2WDC | pdb_00002wdc

Termus thermophilus Sulfate thiohydrolase SoxB in complex with glycerol

• PDB DOI: https://doi.org/10.2210/pdb2WDC/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-24 Released: 2009-06-16 
• Deposition Author(s): Sauve, V., Roversi, P., Leath, K.J., Garman, E.F., Antrobus, R., Lea, S.M., Berks, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.193 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Mechanism for the Hydrolysis of a Sulfur-Sulfur Bond Based on the Crystal Structure of the Thiosulfohydrolase Soxb.

Sauve, V., Roversi, P., Leath, K.J., Garman, E.F., Antrobus, R., Lea, S.M., Berks, B.C.

(2009) J Biological Chem 284: 21707

• PubMed: 19535341 
• DOI: https://doi.org/10.1074/jbc.M109.002709
• Primary Citation Related Structures: 
  2WDC, 2WDD, 2WDE, 2WDF


• PubMed Abstract: 
  

  SoxB is an essential component of the bacterial Sox sulfur oxidation pathway. SoxB contains a di-manganese(II) site and is proposed to catalyze the release of sulfate from a protein-bound cysteine S-thiosulfonate. A direct assay for SoxB activity is described. The structure of recombinant Thermus thermophilus SoxB was determined by x-ray crystallography to a resolution of 1.5 A. Structures were also determined for SoxB in complex with the substrate analogue thiosulfate and in complex with the product sulfate. A mechanistic model for SoxB is proposed based on these structures.

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Organizational Affiliation: 
• Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 64 kDa 
• Atom Count: 5,085 
• Modeled Residue Count: 542 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SULFUR OXIDATION PROTEIN SOXB	A	562	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72IT0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IT0  Go to UniProtKB:  Q72IT0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
TBU	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	TERTIARY-BUTYL ALCOHOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], I [auth A], J [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	Q [auth A], R [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.193 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.345	α = 90
b = 86.456	β = 90
c = 95.974	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
XPREP	data reduction
SCALA	data scaling
SHELXD	phasing
SHARP	phasing
SOLOMON	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Sauve, V., Roversi, P., Leath, K.J., Garman, E.F., Antrobus, R., Lea, S.M., Berks, B.C.

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2015-08-19
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Version format compliance
• Version 1.2: 2017-07-05
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other