9Y8H | pdb_00009y8h

Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans in complex with phosphono carbamate

• PDB DOI: https://doi.org/10.2210/pdb9Y8H/pdb

• Classification: TRANSFERASE
• Organism(s): Paraburkholderia xenovorans LB400
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-11 Released: 2025-09-24 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.252 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans in complex with phosphono carbamate

Liu, L., Lovell, S., Battaile, K.P.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.77 kDa 
• Atom Count: 2,625 
• Modeled Residue Count: 327 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A	339	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: argF, Bxe_C0747 EC: 2.1.3.3
UniProt
Find proteins for Q13H08 (Paraburkholderia xenovorans (strain LB400)) Explore Q13H08  Go to UniProtKB:  Q13H08

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CP (Subject of Investigation/LOI)	B [auth A]	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H4 N O5 P FFQKYPRQEYGKAF-UHFFFAOYSA-N
PO4	C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.252 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39Y8H

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.498	α = 90
b = 131.498	β = 90
c = 131.498	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release