› 3occ

X-ray diffraction
1.7Å resolution

Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis

Released:
DOI: 10.2210/pdb3occ/pdb
PDB entry 3occ coloured by chain, front view.
PDB entry 3occ coloured by chain, side view.
PDB entry 3occ coloured by chain, top view.
Source organism: Yersinia pseudotuberculosis YPIII
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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109317 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Purine nucleoside phosphorylase DeoD-type Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 239 amino acids
Theoretical weight: 25.97 KDa
Source organism: Yersinia pseudotuberculosis YPIII
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B1JL34 (Residues: 1-239; Coverage: 100%)
Gene names: YPK_3624, deoD
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

2 bound ligands:
Ligand DIH 6 x DIH
Ligand PO4 6 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 91.647Å b: 109.829Å c: 154.747Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.151 0.149 0.181
Expression system: Escherichia coli BL21(DE3)

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