7AZT | pdb_00007azt

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

• PDB DOI: https://doi.org/10.2210/pdb7AZT/pdb

• Classification: LYASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-11-17 Released: 2021-08-18 
• Deposition Author(s): Cellini, A., Wahlgren, W.Y., Henry, L., Westenhoff, S., Pandey, S.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.208 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

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

• PubMed: 34342273 
• DOI: https://doi.org/10.1107/S2059798321005830
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden.
Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA.
Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
Department of Biology, Northeastern Illinois University, 5500 North St Louis Avenue, Chicago, IL 60625, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.1 kDa 
• Atom Count: 4,168 
• Modeled Residue Count: 502 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RE11660p	A	502	Drosophila melanogaster	Mutation(s): 0  Gene Names: phr6-4, CG2488
UniProt
Find proteins for Q8SXK5 (Drosophila melanogaster) Explore Q8SXK5  Go to UniProtKB:  Q8SXK5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.208 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.63	α = 90
b = 91.64	β = 90
c = 115.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-18 
Deposition Author(s): Cellini, A., Wahlgren, W.Y., Henry, L., Westenhoff, S., Pandey, S.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History  

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