P21 crystal structure of the tetraheme cytochrome c3 from Shewanella oneidensis MR1

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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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: https://doi.org/10.1074/jbc.M203866200
  • Primary Citation of Related Structures:  
    1M1P, 1M1Q, 1M1R

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small tetraheme cytochrome c
A, B, C, D, E
A, B, C, D, E, F
91Shewanella oneidensisMutation(s): 0 
Find proteins for Q8EDL6 (Shewanella oneidensis (strain MR-1))
Explore Q8EDL6 
Go to UniProtKB:  Q8EDL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EDL6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEC

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
EA [auth F]
FA [auth F]
AA [auth E],
BA [auth E],
CA [auth E],
EA [auth F],
FA [auth F],
GA [auth F],
H [auth A],
HA [auth F],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth E]
C34 H34 Fe N4 O4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth F],
G [auth A],
L [auth B],
Q [auth C]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.69α = 90
b = 34.005β = 110.49
c = 108.313γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-04-03
    Changes: Data collection, Database references, Refinement description