3CVX

Drosophila melanogaster (6-4) photolyase H369M mutant bound to ds DNA with a T-T (6-4) photolesion

PDB DOI: https://doi.org/10.2210/pdb3CVX/pdb
NAKB: 3CVX

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:
0.282 (Depositor), 0.260 (DCC)
R-Value Work:
0.230 (Depositor), 0.220 (DCC)
R-Value Observed:
0.233 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure and mechanism of a coenzyme 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.

Macromolecule Content

Total Structure Weight: 72.87 kDa
Atom Count: 4,789
Modelled Residue Count: 532
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: 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8SXK5
Sequence Annotations Expand
Reference Sequence LOADING

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] mmCIF 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: 3.20 Å
R-Value Free: 0.282 (Depositor), 0.260 (DCC)
R-Value Work: 0.230 (Depositor), 0.220 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.41	α = 90
b = 89.04	β = 90
c = 90.16	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Barends, T.R.M.

Schlichting, I.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.