4OP9

Urate OXIDASE IN COMPLEX WITH 8-AZAXANTHINE

• PDB DOI: https://doi.org/10.2210/pdb4OP9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus flavus
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2014-02-05 Released: 2014-03-19 
• Deposition Author(s): Colloc'h, N., Prange, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.191 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

Functional relevance of the internal hydrophobic cavity of urate oxidase.

Colloc'h, N., Prange, T.

(2014) FEBS Lett 588: 1715-1719

• PubMed: 24657440 
• DOI: https://doi.org/10.1016/j.febslet.2014.03.017
• Primary Citation of Related Structures:  
  4OP6, 4OP9


• PubMed Abstract: 
  

  Urate oxidase from Aspergillus flavus is a 135 kDa homo-tetramer which has a hydrophobic cavity buried within each monomer and located close to its active site. Crystallographic studies under moderate gas pressure and high hydrostatic pressure have shown that both gas presence and high pressure would rigidify the cavity leading to an inhibition of the catalytic activity. Analysis of the cavity volume variations and functional modifications suggest that the flexibility of the cavity would be an essential parameter for the active site efficiency. This cavity would act as a connecting vessel to give flexibility to the neighboring active site, and its expansion under pure oxygen pressure reveals that it might serve as a transient reservoir on its pathway to the active site.

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Organizational Affiliation: 

CERVoxy Team, ISTCT UMR 6301, CNRS, Centre Cyceron, Caen, France; ISTCT UMR 6301, CEA, DSV/I2BM, Caen, France; ISTCT UMR 6301, Université de Caen Basse-Normandie, Normandie Université, Caen, France. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 34.36 kDa 
• Atom Count: 2,616 
• Modelled Residue Count: 296 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uricase	A	302	Aspergillus flavus	Mutation(s): 1  Gene Names: uaZ, uox EC: 1.7.3.3
UniProt
Find proteins for Q00511 (Aspergillus flavus) Explore Q00511  Go to UniProtKB:  Q00511

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZA	B [auth A]	8-AZAXANTHINE C4 H3 N5 O2 KVGVQTOQSNJTJI-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.191 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.109	α = 90
b = 96.175	β = 90
c = 105.407	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): Colloc'h, N., Prange, T.

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2021-09-15
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Refinement description