› 4cdm

X-ray diffraction
2.7Å resolution

Crystal structure of M. mazei photolyase soaked with synthetic 8-HDF

Released:
DOI: 10.2210/pdb4cdm/pdb
PDB entry 4cdm coloured by chain, front view.
PDB entry 4cdm coloured by chain, side view.
PDB entry 4cdm coloured by chain, top view.
Source organism: Methanosarcina mazei Go1
Primary publication:
Structural and evolutionary aspects of antenna chromophore usage by class II photolyases.
Kiontke S, Gnau P, Haselsberger R, Batschauer A, Essen LO
J Biol Chem 289 19659-69 (2014)
PMID: 24849603

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: 482 amino acids
Theoretical weight: 55.12 KDa
Source organism: Methanosarcina mazei Go1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8PYK9 (Residues: 3-464; Coverage: 100%)
Gene name: MM_0852
Sequence domains: DNA photolyase
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD
3 bound ligands:
Ligand FO1 1 x FO1
Ligand SO4 4 x SO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P43212
Unit cell:
a: 69.89Å b: 69.89Å c: 245.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.206 0.27
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions.
Greening et al. (2016)
7 more

1 mention without citation

Structural and evolutionary aspects of antenna chromophore usage by class II photolyases.
Kiontke et al. (2014)