4XFP

Crystal Structure of Highly Active Mutant of Bacillus sp. TB-90 Urate Oxidase

• PDB DOI: https://doi.org/10.2210/pdb4XFP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus sp. TB-90
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): Yes 


• Deposited: 2014-12-28 Released: 2016-01-13 
• Deposition Author(s): Hibi, T., Hayashi, Y., Kawamura, A., Itoh, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.184 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 

Literature

Glycine Substitution of Surface Proline 287 Involves Entropic Enhancement of Bacillus sp. TB-90 Uricase Activity

Hibi, T., Hayashi, Y., Kawamura, A., Itoh, T., Fukada, H., Kishimoto, T., Nishiya, Y.

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)

Macromolecule Content

• Total Structure Weight: 145.89 kDa 
• Atom Count: 10,739 
• Modelled Residue Count: 1,176 
• Deposited Residue Count: 1,268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urate oxidase	A, B, C, D	317	Bacillus sp. TB-90	Mutation(s): 1  Gene Names: uao EC: 1.7.3.3
UniProt
Find proteins for Q45697 (Bacillus sp. (strain TB-90)) Explore Q45697  Go to UniProtKB:  Q45697

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZA	E [auth A], H [auth B], J [auth C], M [auth D]	8-AZAXANTHINE C4 H3 N5 O2 KVGVQTOQSNJTJI-UHFFFAOYSA-N
SO4	G [auth A], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F [auth A], I [auth B], K [auth C], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.184 
• R-Value Work: 0.156 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.135	α = 90
b = 145.195	β = 90
c = 71.141	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Hibi, T., Hayashi, Y., Kawamura, A., Itoh, T.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description