7QUT | pdb_00007qut

serial synchrotron crystallographic structure of Drosophila Melanogaster (6-4) photolyase

• PDB DOI: https://doi.org/10.2210/pdb7QUT/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-18 Released: 2022-04-13 
• Deposition Author(s): Cellini, A., Weixiao, Y.W., Kumar, M.S., Westenhoff, S.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Structural basis of the radical pair state in photolyases and cryptochromes.

Cellini, A., Shankar, M.K., Wahlgren, W.Y., Nimmrich, A., Furrer, A., James, D., Wranik, M., Aumonier, S., Beale, E.V., Dworkowski, F., Standfuss, J., Weinert, T., Westenhoff, S.

(2022) Chem Commun (Camb) 58: 4889-4892

• PubMed: 35352724 
• DOI: https://doi.org/10.1039/d2cc00376g
• Primary Citation Related Structures: 
  7QUT


• PubMed Abstract: 
  

  We present the structure of a photoactivated animal (6-4) photolyase in its radical pair state, captured by serial crystallography. We observe how a conserved asparigine moves towards the semiquinone FAD chromophore and stabilizes it by hydrogen bonding. Several amino acids around the final tryptophan radical rearrange, opening it up to the solvent. The structure explains how the protein environment stabilizes the radical pair state, which is crucial for function of (6-4) photolyases and cryptochromes.

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Organizational Affiliation: 
• Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden. [e-mail].
Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland.
Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland.
Photon Science Division - Laboratory for Synchrotron Radiation and Femtochemistry (LSF), Paul Scherrer Institut, 5232 Villigen, Switzerland.
Department of Chemistry-BMC, University of Uppsala, Husargatan 3, 75237 Uppsala, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.73 kDa 
• Atom Count: 4,277 
• Modeled Residue Count: 500 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RE11660p	A	508	Drosophila melanogaster	Mutation(s): 0  Gene Names: phr6-4, CG2488 EC: 4.1.99.3
UniProt
Find proteins for Q0E8P0 (Drosophila melanogaster) Explore Q0E8P0  Go to UniProtKB:  Q0E8P0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.6	α = 90
b = 103.6	β = 90
c = 52.08	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Cellini, A., Weixiao, Y.W., Kumar, M.S., Westenhoff, S.

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Funding Organization	Location	Grant Number
European Commission	European Union	MolStuctDyn

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2022-04-27
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description