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X-ray diffraction
1.64Å resolution

crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis

Released:
DOI: 10.2210/pdb3odg/pdb
PDB entry 3odg coloured by chain, front view.
PDB entry 3odg coloured by chain, side view.
PDB entry 3odg coloured by chain, top view.
Source organism: Yersinia pseudotuberculosis
Entry authors: Kim J, Ramagopal UA, Burley SK, Almo SC, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179271 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase Chain: A
Molecule details ›
Chain: A
Length: 287 amino acids
Theoretical weight: 30.94 KDa
Source organism: Yersinia pseudotuberculosis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q66D48 (Residues: 1-287; Coverage: 100%)
Gene names: YPTB1201, xapA
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand XAN 1 x XAN
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P63
Unit cell:
a: 96.47Å b: 96.47Å c: 48.906Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.157 0.155 0.187
Expression system: Escherichia coli BL21(DE3)

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