3DR0

Structure of reduced cytochrome c6 from Synechococcus sp. PCC 7002


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.107 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Atomic-resolution structure of reduced cyanobacterial cytochrome c6 with an unusual sequence insertion

Bialek, W.Krzywda, S.Jaskolski, M.Szczepaniak, A.

(2009) Febs J. 276: 4426-4436

  • DOI: 10.1111/j.1742-4658.2009.07150.x
  • Also Cited By: 4EID, 4EIC

  • PubMed Abstract: 
  • The structure of the reduced form of cytochrome c(6) from the mesophilic cyanobacterium Synechococcus sp. PCC 7002 has been determined at 1.2 A and refined to an R-factor of 0.107. This protein is unique among all known cytochromes c(6), owing to the ...

    The structure of the reduced form of cytochrome c(6) from the mesophilic cyanobacterium Synechococcus sp. PCC 7002 has been determined at 1.2 A and refined to an R-factor of 0.107. This protein is unique among all known cytochromes c(6), owing to the presence of an unusual seven-residue insertion, KDGSKSL(44-50), which differs from the insertion found in the recently discovered plant cytochromes c(6A). Furthermore, the present protein is unusual because of its very high content (36%) of the smallest residues (glycine and alanine). The structure reveals that the overall fold of the protein is similar to that of other class I c-type cytochromes, despite the presence of the specific insertion. The insertion is located within the most variable region of the cytochrome c(6) sequence, i.e. between helices II and III. The first six residues [KDGSKS(44-49)] form a loop, whereas the last residue, Leu50, extends the N-terminal beginning of helix III. Several specific noncovalent interactions are found inside the insertion, as well as between the insertion and the rest of the protein. The crystal structure contains three copies of the cytochrome c(6) molecule per asymmetric unit, and is characterized by an unusually high packing density, with solvent occupying barely 17.58% of the crystal volume.


    Related Citations: 
    • Deeply branching c6-like cytochromes of cyanobacteria
      Bialek, W.,Nelson, M.,Tamiola, K.,Kallas, T.,Szczepaniak, A.
      (2008) Biochemistry 47: 5515
    • Cytochrome c6 from Synechococcus sp. PCC 7002
      Nomura, C.,Bryant, D.A.
      (1999) The Phototrophic Prokaryotes --: 269


    Organizational Affiliation

    Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c6
A, B, C
93Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6)Mutation(s): 0 
Gene Names: petJ
Find proteins for O30881 (Synechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Go to UniProtKB:  O30881
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C
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: 1.23 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.107 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 82.879α = 90.00
b = 82.879β = 90.00
c = 28.277γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
MAR345dtbdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-04-25
    Type: Database references