6TSY

Cytochrome c6 from Thermosynechococcus elongatus in a monoclinic space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structures of native cytochrome c6from Thermosynechococcus elongatus in two different space groups and implications for its oligomerization.

Falke, S.Feiler, C.Chapman, H.Sarrou, I.

(2020) Acta Crystallogr F Struct Biol Commun 76: 444-452

  • DOI: https://doi.org/10.1107/S2053230X20010249
  • Primary Citation of Related Structures:  
    6TR1, 6TSY

  • PubMed Abstract: 

    Native cytochrome c 6 was purified from an extract of strain BP-1 of the thermophilic cyanobacterium Thermosynechococcus elongatus. The protein was crystallized, and with only slight modifications of the buffer and vapour-diffusion conditions two different space groups were observed, namely H3 and C2. Both crystal structures were solved; they contained three and six molecules per asymmetric unit and were refined to 1.7 and 2.25 Å resolution, respectively. To date, the structure of native cytochrome c 6 from T. elongatus has only been reported as a monomer using NMR spectroscopy, i.e. without addressing putative oligomerization, and related structures have only previously been solved using X-ray crystallography after recombinant gene overexpression in Escherichia coli. The reported space groups of related cyanobacterial cytochrome c 6 structures differ from those reported here. Interestingly, the protein-protein interfaces that were observed utilizing X-ray crystallography could also explain homo-oligomerization in solution; specifically, trimerization is indicated by infra-red dynamic light scattering and blue native gel electrophoresis in solution. Trimers were also detected by mass spectrometry. Furthermore, there is an indication of post-translational methylation in the crystal structure. Additionally, the possibility of modifying the crystal size and the redox activity in the context of photosynthesis is shaping the investigated cytochrome as a highly suitable model protein for advanced serial crystallography at highly brilliant X-ray free-electron laser sources.


  • Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c6
A, B, C, D, E
A, B, C, D, E, F
87Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A3X9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A3X9 
Go to UniProtKB:  P0A3X9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3X9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.019α = 90
b = 109.905β = 100.89
c = 55.402γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references, Derived calculations
  • Version 1.2: 2020-09-16
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description