9ZPB | pdb_00009zpb

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

PDB DOI: https://doi.org/10.2210/pdb9ZPB/pdb

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

Deposited: 2025-12-16 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: 2.19 Å
R-Value Free:
0.204 (Depositor), 0.205 (DCC)
R-Value Work:
0.174 (Depositor), 0.178 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 172.25 kDa
Atom Count: 12,244
Modeled Residue Count: 1,549
Deposited Residue Count: 1,588
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13UJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	E [auth A], H [auth B], M [auth C], P [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain P [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	K [auth B], N [auth C], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B]	G [auth A], L [auth B], O [auth C], R [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.204 (Depositor), 0.205 (DCC)
R-Value Work: 0.174 (Depositor), 0.178 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.005	α = 90
b = 170.156	β = 90
c = 170.322	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

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