5TLC | pdb_00005tlc

Crystal structure of BdsA from Bacillus subtilis WU-S2B

• PDB DOI: https://doi.org/10.2210/pdb5TLC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-11 Released: 2017-05-03 
• Deposition Author(s): Okai, M., Lee, W.C., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Crystal structure of dibenzothiophene sulfone monooxygenase BdsA from Bacillus subtilis WU-S2B

Okai, M., Lee, W.C., Guan, L.J., Ohshiro, T., Izumi, Y., Tanokura, M.

(2017) Proteins 85: 1171-1177

• PubMed: 28205250 
• DOI: https://doi.org/10.1002/prot.25267
• Primary Citation Related Structures: 
  5TLC


• PubMed Abstract: 
  

  The dibenzothiophene (DBT) sulfone monooxygenase BdsA from Bacillus subtilis WU-S2B catalyzes the conversion of DBT sulfone to 2'-hydroxybiphenyl 2-sulfinate. We report the crystal structures of BdsA at a resolution of 2.80 Å. BdsA exists as a homotetramer with a dimer-of-dimers configuration in the crystal, and the interaction between E288 and R296 in BdsA is important for tetramer formation. A structural comparison with homologous proteins shows that the orientation and location of the α9-α12 helices in BdsA are closer to those of the closed form than those of the open form in the EDTA monooxygenase EmoA. Proteins 2017; 85:1171-1177. © 2017 Wiley Periodicals, Inc.

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, 108-8477, Japan.
Food Processing Institute, Heilongjiang Academy of Agricultural Sciences, Nangang District, Harbin, 150086, China.
Department of Biotechnology, Tottori University, Tottori, 680-8552, Japan.

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: 198.84 kDa 
• Atom Count: 12,884 
• Modeled Residue Count: 1,657 
• Deposited Residue Count: 1,812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dibenzothiophene desulfurization enzyme A	A, B, C, D	453	Bacillus subtilis	Mutation(s): 0  Gene Names: bdsA
UniProt
Find proteins for Q8GRC7 (Bacillus subtilis) Explore Q8GRC7  Go to UniProtKB:  Q8GRC7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.274 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.126	α = 90
b = 84.126	β = 90
c = 269.456	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Okai, M., Lee, W.C., Tanokura, M.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references