35YG | pdb_000035yg

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (Apo)

• PDB DOI: https://doi.org/10.2210/pdb35YG/pdb

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


• Deposited: 2026-05-21 Released: 2026-06-03 
• 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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.275 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (Apo)

Liu, L., Lovell, S., Battaile, K.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 85.6 kDa 
• Atom Count: 5,771 
• Modeled Residue Count: 769 
• Deposited Residue Count: 794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N5-carboxyaminoimidazole ribonucleotide synthase	A, B	397	Paraburkholderia xenovorans LB400	Mutation(s): 0  Gene Names: purK, Bxe_A0694 EC: 6.3.4.18
UniProt
Find proteins for Q13UJ9 (Paraburkholderia xenovorans (strain LB400)) Explore Q13UJ9  Go to UniProtKB:  Q13UJ9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.275 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.301	α = 90
b = 86.128	β = 97.87
c = 51.93	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: 2026-06-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

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: 2026-06-03
  Type: Initial release