Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Observed: 0.167 

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Three-dimensional structure of cytochrome c' from two Alcaligenes species and the implications for four-helix bundle structures.

Dobbs, A.J.Anderson, B.F.Faber, H.R.Baker, E.N.

(1996) Acta Crystallogr D Biol Crystallogr 52: 356-368

  • DOI: https://doi.org/10.1107/S0907444995008328
  • Primary Citation of Related Structures:  
    1CGN, 1CGO

  • PubMed Abstract: 

    The three-dimensional structures of two cytochromes c' have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c' from Alcaligenes sp was determined by molecular replacement supplemented with the iron anomalous scattering and the use of a single isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8 A resolution. The final model, comprising 956 protein atoms (one monomer) and 89 water molecules, has a final R value of 0.188 for all data in the range 20.0-1.8 A resolution (14 673 reflections). The structure of the cytochrome c' from Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s. deviation for all atoms 0.36 A). Although its amino-acid sequence has not been determined chemically, only four differences from that of Alcaligenes sp cytochrome c' were identified by the X-ray analysis. The final model for Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75 water molecules, gave a final R factor of 0.167 for all data in the range 20.0-2.15 A (8220 reflections). The cytochrome c' monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very few cross-linking hydrogen bonds between the helices, the principal side-chain hydrogen bonding involving one of the haem propionates and a conserved Arg residue. The cytochrome c' dimer is created by a crystallographic twofold axis. Monomer-monomer contacts primarily involve the two A helices, with size complementarity of side chains in a central solvent-excluded portion of the interface and hydrogen bonding at the periphery. Both species have a pyroglutamic acid N-terminal residue. The haem iron is five-coordinate, 0.32 A out of the haem plane towards the fifth ligand, His120. The unusual magnetic properties of the Fe atom may be linked to a conserved basic residue, Arg124, adjacent to His120.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C127Achromobacter xylosoxidansMutation(s): 0 
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans)
Explore P00138 
Go to UniProtKB:  P00138
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00138
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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PCA
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Observed: 0.167 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.6α = 90
b = 54.6β = 90
c = 180.4γ = 120
Software Package:
Software NamePurpose
SUPPLIEDdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Other, Polymer sequence
  • Version 3.0: 2020-01-22
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary