4NF2 | pdb_00004nf2

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

PDB DOI: https://doi.org/10.2210/pdb4NF2/pdb

Classification: TRANSFERASE
Organism(s): Bacillus anthracis str. 'Ames Ancestor
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2013-10-30 Released: 2013-11-13
Deposition Author(s): Shabalin, I.G., Handing, K., Cymborowski, M.T., Stam, J., Winsor, J., Shuvalova, L., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.170 (Depositor), 0.186 (DCC)
R-Value Work:
0.145 (Depositor)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 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., Handing, K., Cymborowski, M.T., Stam, J., Winsor, J., Shuvalova, L., Anderson, W.F., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 115.53 kDa
Atom Count: 8,220
Modeled Residue Count: 921
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A, B, C	340	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 2 Gene Names: argF, BAS4036, BA_4351, GBAA_4351 EC: 2.1.3.3
UniProt
Find proteins for Q81M99 (Bacillus anthracis) Explore Q81M99 Go to UniProtKB: Q81M99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81M99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CP Query on CP Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B], L [auth C]	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H₄ N O₅ P FFQKYPRQEYGKAF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain L [auth C]
NVA Query on NVA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C]	E [auth A], I [auth B], M [auth C]	NORVALINE C₅ H₁₁ N O₂ SNDPXSYFESPGGJ-BYPYZUCNSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C]	F [auth A], G [auth A], H [auth B], K [auth B], N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.170 (Depositor), 0.186 (DCC)
R-Value Work: 0.145 (Depositor)
R-Value Observed: 0.147 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.893	α = 90
b = 99.893	β = 90
c = 118.989	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-11-13

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2013-11-13
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