Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 63998.69 
• Atom Count: 4521 
• Residue Count: 562 
• Unique protein chains: 1

2WDC

Termus thermophilus Sulfate thiohydrolase SoxB in complex with glycerol

• DOI: 10.2210/pdb2WDC/pdb

• Classification: HYDROLASE
• Organism(s): Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
• Expression System: Escherichia coli


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 

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.Biol.Chem. 284: 21707

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


• 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.

---

Organizational Affiliation: 

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
TBU	A	TERTIARY-BUTYL ALCOHOL 2-METHYL-2-PROPANOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.193 
• R-Value Work: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 71.345	α = 90.00
b = 86.456	β = 90.00
c = 95.974	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-24 
• 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
  Type: Atomic model, Derived calculations, Non-polymer description, Other, Version format compliance
• Version 1.2: 2017-07-05
  Type: Data collection