1GDV

CRYSTAL STRUCTURE OF CYTOCHROME C6 FROM RED ALGA PORPHYRA YEZOENSIS AT 1.57 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of cytochrome c6 from the red alga Porphyra yezoensis at 1. 57 A resolution.

Yamada, S.Park, S.Y.Shimizu, H.Koshizuka, Y.Kadokura, K.Satoh, T.Suruga, K.Ogawa, M.Isogai, Y.Nishio, T.Shiro, Y.Oku, T.

(2000) Acta Crystallogr.,Sect.D 56: 1577-1582


  • PubMed Abstract: 
  • The crystal structure of cytochrome c(6) from the red alga Porphyra yezoensis has been determined at 1.57 A resolution. The crystal is tetragonal and belongs to space group P4(3)2(1)2, with unit-cell parameters a = b = 49.26 (3), c = 83.45 (4) A and ...

    The crystal structure of cytochrome c(6) from the red alga Porphyra yezoensis has been determined at 1.57 A resolution. The crystal is tetragonal and belongs to space group P4(3)2(1)2, with unit-cell parameters a = b = 49.26 (3), c = 83.45 (4) A and one molecule per asymmetric unit. The structure was solved by the molecular-replacement method and refined with X-PLOR to an R factor of 19.9% and a free R factor of 25.4%. The overall structure of cytochrome c(6) follows the topology of class I c-type cytochromes in which the heme prosthetic group covalently binds to Cys14 and Cys17, and the iron has an octahedral coordination with His18 and Met58 as the axial ligands. The sequence and the structure of the eukaryotic red algal cytochrome c(6) are very similar to those of a prokaryotic cyanobacterial cytochrome c(6) rather than those of eukaryotic green algal c(6) cytochromes.


    Organizational Affiliation

    Department of Biological Chemistry, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C6
A
85Pyropia yezoensisGene Names: petJ
Find proteins for Q8WKJ8 (Pyropia yezoensis)
Go to UniProtKB:  Q8WKJ8
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 49.260α = 90.00
b = 49.260β = 90.00
c = 83.450γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
CCP4data scaling
MOSFLMdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance