Crystal Structure of Cytochrome c555 from Aquifex aeolicus

Experimental Data Snapshot

  • Resolution: 1.15 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 

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Hyperstability and crystal structure of cytochrome c(555) from hyperthermophilic Aquifex aeolicus

Obuchi, M.Kawahara, K.Motooka, D.Nakamura, S.Yamanaka, M.Takeda, T.Uchiyama, S.Kobayashi, Y.Ohkubo, T.Sambongi, Y.

(2009) Acta Crystallogr D Biol Crystallogr 65: 804-813

  • DOI: https://doi.org/10.1107/S0907444909017314
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In order to elucidate the relationship between the stability and the structure of the monohaem cytochrome c(555) (AA c(555)) from the hyperthermophilic bacterium Aquifex aeolicus, chemical denaturation and crystal structure determination were carried out. AA c(555) exhibited higher stability than the thermophilic Hydrogenobacter thermophilus cytochrome c(552) (HT c(552)), which is one of the most stable cytochromes c. The three-dimensional crystal structure of AA c(555), which was determined using the multiple anomalous dispersion technique at 1.15 A resolution, included a unique 14-residue extra helix, while the side-chain interactions of several amino-acid residues responsible for the stability of HT c(552) were conserved in AA c(555). The side chain of the Met61 residue in the extra helix was aligned towards the haem, forming a coordination bond between the Met S and haem Fe atoms. In other cytochromes c the corresponding regions always form Omega loops which also include the haem-liganding Met residue and are known to be involved in the initial step in cytochrome c denaturation. The formation of the extra helix in AA c(555) results in the highest helix content, 59.8%, among the monohaem cytochromes c. The extra helix should mainly contribute to the hyperstability of AA c(555) and is presumed to be a novel strategy of cytochromes c for adaptation to a hyperthermophilic environment.

  • Organizational Affiliation

    Hiroshima University, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c55287Aquifex aeolicusMutation(s): 0 
Gene Names: cycB2aq_1550
Find proteins for O67504 (Aquifex aeolicus (strain VF5))
Explore O67504 
Go to UniProtKB:  O67504
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67504
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.15 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.529α = 90
b = 32.993β = 115.05
c = 49.668γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations