2WQ6

Structure of the 6-4 photolyase of D. melanogaster in complex with the non-natural N4-methyl T(Dewar)C lesion

PDB DOI: https://doi.org/10.2210/pdb2WQ6/pdb
NAKB: 2WQ6

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

Deposited: 2009-08-14 Released: 2010-02-23
Deposition Author(s): Glas, A.F., Kaya, E., Schneider, S., Maul, M.J., Carell, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.228
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

DNA (6-4) Photolyases Reduce Dewar Isomers for Isomerization Into (6-4) Lesions

Glas, A.F., Kaya, E., Schneider, S., Heil, K., Fazio, D., Maul, M.J., Carell, T.

(2010) J Am Chem Soc 132: 3254

PubMed: 20166732 Search on PubMed
DOI: https://doi.org/10.1021/ja910917f
Primary Citation of Related Structures:
2WQ6, 2WQ7

PubMed Abstract:
Repair of the Dewar valence isomers by (6-4) photolyases proceeds via an enzyme catalyzed ring-opening reaction of the Dewar lesion to the (6-4) photoproduct.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 72.89 kDa
Atom Count: 5,005
Modelled Residue Count: 538
Deposited Residue Count: 573
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RE11660P	A	543	Drosophila melanogaster	Mutation(s): 0 EC: 4.1.99.3
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: 2
Molecule	Chains	Length	Organism	Image
5'-D(APCPAPGPCPGPGPTDYPCDWPGP* CPAPAPGPT)-3'	B [auth C]	15	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(TPAPCPCPTPGPCPGPAPCP* CPGPCPTPG)-3'	C [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: 2.30 Å
R-Value Free: 0.228
R-Value Work: 0.201
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.169	α = 90
b = 87.486	β = 90
c = 91.856	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-23
Type: Initial release
Version 1.1: 2011-11-09
Changes: Database references, Derived calculations, Refinement description, Version format compliance
Version 1.2: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description