3CVW | pdb_00003cvw

Drosophila melanogaster (6-4) photolyase H365N mutant bound to ds DNA with a T-T (6-4) photolesion and cofactor F0

• PDB DOI: https://doi.org/10.2210/pdb3CVW/pdb
• NAKB: 3CVW

• Classification: Lyase/DNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-04-20 Released: 2009-10-13 
• Deposition Author(s): Maul, M.J., Barends, T.R.M., Glas, A.F., Cryle, M.J., Schlichting, I., Carell, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.329 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.275 (Depositor) 

Literature

Structure and mechanism of a cofactor f0 accelerated (6-4) photolyase from the fruit fly

Maul, M.J., Barends, T., Glas, A.F., Cryle, M.J., Schneider, S., Domratcheva, T., Schlichting, I., Carell, T.

To be published.

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: 73.22 kDa 
• Atom Count: 4,817 
• Modeled Residue Count: 532 
• Deposited Residue Count: 573 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RE11660p	C [auth A]	543	Drosophila melanogaster	Mutation(s): 1  Gene Names: phr64-520
UniProt
Find proteins for Q8SXK5 (Drosophila melanogaster) Explore Q8SXK5  Go to UniProtKB:  Q8SXK5

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DGP*DGP*(64T)P*(5PY)P*DGP*DCP*DAP*DGP*DGP*DT)-3')	A [auth C]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DTP*DAP*DCP*DCP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DTP*DG)-3')	B [auth D]	15	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FO1	E [auth A]	1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol C16 H17 N3 O7 AUEILLWDYUBWCM-XQQFMLRXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.329 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.275 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.47	α = 90
b = 89.51	β = 90
c = 89.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Maul, M.J., Barends, T.R.M., Glas, A.F., Cryle, M.J., Schlichting, I., Carell, T.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection