4NF2

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.170 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Starting Model: experimental

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.

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: 115.53 kDa 
• Atom Count: 8,220 
• Modelled Residue Count: 921 
• Deposited Residue Count: 1,020 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CP	D [auth A], J [auth B], L [auth C]	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H4 N O5 P FFQKYPRQEYGKAF-UHFFFAOYSA-N
NVA	E [auth A], I [auth B], M [auth C]	NORVALINE C5 H11 N O2 SNDPXSYFESPGGJ-BYPYZUCNSA-N
CL	F [auth A], G [auth A], H [auth B], K [auth B], N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.170 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m34nf2

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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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