6A4M | pdb_00006a4m

Structure of urate oxidase from Bacillus subtilis 168

• PDB DOI: https://doi.org/10.2210/pdb6A4M/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-06-20 Released: 2019-06-26 
• Deposition Author(s): Jiang, Y.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Urate Oxidase from Bacillus Subtilis 168

Nayab, A., Moududee, S.A., Shi, Y., Jiang, Y., Gong, Q.

(2019) Crystallogr Rep 64: 1126-1133

• DOI: https://doi.org/10.1134/S1063774519070149

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 34.75 kDa 
• Atom Count: 2,180 
• Modeled Residue Count: 269 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uric acid degradation bifunctional protein PucL	A	305	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: pucL, yunL, BSU32450 EC: 4.1.1.97 (PDB Primary Data), 1.7.3.3 (PDB Primary Data)
UniProt
Find proteins for O32141 (Bacillus subtilis (strain 168)) Explore O32141  Go to UniProtKB:  O32141

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.05	α = 90
b = 133.05	β = 90
c = 90.227	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Jiang, Y.Y.

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2020-03-11
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description