Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

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This is version 1.5 of the entry. See complete history


Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.

Wilmanns, M.Lappalainen, P.Kelly, M.Sauer-Eriksson, E.Saraste, M.

(1995) Proc Natl Acad Sci U S A 92: 11955-11959

  • DOI: https://doi.org/10.1073/pnas.92.26.11955
  • Primary Citation of Related Structures:  
    1CYW, 1CYX

  • PubMed Abstract: 

    Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.

  • Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYOA205Escherichia coliMutation(s): 0 
EC: 1.10.3
Find proteins for P0ABJ1 (Escherichia coli (strain K12))
Explore P0ABJ1 
Go to UniProtKB:  P0ABJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABJ1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.6α = 90
b = 84.1β = 90
c = 94.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Other
  • Version 1.4: 2022-08-17
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.5: 2024-02-07
    Changes: Data collection