4EID | pdb_00004eid

Crystal structure of cytochrome c6 Q57V mutant from Synechococcus sp. PCC 7002


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 
    0.176 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.138 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.139 (Depositor) 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history


Literature

Insights into the relationship between the haem-binding pocket and the redox potential of c6 cytochromes: four atomic resolution structures of c6 and c6-like proteins from Synechococcus sp. PCC 7002.

Bialek, W.Krzywda, S.Zatwarnicki, P.Jaskolski, M.Kolesinski, P.Szczepaniak, A.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2823-2832

  • DOI: https://doi.org/10.1107/S1399004714013108
  • Primary Citation of Related Structures:  
    4EIC, 4EID, 4EIE, 4EIF

  • PubMed Abstract: 

    The structure of cytochrome c6C from the mesophilic cyanobacterium Synechococcus sp. PCC 7002 has been determined at 1.03 Å resolution. This is the first structural report on the recently discovered cyanobacterial cytochrome c6-like proteins found in marine and nitrogen-fixing cyanobacteria. Despite high similarity in the overall three-dimensional fold between cytochromes c6 and c6C, the latter shows saliently different electrostatic properties in terms of surface charge distribution and dipole moments. Its midpoint redox potential is less than half of the value for typical c6 cytochromes and results mainly from the substitution of one residue in the haem pocket. Here, high-resolution crystal structures of mutants of both cytochromes c6 and c6C are presented, and the impact of the mutation of specific residues in the haem-binding pocket on the redox potential is discussed. These findings contribute to the elucidation of the structure-function relationship of c6-like cytochromes.


  • Organizational Affiliation
    • Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c693Picosynechococcus sp. PCC 7002Mutation(s): 1 
Gene Names: petJpetJ1SYNPCC7002_A0167
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: 1.13 Å
  • R-Value Free:  0.176 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.138 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.139 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.781α = 90
b = 27.637β = 101.16
c = 44.099γ = 90
Software Package:
Software NamePurpose
AUTOMARdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection
  • Version 2.0: 2021-03-10
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-10-30
    Changes: Structure summary
  • Version 2.3: 2025-11-12
    Changes: Database references