3CVY

Drosophila melanogaster (6-4) photolyase bound to repaired ds DNA

PDB DOI: https://doi.org/10.2210/pdb3CVY/pdb
NAKB: 3CVY

Classification: Lyase/DNA
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-04-20 Released: 2008-11-04
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: 2.70 Å
R-Value Free: 0.266
R-Value Work: 0.212
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure and mechanism of a DNA (6-4) photolyase.

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

(2008) Angew Chem Int Ed Engl 47: 10076-10080

PubMed: 18956392 Search on PubMed
DOI: https://doi.org/10.1002/anie.200804268
Primary Citation of Related Structures:
3CVU, 3CVY

Organizational Affiliation

Centre for Integrative Protein Science, Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany.

Macromolecule Content

Total Structure Weight: 72.88 kDa
Atom Count: 4,781
Modelled Residue Count: 531
Deposited Residue Count: 573
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RE11660p	C [auth A]	543	Drosophila melanogaster	Mutation(s): 0 Gene Names: phr64-520
UniProt
Find proteins for Q8SXK5 (Drosophila melanogaster) Explore Q8SXK5 Go to UniProtKB: Q8SXK5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8SXK5
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(DAPDCPDAPDGPDCPDGPDGPDTPDTPDGPDCPDAPDGPDGP*DT)-3')	A [auth C]	15	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(DTPDAPDCPDCPDTPDGPDCPDAPDAPDCPDCPDGPDCPDTP*DG)-3')	B [auth D]	15	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.266
R-Value Work: 0.212
R-Value Observed: 0.215
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.36	α = 90
b = 88.84	β = 90
c = 86.59	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-11-04
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: 2024-02-21
Changes: Data collection, Database references, Derived calculations