1H21

A novel iron centre in the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

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This is version 1.3 of the entry. See complete history


Literature

A Novel Iron Centre in the Split-Soret Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774

Abreu, I.A.Lourenco, A.I.Xavier, A.V.Legall, J.Coelho, A.V.Matias, P.M.Pinto, D.M.Armenia Carrondo, M.Teixeira, M.Saraiva, L.M.

(2003) J Biol Inorg Chem 8: 360

  • DOI: https://doi.org/10.1007/s00775-002-0426-3
  • Primary Citation of Related Structures:  
    1H21

  • PubMed Abstract: 

    The facultative sulfate/nitrate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 harbours a split-Soret cytochrome c. This cytochrome is a homodimeric protein, having two bis-histidinyl c-type haems per monomer. It has an unique architecture at the haem domain: each haem has one of the coordinating histidines provided by the other monomer, and in each monomer the haems are parallel to each other, almost in van der Waals contact. This work reports the cloning and sequencing of the gene encoding for this cytochrome and shows, by transcriptional analysis, that it is more expressed in nitrate-grown cells than in sulfate-grown ones. In addition, the gene-deduced amino acid sequence revealed two new cysteine residues that could be involved in the binding of a non-haem iron centre. Indeed, the presence of a novel type of an iron-sulfur centre (possibly of the [2Fe-2S] type) was demonstrated by EPR spectroscopy, and putative models for its localization and structure in the cytochrome molecule are proposed on the basis of the so-far-known 3D crystallographic structure of the aerobically purified split-Soret cytochrome, which lacks this centre.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SPLIT-SORET CYTOCHROME C
A, B, C, D
247Desulfovibrio desulfuricansMutation(s): 0 
UniProt
Find proteins for P81040 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore P81040 
Go to UniProtKB:  P81040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81040
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.06α = 90
b = 100.13β = 90
c = 109.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
X-PLORrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-20
    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: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary