› 5o8d

X-ray diffraction
2Å resolution

Mutant of class II CPD photolyase from Methanosarcina mazei - Y345F

Released:
DOI: 10.2210/pdb5o8d/pdb
PDB entry 5o8d coloured by chain, front view.
PDB entry 5o8d coloured by chain, side view.
PDB entry 5o8d coloured by chain, top view.
Source organism: Methanosarcina mazei Go1
Primary publication:
Nicotinamide Adenine Dinucleotides Arrest Photoreduction of Class II DNA Photolyases in FADH˙ State.
Ignatz E, Geisselbrecht Y, Kiontke S, Essen LO
Photochem Photobiol 94 81-87 (2018)
PMID: 28858395

Function and Biology Details

Reaction catalysed: 
Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185827 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyribodipyrimidine photo-lyase Chain: A
Molecule details ›
Chain: A
Length: 484 amino acids
Theoretical weight: 55.35 KDa
Source organism: Methanosarcina mazei Go1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8PYK9 (Residues: 1-464; Coverage: 100%)
Gene name: MM_0852
Sequence domains: DNA photolyase
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD
2 bound ligands:
Ligand SO4 8 x SO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P43212
Unit cell:
a: 69.93Å b: 69.93Å c: 245.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.177 0.218
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Sub-nanosecond tryptophan radical deprotonation mediated by a protein-bound water cluster in class II DNA photolyases.
Müller et al. (2018)
2 more