2FUB | pdb_00002fub

Crystal structure of urate oxidase at 140 MPa

• PDB DOI: https://doi.org/10.2210/pdb2FUB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus flavus
• Mutation(s): No 


• Deposited: 2006-01-26 Released: 2006-02-14 
• Deposition Author(s): Colloc'h, N., Girard, E., Fourme, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.213 (Depositor), 0.158 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

High pressure macromolecular crystallography: The 140-MPa crystal structure at 2.3 A resolution of urate oxidase, a 135-kDa tetrameric assembly

Colloc'h, N., Girard, E., Dhaussy, A.-C., Kahn, R., Ascone, I., Mezouar, M., Fourme, R.

(2006) Biochim Biophys Acta 1764: 391-397

• PubMed: 16478683 
• DOI: https://doi.org/10.1016/j.bbapap.2006.01.006
• Primary Citation Related Structures: 
  2FUB


• PubMed Abstract: 
  

  We report the three-dimensional structure determined by high-pressure macromolecular crystallography (HPMX) of a 135-kDa homo-tetrameric enzyme, urate oxidase from Aspergillus flavus complexed with its potent inhibitor 8-azaxanthin. Urate oxidase crystals are quite sensitive to pressure, as three-dimensional order is lost at about 180 MPa. A highly complete 2.3 A resolution data set was collected at 140 MPa, close to the critical pressure. Crystal structures at atmospheric pressure and at high pressure were refined in the orthorhombic space group I222 with final crystallographic R factors 14.1% and 16.1%, respectively. The effect of pressure on temperature factors, ordered water molecules, hydrogen bond lengths, contacts, buried surface areas as well as cavity volume was investigated. Results suggest that the onset of disruption of the tetrameric assembly by pressure has been captured in the crystalline state.

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Organizational Affiliation: 
• Centre CYCERON, UMR 6185 Université de Caen-CNRS, Bd Becquerel, 14074 Caen, France.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 34.43 kDa 
• Atom Count: 2,500 
• Modeled Residue Count: 295 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uricase	A	301	Aspergillus flavus	Mutation(s): 0  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
CYS	C [auth A]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.213 (Depositor), 0.158 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.18	α = 90
b = 95.63	β = 90
c = 104.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Colloc'h, N., Girard, E., Fourme, R.

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-09-15
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Derived calculations
• Version 1.6: 2024-10-30
  Changes: Structure summary