1XE3

Crystal Structure of purine nucleoside phosphorylase DeoD from Bacillus anthracis

• PDB DOI: https://doi.org/10.2210/pdb1XE3/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-09 Released: 2004-10-26 
• Deposition Author(s): Grenha, R., Levdikov, V.M., Fogg, M., Blagova, E.V., Brannigan, J.A., Wilkinson, A.J., Wilson, K.S., Structural Proteomics in Europe (SPINE)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.235 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Structure of purine nucleoside phosphorylase (DeoD) from Bacillus anthracis.

Grenha, R., Levdikov, V.M., Fogg, M.J., Blagova, E.V., Brannigan, J.A., Wilkinson, A.J., Wilson, K.S.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 459-462

• PubMed: 16511068 
• DOI: https://doi.org/10.1107/S174430910501095X
• Primary Citation of Related Structures:  
  1XE3


• PubMed Abstract: 
  

  Protein structures from the causative agent of anthrax (Bacillus anthracis) are being determined as part of a structural genomics programme. Amongst initial candidates for crystallographic analysis are enzymes involved in nucleotide biosynthesis, since these are recognized as potential targets in antibacterial therapy. Purine nucleoside phosphorylase is a key enzyme in the purine-salvage pathway. The crystal structure of purine nucleoside phosphorylase (DeoD) from B. anthracis has been solved by molecular replacement at 2.24 A resolution and refined to an R factor of 18.4%. This is the first report of a DeoD structure from a Gram-positive bacterium.

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Organizational Affiliation: 

Department of Chemistry, University of York, York YO10 5YW, England.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 161.56 kDa 
• Atom Count: 11,450 
• Modelled Residue Count: 1,402 
• Deposited Residue Count: 1,470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
purine nucleoside phosphorylase	A, B, C, D, E, F	245	Bacillus anthracis	Mutation(s): 0  Gene Names: deoD EC: 2.4.2.1
UniProt
Find proteins for Q81T09 (Bacillus anthracis) Explore Q81T09  Go to UniProtKB:  Q81T09

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	G [auth A], H [auth B], I [auth C], J [auth C], K [auth D], L [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.235 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.861	α = 90
b = 128.257	β = 90
c = 223.565	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Grenha, R., Levdikov, V.M., Fogg, M., Blagova, E.V., Brannigan, J.A., Wilkinson, A.J., Wilson, K.S., Structural Proteomics in Europe (SPINE)

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description