3Q2O | pdb_00003q2o

Crystal Structure of purK: N5-carboxyaminoimidazole ribonucleotide synthetase

• PDB DOI: https://doi.org/10.2210/pdb3Q2O/pdb

• Classification: LYASE
• Organism(s): Bacillus anthracis str. A0248
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-20 Released: 2011-10-26 
• Deposition Author(s): Fung, L.W., Tuntland, M.L., Santarsiero, B.D., Johnson, M.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structure of N(5)-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis.

Tuntland, M.L., Johnson, M.E., Fung, L.W., Santarsiero, B.D.

(2011) Acta Crystallogr D Biol Crystallogr 67: 870-874

• PubMed: 21931218 
• DOI: https://doi.org/10.1107/S0907444911029210
• Primary Citation Related Structures: 
  3Q2O


• PubMed Abstract: 
  

  The apo structure of N5-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis (baPurK) with Mg2+ in the active site is reported at 1.96 Å resolution. PurK is an enzyme in the purine-biosynthetic pathway, unique to prokaryotes, that converts 5-aminoimidazole ribonucleotide to N5-carboxyaminoimidazole ribonucleotide and has been suggested as a potential antimicrobial drug target. Two interesting features of baPurK are a flexible B-loop (residues 149/150-157) that is in close contact with the active site and the binding of Mg2+ to the active site without additional ligands.

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Organizational Affiliation: 
• Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 86.47 kDa 
• Atom Count: 6,257 
• Modeled Residue Count: 754 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylaminoimidazole carboxylase, ATPase subunit	A, B	389	Bacillus anthracis str. A0248	Mutation(s): 0  Gene Names: BAA_0344, purK EC: 4.1.1.21

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.43	α = 90
b = 82.445	β = 90
c = 166.621	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-26 
Deposition Author(s): Fung, L.W., Tuntland, M.L., Santarsiero, B.D., Johnson, M.E.

Revision History  

• Version 1.0: 2011-10-26
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description