1CO6

CRYSTAL STRUCTURE OF FERROCYTOCHROME C2 FROM RHODOPSEUDOMONAS VIRIDIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1006/jmbi.1995.0491
  • Also Cited By: 1HH7

  • 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 ...

    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.


    Related Citations: 
    • Application of Automatic Molecular-Replacement Procedure to Crystal Structure Analysis of Cytochrrome c2 from Rhodopseudomonas Viridis
      Miki, K.,Sogabe, S.,Uno, A.,Ezoe, T.,Kasai, N.,Saeda, M.,Matsuura, Y.,Miki, M.
      (1994) Acta Crystallogr.,Sect.D 50: 271
    • Structure Similarity of Cytochrrome c2 from Rhodopseudomonas Viridis to Mitochondrial Cytochrome C Revealed by its Crystal Structure at 2.7 A Resokution
      Sogabe, S.,Ezoe, T.,Kasai, N.,Saeda, M.,Uno, A.,Miki, M.,Miki, K.
      (1994) FEBS Lett. 345: 5


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CYTOCHROME C2)
A
107Blastochloris viridisMutation(s): 0 
Gene Names: cycA
Find proteins for P00083 (Blastochloris viridis)
Go to UniProtKB:  P00083
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.182 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.130α = 90.00
b = 76.130β = 90.00
c = 40.400γ = 120.00
Software Package:
Software NamePurpose
PROTEINdata scaling
PROLSQrefinement
PHASERphasing
WEISdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-06-05 
  • Released Date: 1999-06-18 
  • Deposition Author(s): Miki, K., Sogabe, S.

Revision History 

  • Version 1.0: 1999-06-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description