1CYC

THE CRYSTAL STRUCTURE OF BONITO (KATSUO) FERROCYTOCHROME C AT 2.3 ANGSTROMS RESOLUTION. II. STRUCTURE AND FUNCTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of bonito (katsuo) ferrocytochrome c at 2.3 A resolution. II. Structure and function.

Tanaka, N.Yamane, T.Tsukihara, T.Ashida, T.Kakudo, M.

(1975) J.Biochem.(Tokyo) 77: 147-162


  • PubMed Abstract: 
  • The structure analysis of bonito heart ferrocytochrome c was carried out at 2.3 A resolution by X-ray diffraction, and a Kendrew-type skeletal model was built up. This molecule has an overall egg shape, 35 A in height, 30 A in width and 23 A in thick ...

    The structure analysis of bonito heart ferrocytochrome c was carried out at 2.3 A resolution by X-ray diffraction, and a Kendrew-type skeletal model was built up. This molecule has an overall egg shape, 35 A in height, 30 A in width and 23 A in thickness; the 5th ligand of the heme iron atom is the N-epsilon atom of the His-18 imidazole ring and the 6th is the Met-80 sulfur atom. Distinct alpha-helix regions are found between the N-terminus and reside 11, between 60 and 69, and between 90 and the C-terminus. The most distinct difference between the conformation of the present molecule and that of the horse oxidized molecule is the location of the Phe-82 phenyl ring. In the present reduced molecule, the phyenyl ring is in closer contact with the iron atom and gives influences on the character of the iron atom. Inside the molecule, at the lower part of the heme pocket, there is an extended hydrogen bond network including the propionic acid residues of the heme group. Both Phe-82 and the hydrogen bond network may play a key role in the function of this molecule.


    Related Citations: 
    • Oxidation of a Ferrocytochrome C in the Crystalline State-Structural Change and Anion Binding
      Tsukihara, T.,Yamane, T.,Tanaka, N.,Ashida, T.,Kakudo, M.
      (1973) J.Biochem.(Tokyo) 73: 1163
    • The Crystal Structure of Bonito (Katsuo) Ferrocytochrome C at 4 Angstroms Resolution
      Ashida, T.,Ueki, T.,Tsukihara, T.,Sugihara, A.,Takano, T.,Kakudo, M.
      (1971) J.Biochem.(Tokyo) 70: 913
    • The Crystal Structure of Bonito (Katsuo) Ferrocytochrome C at 2.3 Angstroms Resolution
      Ashida, T.,Tanaka, N.,Yamane, T.,Tsukihara, T.,Kakudo, M.
      (1973) J.Biochem.(Tokyo) 73: 463
    • The Amino Acid Sequence of Cytochrome C from Bonito (Katsuwonus Pelamis, Linnaeus)
      Nakayama, T.,Titani, K.,Narita, K.
      (1971) J.Biochem.(Tokyo) 70: 311



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERROCYTOCHROME C
A, B
103Katsuwonus pelamisGene Names: cyc
Find proteins for P00025 (Katsuwonus pelamis)
Go to UniProtKB:  P00025
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
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: 2.3 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.680α = 90.00
b = 84.580β = 90.00
c = 37.830γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1976-10-06
    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