1CCR

STRUCTURE OF RICE FERRICYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of rice ferricytochrome c at 2.0 A resolution.

Ochi, H.Hata, Y.Tanaka, N.Kakudo, M.Sakurai, T.Aihara, S.Morita, Y.

(1983) J.Mol.Biol. 166: 407-418


  • PubMed Abstract: 
  • The crystal structure of ferricytochrome c from rice embryos has been solved by X-ray diffraction to a resolution of 2.0 A, applying a single isomorphous replacement method with anomalous scattering effects. The initial molecular model was built on a ...

    The crystal structure of ferricytochrome c from rice embryos has been solved by X-ray diffraction to a resolution of 2.0 A, applying a single isomorphous replacement method with anomalous scattering effects. The initial molecular model was built on a graphics display system and was refined by the Hendrickson and Konnert method. The R factor was reduced to 0.25. Rice cytochrome c consists of III amino acid residues. In comparison with animal cytochromes c, the peptide chain extends for eight residues at the N-terminal end, which is characteristic for plant cytochromes c. These additional residues display a collagen-like conformation and an irregular reverse turn, and are located around the C-terminal alpha-helix on the surface or the rear side of the molecule. Two hydrogen bonds between the carbonyl oxygen of the N-terminal acetyl group and O eta of Tyr65, and between the peptide carbonyl oxygen of Pro-1 and O epsilon 1 of Gln89, are involved in holding these eight residues on the molecular surface, where Tyr65 and Gln89 are invariant in plant cytochromes c. Except for the extra eight residues, the main-chain conformations of both rice and tuna cytochromes c are essentially identical, though small local conformational differences are found at residues 24, 25, 56 and 57.


    Related Citations: 
    • Amino Acid Sequence of Cytochrome C from Rice
      Mori, E.,Morita, Y.
      (1980) J.Biochem.(Tokyo) 87: 249
    • Studies on Respiratory Enzymes in Rice Kernel. Part I. Isolation and Purification of Cytochrome C and Peroxidase 556 from Rice Embryo
      Mori, Y.,Ida, S.
      (1968) Agric.Biol.Chem. 32: 441
    • A Preliminary Crystallographic Investigation of Rice Cytochrome C
      Morita, Y.,Ida, S.
      (1972) J.Mol.Biol. 71: 807



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C
A
112Oryza sativa subsp. japonicaMutation(s): 0 
Gene Names: CC-1
Find proteins for Q0DI31 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q0DI31
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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
A
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.190 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 43.780α = 90.00
b = 43.780β = 90.00
c = 110.050γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1983-04-21
    Type: Initial release
  • Version 1.1: 2008-03-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other