› 4d13

X-ray diffraction
1.3Å resolution

Crystal structure of cofactor-free urate oxidase in complex with its 5-peroxoisourate intermediate (X-ray dose, 2.2 kGy)

Released:
DOI: 10.2210/pdb4d13/pdb
PDB entry 4d13 coloured by chain, front view.
PDB entry 4d13 coloured by chain, side view.
PDB entry 4d13 coloured by chain, top view.
Source organism: Aspergillus flavus
Primary publication:
Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase.
Bui S, von Stetten D, Jambrina PG, Prangé T, Colloc'h N, de Sanctis D, Royant A, Rosta E, Steiner RA
Angew Chem Int Ed Engl 53 13710-4 (2014)
PMID: 25314114

Function and Biology Details

Reaction catalysed: 
Urate + O(2) + H(2)O = 5-hydroxyisourate + H(2)O(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169432 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uricase Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.29 KDa
Source organism: Aspergillus flavus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00511 (Residues: 1-302; Coverage: 100%)
Gene names: Uox, uaZ
Sequence domains: Uricase
Structure domains: Urate Oxidase;

Ligands and Environments

2 bound ligands:
Ligand IUP 1 x IUP
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: I222
Unit cell:
a: 79.93Å b: 95.08Å c: 104.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.109 0.108 0.132
Expression system: Escherichia coli

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Citations

3 review citations

Radiation damage to macromolecules: kill or cure?
Garman et al. (2015)
2 more