2DGE

Crystal structure of oxidized cytochrome C6A from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


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

  • 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 Ang ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c6
A, B, C, D
105Arabidopsis thalianaMutation(s): 0 
Gene Names: PETJ
Find proteins for Q93VA3 (Arabidopsis thaliana)
Go to UniProtKB:  Q93VA3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
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: 1.5 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.186 
  • 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
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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