7AYV

X-ray crystallographic structure of (6-4)photolyase from Drosophila melanogaster at cryogenic temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature.

Cellini, A.Yuan Wahlgren, W.Henry, L.Pandey, S.Ghosh, S.Castillon, L.Claesson, E.Takala, H.Kubel, J.Nimmrich, A.Kuznetsova, V.Nango, E.Iwata, S.Owada, S.Stojkovic, E.A.Schmidt, M.Ihalainen, J.A.Westenhoff, S.

(2021) Acta Crystallogr D Struct Biol 77: 1001-1009

  • DOI: https://doi.org/10.1107/S2059798321005830
  • Primary Citation of Related Structures:  
    7AYV, 7AZT

  • PubMed Abstract: 

    (6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 Å resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 Å resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RE11660p502Drosophila melanogasterMutation(s): 0 
Gene Names: phr6-4CG2488
UniProt
Find proteins for Q8SXK5 (Drosophila melanogaster)
Explore Q8SXK5 
Go to UniProtKB:  Q8SXK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8SXK5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.903α = 90
b = 88.933β = 90
c = 114.022γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description