1CCR

STRUCTURE OF RICE FERRICYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 
    0.190 (Depositor), 0.180 (DCC) 

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Ligand Structure Quality Assessment 

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This is version 2.0 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

  • DOI: https://doi.org/10.1016/s0022-2836(83)80092-8
  • Primary Citation of Related Structures:  
    1CCR

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C112Oryza sativaMutation(s): 0 
UniProt
Find proteins for Q0DI31 (Oryza sativa subsp. japonica)
Explore Q0DI31 
Go to UniProtKB:  Q0DI31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0DI31
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
B [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
A
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work:  0.190 (Depositor), 0.180 (DCC) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.78α = 90
b = 43.78β = 90
c = 110.05γ = 120

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HECClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1983-04-21
    Type: Initial release
  • Version 1.1: 2008-03-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2021-03-03
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary