Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Work: 0.182 

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This is version 2.1 of the entry. See complete history


Refined crystal structure of ferrocytochrome c2 from Rhodopseudomonas viridis at 1.6 A resolution.

Sogabe, S.Miki, K.

(1995) J Mol Biol 252: 235-246

  • DOI: https://doi.org/10.1006/jmbi.1995.0491
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The three-dimensional structure of ferrocytochrome c2 from the purple photosynthetic bacterium Rhodopseudomonas viridis has been refined to a final R-factor of 18.2% for 15,014 unique reflections collected by synchrotron radiation between 6.0 and 1.6 A resolution. The refined model includes 107 amino acid residues, one heme prosthetic group and 125 water molecules. The root-mean-square deviations from the ideal bond lengths and angles were 0.014 A and 3.0 degrees, respectively. The atomic coordinate error was estimated to be less than 0.3 A. A structure comparison of this cytochrome c2 with those of the other c-type cytochromes demonstrated that these cytochromes exhibit a high degree of structural similarity with the exception of the surface loop and the terminal region of the polypeptide chain. The deletion of an intrahelical amino residue distorted the conformation of the alpha-helix and it divided into two pieces. The C-terminal extension of the polypeptide chain caused significant conformational changes of the contact residues compared with the other c-type cytochromes. Of the water molecules conserved in various c-type cytochromes, two are located internally in the vicinity of the heme group. One of these water molecules found in this cytochrome c2 is evolutionarily conserved among eukaryotic cytochromes c. This water molecule is located in the heme proximate environment in a position similar to that of eukaryotic cytochromes c. The position of this water molecule is associated with the oxidation state of the heme iron in electron transfer.

  • Organizational Affiliation

    Research Laboratory of Resources Utilization, Tokyo Institute of Technology Nagatsuta, Yokohama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (CYTOCHROME C2)107Blastochloris viridisMutation(s): 0 
Gene Names: cycA
Membrane Entity: Yes 
Find proteins for P00083 (Blastochloris viridis)
Explore P00083 
Go to UniProtKB:  P00083
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00083
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: 1.60 Å
  • R-Value Work: 0.182 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.13α = 90
b = 76.13β = 90
c = 40.4γ = 120
Software Package:
Software NamePurpose
WEISdata reduction
PROTEINdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-08-09
    Changes: Data collection, Database references, Refinement description