1M1R

Reduced p222 crystal structure of the tetraheme cytochrome c of Shewanella oneidensis MR1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures at atomic resolution reveal the novel concept of 'electron-harvesting' as a role for the small tetraheme cytochrome c

Leys, D.Meyer, T.E.Tsapin, A.I.Nealson, K.H.Cusanovich, M.A.Van Beeumen, J.J.

(2002) J.Biol.Chem. 277: 35703-35711

  • DOI: 10.1074/jbc.M203866200
  • Primary Citation of Related Structures:  1M1P, 1M1Q

  • PubMed Abstract: 
  • The genus Shewanella produces a unique small tetraheme cytochrome c that is implicated in the iron oxide respiration pathway. It is similar in heme content and redox potential to the well known cytochromes c(3) but related in structure to the cytochr ...

    The genus Shewanella produces a unique small tetraheme cytochrome c that is implicated in the iron oxide respiration pathway. It is similar in heme content and redox potential to the well known cytochromes c(3) but related in structure to the cytochrome c domain of soluble fumarate reductases from Shewanella sp. We report the crystal structure of the small tetraheme cytochrome c from Shewanella oneidensis MR-1 in two crystal forms and two redox states. The overall fold and heme core are surprisingly different from the soluble fumarate reductase structures. The high resolution obtained for an oxidized orthorhombic crystal (0.97 A) revealed several flexible regions. Comparison of the six monomers in the oxidized monoclinic space group (1.55 A) indicates flexibility in the C-terminal region containing heme IV. The reduced orthorhombic crystal structure (1.02 A) revealed subtle differences in the position of several residues, resulting in decreased solvent accessibility of hemes and the withdrawal of a positive charge from the molecular surface. The packing between monomers indicates that intermolecular electron transfer between any heme pair is possible. This suggests there is no unique site of electron transfer on the surface of the protein and that electron transfer partners may interact with any of the hemes, a process termed "electron-harvesting." This optimizes the efficiency of intermolecular electron transfer by maximizing chances of productive collision with redox partners.


    Organizational Affiliation

    Laboratory of Protein Biochemistry and Protein Engineering, Department of Biochemistry, Physiology, and Microbiology, K.L. Ledeganckstraat 35, 9000 Gent, Belgium. dl37@le.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SMALL tetraheme cytochrome c
A
91Shewanella oneidensis (strain MR-1)Gene Names: cctA
Find proteins for Q8EDL6 (Shewanella oneidensis (strain MR-1))
Go to UniProtKB:  Q8EDL6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.02 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.882α = 90.00
b = 48.107β = 90.00
c = 58.234γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance