1H33

Oxidised SoxAX complex from Rhodovulum sulfidophilum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.217 (Depositor) 
  • R-Value Work: 
    0.179 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

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Ligand Structure Quality Assessment 

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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 C261Rhodovulum sulfidophilumMutation(s): 0 
EC: 2.8.5.2
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 C138Rhodovulum 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.217 (Depositor) 
  • R-Value Work:  0.179 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.353α = 90
b = 87.341β = 90
c = 71.654γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HECClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary