Cytochrome c domain of caa3 oxygen oxidoreductase

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Observed: 0.142 

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This is version 2.1 of the entry. See complete history


Structure at 1.3 A resolution of Rhodothermus marinus caa(3) cytochrome c domain.

Srinivasan, V.Rajendran, C.Sousa, F.L.Melo, A.M.Saraiva, L.M.Pereira, M.M.Santana, M.Teixeira, M.Michel, H.

(2005) J Mol Biol 345: 1047-1057

  • DOI: https://doi.org/10.1016/j.jmb.2004.10.069
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The cytochrome c domain of subunit II from the Rhodothermus marinus caa(3) HiPIP:oxygen oxidoreductase, a member of the superfamily of heme-copper-containing terminal oxidases, was produced in Escherichia coli and characterised. The recombinant protein, which shows the same optical absorption and redox properties as the corresponding domain in the holo enzyme, was crystallized and its structure was determined to a resolution of 1.3 A by the multiwavelength anomalous dispersion (MAD) technique using the anomalous dispersion of the heme iron atom. The model was refined to final R(cryst) and R(free) values of 13.9% and 16.7%, respectively. The structure reveals the insertion of two short antiparallel beta-strands forming a small beta-sheet, an interesting variation of the classical all alpha-helical cytochrome c fold. This modification appears to be common to all known caa(3)-type terminal oxidases, as judged by comparative modelling and by analyses of the available amino acid sequences for these enzymes. This is the first high-resolution crystal structure reported for a cytochrome c domain of a caa(3)-type terminal oxidase. The R.marinus caa(3) uses HiPIP as the redox partner. The calculation of the electrostatic potential at the molecular surface of this extra C-terminal domain provides insights into the binding to its redox partner on one side and its interaction with the remaining subunit II on the other side.

  • Organizational Affiliation

    Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Marie-Curie-Str. 15, D-60439 Frankfurt am Main, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME OXIDASE SUBUNIT II99Rhodothermus marinusMutation(s): 0 
Gene Names: rcoxA
EC: (PDB Primary Data), (UniProt)
Find proteins for Q9F3S9 (Rhodothermus marinus)
Explore Q9F3S9 
Go to UniProtKB:  Q9F3S9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F3S9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEC

Download Ideal Coordinates CCD File 
B [auth A]HEME C
C34 H34 Fe N4 O4
Query on TRS

Download Ideal Coordinates CCD File 
C4 H12 N O3
Query on ACT

Download Ideal Coordinates CCD File 
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Observed: 0.142 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.049α = 90
b = 54.049β = 90
c = 91.347γ = 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: 2005-01-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-01-23
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-05-22
    Changes: Data collection, Derived calculations, Refinement description