6RGT | pdb_00006rgt

Crystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid

• PDB DOI: https://doi.org/10.2210/pdb6RGT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus flavus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-04-17 Released: 2020-05-13 
• Deposition Author(s): Bui, S., Lowden, S.R.J., Steiner, R.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.189 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid

Bui, S., Lowden, S.R.J., Steiner, R.A.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.8 kDa 
• Atom Count: 3,316 
• Modeled Residue Count: 301 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MUA	B [auth A]	9-METHYL URIC ACID C6 H6 N4 O3 XJEJWDFDVPDMAS-UHFFFAOYSA-N
TRS	D [auth A], E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.189 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.291	α = 90
b = 95.116	β = 90
c = 104.503	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Bui, S., Lowden, S.R.J., Steiner, R.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/P000169/1

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description