1SP3

Crystal structure of octaheme cytochrome c from Shewanella oneidensis

• PDB DOI: https://doi.org/10.2210/pdb1SP3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Shewanella frigidimarina
• Mutation(s): No 


• Deposited: 2004-03-16 Released: 2004-09-21 
• Deposition Author(s): Mowat, C.G., Rothery, E., Miles, C.S., McIver, L., Doherty, M.K., Drewette, K., Taylor, P., Walkinshaw, M.D., Chapman, S.K., Reid, G.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.252 
• R-Value Work: 0.155 
• R-Value Observed: 0.160 

Literature

Octaheme tetrathionate reductase is a respiratory enzyme with novel heme ligation.

Mowat, C.G., Rothery, E., Miles, C.S., McIver, L., Doherty, M.K., Drewette, K., Taylor, P., Walkinshaw, M.D., Chapman, S.K., Reid, G.A.

(2004) Nat Struct Mol Biol 11: 1023-1024

• PubMed: 15361860 
• DOI: https://doi.org/10.1038/nsmb827
• Primary Citation of Related Structures:  
  1SP3


• PubMed Abstract: 
  

  We have isolated a soluble cytochrome from Shewanella oneidensis that contains eight covalently attached heme groups and determined its crystal structure. One of these hemes exhibits novel ligation of the iron atom by the epsilon-amino group of a lysine residue, despite its attachment via a typical CXXCH motif. This heme is most likely the active site for tetrathionate reduction, a reaction catalyzed efficiently by this enzyme.

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Organizational Affiliation: 

Institute of Cell and Molecular Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 54.58 kDa 
• Atom Count: 4,243 
• Modelled Residue Count: 436 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytochrome c, putative	A	443	Shewanella oneidensis MR-1	Mutation(s): 0  Gene Names: SO4144 (tigr locus)
UniProt
Find proteins for Q8E9W8 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8E9W8  Go to UniProtKB:  Q8E9W8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
SCN	B [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.252 
• R-Value Work: 0.155 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.59	α = 90
b = 61.767	β = 90
c = 185.237	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Mowat, C.G., Rothery, E., Miles, C.S., McIver, L., Doherty, M.K., Drewette, K., Taylor, P., Walkinshaw, M.D., Chapman, S.K., Reid, G.A.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2021-03-03
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary