU3 Go to UniProtKB: A0A0H3NPU3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3NPU3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.186 (Depositor), 0.187 (DCC)
R-Value Work: 0.167 (Depositor), 0.168 (DCC)
R-Value Observed: 0.168 (Depositor)

Diffraction Data:

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.214	α = 90
b = 139.214	β = 90
c = 139.214	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-05-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2019-05-22
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.