4LJI

Crystal structure at 1.5 angstrom resolution of the PsbV2 cytochrome from the cyanobacterium thermosynechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Model: experimental
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Literature

Crystal structure at 1.5 angstrom resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus

Suga, M.Lai, T.-L.Sugiura, M.Shen, J.-R.Boussac, A.

(2013) FEBS Lett 587: 3267-3272

  • DOI: https://doi.org/10.1016/j.febslet.2013.08.023
  • Primary Citation of Related Structures:  
    4LJI

  • PubMed Abstract: 

    PsbV2 is a c-type cytochrome present in a very low abundance in the thermophilic cyanobacterium Thermosynechococcus elongatus. We purified this cytochrome and solved its crystal structure at a resolution of 1.5Å. The protein existed as a dimer in the crystal, and has an overall structure similar to other c-type cytochromes like Cytc6 and Cytc550, for example. However, the 5th and 6th heme iron axial ligands were found to be His51 and Cys101, respectively, in contrast to the more common bis-His or His/Met ligands found in most cytochromes. Although a few other c-type cytochromes were suggested to have this axial coordination, this is the first crystal structure reported for a c-type heme with this unusual His/Cys axial coordination. Previous spectroscopic characterizations of PsbV2 are discussed in relation to its structural properties.


  • Organizational Affiliation

    Laboratory of Biomacromolecular Structure, Graduate School of Natural Science and Technology, Department of Biology, Faculty of Science, Okayama University, 1-1, Naka 3-chome, Tsushima, Kita-ku, Okayama 700-8530, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550-like protein
A, B
141Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJE2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DJE2 
Go to UniProtKB:  Q8DJE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DJE2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.421α = 71.86
b = 38.43β = 82.22
c = 47.779γ = 69.38
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2013-10-16
    Changes: Database references
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description