3DMI

Crystallization and Structural Analysis of Cytochrome c6 from the Diatom Phaeodactylum tricornutum at 1.5 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallization and structural analysis of cytochrome c(6) from the diatom Phaeodactylum tricornutum at 1.5 A resolution

Akazaki, H.Kawai, F.Hosokawa, M.Hama, T.Chida, H.Hirano, T.Lim, B.-K.Sakurai, N.Hakamata, W.Park, S.-Y.Nishio, T.Oku, T.

(2009) Biosci.Biotechnol.Biochem. 73: 189-191

  • DOI: 10.1271/bbb.80472

  • PubMed Abstract: 
  • We determined for the first time the crystal structure of diatom cytochrome c(6) from Phaeodactylum tricornutum at 1.5 A resolution. The overall structure of the protein was classified as a class I c-type cytochrome. The physicochemical properties of ...

    We determined for the first time the crystal structure of diatom cytochrome c(6) from Phaeodactylum tricornutum at 1.5 A resolution. The overall structure of the protein was classified as a class I c-type cytochrome. The physicochemical properties of the protein were examined by denaturation with guanidine hydrochloride and urea, and compared with those of other algal cytochrome c(6).


    Organizational Affiliation

    Bio-Organic Chemistry Laboratory, Graduate School of Bioresource Sciences, Nihon University.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cytochrome c6
A
88Phaeodactylum tricornutumMutation(s): 0 
Gene Names: pet J (PetJ)
Find proteins for Q8GTB5 (Phaeodactylum tricornutum)
Go to UniProtKB:  Q8GTB5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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: 1.5 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 80.385α = 90.00
b = 80.385β = 90.00
c = 80.385γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance