9ZOI | pdb_00009zoi

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ATP complex)

PDB DOI: https://doi.org/10.2210/pdb9ZOI/pdb

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

Deposited: 2025-12-15 Released: 2025-12-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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: 1.93 Å
R-Value Free:
0.196 (Depositor), 0.199 (DCC)
R-Value Work:
0.169 (Depositor), 0.174 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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Literature

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ATP complex)

Liu, L., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 173.02 kDa
Atom Count: 12,509
Modeled Residue Count: 1,548
Deposited Residue Count: 1,588
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N5-carboxyaminoimidazole ribonucleotide synthase	A, B, C, D	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13UJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain O [auth C]	E [auth A], O [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain O [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain T [auth D] MOL2 format, chain K [auth B] MOL2 format, chain T [auth D] mmCIF format, chain K [auth B] mmCIF format, chain T [auth D]	K [auth B], T [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth B] Focus chain T [auth D] Interactions & Density Focus chain K [auth B] Focus chain T [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain L [auth B] MOL2 format, chain U [auth D] MOL2 format, chain L [auth B] mmCIF format, chain U [auth D] mmCIF format, chain L [auth B]	L [auth B], U [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain U [auth D] Interactions & Density Focus chain L [auth B] Focus chain U [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	J [auth B], P [auth C], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain J [auth B] Focus chain P [auth C] Focus chain S [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth A] M [auth B] N [auth B] Q [auth C] G [auth A], H [auth A], M [auth B], N [auth B], Q [auth C], R [auth C], V [auth D], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.196 (Depositor), 0.199 (DCC)
R-Value Work: 0.169 (Depositor), 0.174 (DCC)
R-Value Observed: 0.170 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.007	α = 90
b = 170.436	β = 90
c = 170.508	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

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