1OA1

REDUCED HYBRID CLUSTER PROTEIN (HCP) FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH STRUCTURE AT 1.55A RESOLUTION USING SYNCHROTRON RADIATION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Reduced Hybrid Cluster Proteins (Hcp) from Desulfovibrio Desulfuricans Atcc 27774 and Desulfovibrio Vulgaris (Hildenborough): X-Ray Structures at High Resolution Using Synchrotron Radiation

Aragao, D.Macedo, S.Mitchell, E.P.Romao, C.V.Liu, M.Y.Frazao, C.Saraiva, L.M.Xavier, A.V.Legall, J.Van Dongen, W.M.A.M.Hagen, W.R.Teixeira, M.Carrondo, M.A.Lindley, P.F.

(2003) J Biol Inorg Chem 8: 540

  • DOI: https://doi.org/10.1007/s00775-003-0443-x
  • Primary Citation of Related Structures:  
    1OA0, 1OA1

  • PubMed Abstract: 

    The hybrid cluster proteins from the sulfate reducing bacteria Desulfovibrio desulfuricans ATCC 27774 ( Dd) and Desulfovibrio vulgaris strain Hildenborough ( Dv) have been isolated and crystallized anaerobically. In each case, the protein has been reduced with dithionite and the crystal structure of the reduced form elucidated using X-ray synchrotron radiation techniques at 1.25 A and 1.55 A resolution for Dd and Dv, respectively. Although the overall structures of the proteins are unchanged upon reduction, there are significant changes at the hybrid cluster centres. These include significant movements in the position of the iron atom linked to the persulfide moiety in the oxidized as-isolated proteins and the sulfur atom of the persulfide itself. The nature of these changes is described and the implications with respect to the function of hybrid cluster proteins are discussed.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, Apartado 127, 2781-901 , Oeiras, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYDROXYLAMINE REDUCTASE553Nitratidesulfovibrio vulgarisMutation(s): 0 
EC: 1.7
UniProt
Find proteins for P31101 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P31101 
Go to UniProtKB:  P31101
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31101
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.053α = 90
b = 67.464β = 90
c = 134.955γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-03-29
    Changes: Database references, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-05-01
    Changes: Data collection, Refinement description