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 
  • R-Value Observed: 0.108 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1111/j.1742-4658.2009.07150.x
  • Primary Citation of Related Structures:  
    3DR0

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c6
A, B, C
93Picosynechococcus sp. PCC 7002Mutation(s): 0 
Gene Names: petJ
UniProt
Find proteins for O30881 (Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6))
Explore O30881 
Go to UniProtKB:  O30881
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO30881
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.107 
  • R-Value Observed: 0.108 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.879α = 90
b = 82.879β = 90
c = 28.277γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-25
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description