1H21

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1007/s00775-002-0426-3

  • 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 ...

    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.


    Related Citations: 
    • A Preliminary Analysis of the Three Dimensional Structure of Dimeric Di-Haem Split-Soret Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774 at 2.5 A Resolution Using the MAD Phasing Method: A Novel Cytochrome Fold with a Stacked Haem Arrangement
      Matias, P.M.,Morais, J.,Coelho, A.V.,Meijers, R.,Gonzalez, A.,Thompson, A.W.,Sieker, L.,Legall, J.,Carrondo, M.A.
      (1997) J.Biol.Inorg.Chem. 2: 507


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPLIT-SORET CYTOCHROME C
A, B, C, D
247Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)N/A
Find proteins for P81040 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949))
Go to UniProtKB:  P81040
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download SDF File 
Download CCD File 
A, B, C, D
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 96.060α = 90.00
b = 100.130β = 90.00
c = 109.300γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MLPHAREphasing
X-PLORrefinement
DMphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance