1H31

Oxidised SoxAX complex from Rhodovulum sulfidophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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Literature

Structural Basis for the Oxidation of Thiosulfate by a Sulfur Cycle Enzyme

Bamford, V.A.Bruno, S.Rasmussen, T.Appia-Ayme, C.Cheesman, M.R.Berks, B.C.Hemmings, A.M.

(2002) EMBO J 21: 5599

  • DOI: https://doi.org/10.1093/emboj/cdf566
  • Primary Citation of Related Structures:  
    1H31, 1H32, 1H33

  • PubMed Abstract: 

    Reduced inorganic sulfur compounds are utilized by many bacteria as electron donors to photosynthetic or respiratory electron transport chains. This metabolism is a key component of the biogeochemical sulfur cycle. The SoxAX protein is a heterodimeric c-type cytochrome involved in thiosulfate oxidation. The crystal structures of SoxAX from the photosynthetic bacterium Rhodovulum sulfidophilum have been solved at 1.75 A resolution in the oxidized state and at 1.5 A resolution in the dithionite-reduced state, providing the first structural insights into the enzymatic oxidation of thiosulfate. The SoxAX active site contains a haem with unprecedented cysteine persulfide (cysteine sulfane) coordination. This unusual post-translational modification is also seen in sulfurtransferases such as rhodanese. Intriguingly, this enzyme shares further active site characteristics with SoxAX such as an adjacent conserved arginine residue and a strongly positive electrostatic potential. These similarities have allowed us to suggest a catalytic mechanism for enzymatic thiosulfate oxidation. The atomic coordinates and experimental structure factors have been deposited in the PDB with the accession codes 1H31, 1H32 and 1H33.


  • Organizational Affiliation

    Centre for Metalloprotein Spectroscopy and Biology, School of Biological Sciences and School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIHEME CYTOCHROME C
A, C, E, G
261Rhodovulum sulfidophilumMutation(s): 0 
UniProt
Find proteins for Q939U1 (Rhodovulum sulfidophilum)
Explore Q939U1 
Go to UniProtKB:  Q939U1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ939U1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C
B, D, F, H
138Rhodovulum sulfidophilumMutation(s): 0 
UniProt
Find proteins for Q939U4 (Rhodovulum sulfidophilum)
Explore Q939U4 
Go to UniProtKB:  Q939U4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ939U4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth B]
L [auth C]
M [auth C]
I [auth A],
J [auth A],
K [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth E],
P [auth E],
Q [auth F],
R [auth G],
S [auth G],
T [auth H]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A, C, E, G
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.188α = 90
b = 102.894β = 110.45
c = 114.365γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-07
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance