2CDV

REFINED STRUCTURE OF CYTOCHROME C3 AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined structure of cytochrome c3 at 1.8 A resolution

Higuchi, Y.Kusunoki, M.Matsuura, Y.Yasuoka, N.Kakudo, M.

(1984) J.Mol.Biol. 172: 109-139


  • PubMed Abstract: 
  • The structure of cytochrome c3 from the sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki has been successfully refined at 1.8 A resolution. The crystallographic R factor is 0.176 for 9907 significant reflections. The isotropic temperature f ...

    The structure of cytochrome c3 from the sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki has been successfully refined at 1.8 A resolution. The crystallographic R factor is 0.176 for 9907 significant reflections. The isotropic temperature factors of individual atoms were refined and a total of 47 water molecules located on the difference map were incorporated in the refinement. The four heme groups are closely packed, with adjacent pairs of heme planes being nearly perpendicular to each other. The fifth and the sixth ligands of the heme iron atoms are histidine residues with N epsilon 2-Fe distances ranging from 1.88 A to 2.12 A. The histidine co-ordination to the heme iron is different for each heme group. The heme groups are all highly exposed to solvent, although the actual regions exposed differ among the hemes. The four heme groups are located in different environments, and the heme planes are deformed from planarity. The differences in the heme structures and their environments indicate that the four heme groups are non-equivalent. The chemical as well as the physical properties of cytochrome c3 should be interpreted in terms of the structural non-equivalence of the heme groups. The characteristic secondary structural non-equivalence of the heme groups. The characteristic secondary structures of the polypeptide chain of this molecule are three short alpha-helices, two short beta-strands and ten reverse turns.


    Related Citations: 
    • The Structure of Cytochrome C3 from Desulfovibrio Vulgaris Miyazaki at 2.5 Angstroms Resolution
      Higuchi, Y.,Bando, S.,Kusunoki, M.,Matsuura, Y.,Yasuoka, N.,Kakudo, M.,Yamanaka, T.,Yagi, T.,Inokuchi, H.
      (1981) J.Biochem.(Tokyo) 89: 1659
    • Crystallographic Data for Cytochrome C3 from Two Strains of Desulfovibrio Vulgaris, Miyazaki
      Bando, S.,Matsuura, Y.,Tanaka, N.,Yasuoka, N.,Kakudo, M.,Yagi, T.,Inokuchi, H.
      (1979) J.Biochem.(Tokyo) 86: 269
    • On Cytochrome C3 Folding
      Higuchi, Y.,Kusunoki, M.,Yasuoka, N.,Kakudo, M.,Yagi, T.
      (1981) J.Biochem.(Tokyo) 90: 1715
    • Amino Acid Sequence of Cytochrome C3 from Desulfovibrio Vulgaris, Miyazaki
      Shinkai, W.,Hase, T.,Yagi, T.,Matsubara, H.
      (1980) J.Biochem.(Tokyo) 87: 1747



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C3
A
107Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 0 
Find proteins for P00132 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P00132
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: 1.8 Å
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.900α = 90.00
b = 68.100β = 90.00
c = 34.900γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1984-02-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other