5YJ2 | pdb_00005yj2

Crystal structure of Bacillus sp. TB-90 urate oxidase without dehydration

• PDB DOI: https://doi.org/10.2210/pdb5YJ2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus sp. TB-90
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2017-10-07 Released: 2018-10-10 
• Deposition Author(s): Hibi, T., Itoh, T., Nishiya, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal structure of Bacillus sp. TB-90 urate oxidase without dehydration

Hibi, T., Itoh, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 144.02 kDa 
• Atom Count: 11,056 
• Modeled Residue Count: 1,212 
• Deposited Residue Count: 1,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uric acid degradation bifunctional protein	A, B, C, D	312	Bacillus sp. TB-90	Mutation(s): 0  Gene Names: uao EC: 4.1.1.97 (PDB Primary Data), 1.7.3.3 (PDB Primary Data)
UniProt
Find proteins for Q45697 (Bacillus sp. (strain TB-90)) Explore Q45697  Go to UniProtKB:  Q45697

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZA (Subject of Investigation/LOI)	E [auth A], H [auth B], M [auth C], P [auth D]	8-AZAXANTHINE C4 H3 N5 O2 KVGVQTOQSNJTJI-UHFFFAOYSA-N
SO4	J [auth B], L [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MXE	G [auth A], K [auth B], O [auth C]	2-METHOXYETHANOL C3 H8 O2 XNWFRZJHXBZDAG-UHFFFAOYSA-N
OXY (Subject of Investigation/LOI)	F [auth A], I [auth B], N [auth C], Q [auth D]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A, B, C, D	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.073	α = 90
b = 143.895	β = 90
c = 70.231	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Hibi, T., Itoh, T., Nishiya, Y.

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Experimental preparation, Structure summary
• Version 1.2: 2025-04-09
  Changes: Data collection, Database references, Structure summary