2DGE

Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of oxidized cytochrome c(6A) from Arabidopsis thaliana

Chida, H.Yokoyama, T.Kawai, F.Nakazawa, A.Akazaki, H.Takayama, Y.Hirano, T.Suruga, K.Satoh, T.Yamada, S.Kawachi, R.Unzai, S.Nishio, T.Park, S.-Y.Oku, T.

(2006) FEBS Lett 580: 3763-3768

  • DOI: 10.1016/j.febslet.2006.05.067
  • Primary Citation of Related Structures:  
    2DGE

  • PubMed Abstract: 
  • Compared with algal and cyanobacterial cytochrome c(6), cytochrome c(6A) from higher plants contains an additional loop of 12 amino acid residues. We have determined the first crystal structure of cytochrome c(6A) from Arabidopsis thaliana at 1.5 Angstrom resolution in order to help elucidate its function ...

    Compared with algal and cyanobacterial cytochrome c(6), cytochrome c(6A) from higher plants contains an additional loop of 12 amino acid residues. We have determined the first crystal structure of cytochrome c(6A) from Arabidopsis thaliana at 1.5 Angstrom resolution in order to help elucidate its function. The overall structure of cytochrome c(6A) follows the topology of class I c-type cytochromes in which the heme prosthetic group covalently binds to Cys16 and Cys19, and the iron has octahedral coordination with His20 and Met60 as the axial ligands. Two cysteine residues (Cys67 and Cys73) within the characteristic 12 amino acids loop form a disulfide bond, contributing to the structural stability of cytochrome c(6A). Our model provides a chemical basis for the known low redox potential of cytochrome c(6A) which makes it an unsuitable electron carrier between cytochrome b(6)f and PSI.


    Organizational Affiliation

    Bio-organic Chemistry Laboratory, Graduate School of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa-shi, Kanagawa 252-8510, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c6A, B, C, D105Arabidopsis thalianaMutation(s): 0 
Gene Names: ATC6PETJAt5g45040K21C13.23
UniProt
Find proteins for Q93VA3 (Arabidopsis thaliana)
Explore Q93VA3 
Go to UniProtKB:  Q93VA3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93VA3
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.443α = 82.51
b = 51.843β = 62.08
c = 53.685γ = 63.26
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance