› 4ogl

X-ray diffraction
1.25Å resolution

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution

Released:
DOI: 10.2210/pdb4ogl/pdb
PDB entry 4ogl coloured by chain, front view.
PDB entry 4ogl coloured by chain, side view.
PDB entry 4ogl coloured by chain, top view.
Source organism: Vibrio cholerae O1 biovar El Tor str. N16961
Primary publication:
X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at 1.25 A resolution
Prokofev II, Lashkov AA, Gabdoulkhakov AG, Balaev T, Seregina AS, Mironov C, Betzel C, Mikhailov AM
Crystallogr. Rep. (2016)

Function and Biology Details

Reaction catalysed: 
Uridine + phosphate = uracil + 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-192083 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine phosphorylase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 253 amino acids
Theoretical weight: 27.11 KDa
Source organism: Vibrio cholerae O1 biovar El Tor str. N16961
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KT71 (Residues: 6-258; Coverage: 98%)
Gene name: VC_1034
Sequence domains: Phosphorylase superfamily
Structure domains: Nucleoside phosphorylase domain

Ligands and Environments

5 bound ligands:
Ligand TDR 6 x TDR
Ligand EDO 9 x EDO
Ligand GOL 6 x GOL
Ligand NA 3 x NA
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, DESY BEAMLINE P11
Spacegroup: P21
Unit cell:
a: 92.748Å b: 96.499Å c: 92.776Å
α: 90° β: 119.99° γ: 90°
R-values:
R R work R free
0.117 0.115 0.147
Expression system: Escherichia coli

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