› 7yee

X-ray diffraction
2.15Å resolution

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-241179 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Deoxyribodipyrimidine photo-lyase Chains: A, B
Molecule details ›
Chains: A, B
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
CPD photolesion containing DNA Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.57 KDa
Source organism: synthetic construct
Expression system: Not provided
complementary oligonucleotide to the CPD containing DNA Chains: D, F
CPD photolesion containing DNA Chain: E

Ligands and Environments


Cofactor: Ligand FAD 2 x FAD
1 bound ligand:
Ligand SO4 1 x SO4
1 modified residue:
Ligand TTD 1 x TTD

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SwissFEL ARAMIS BEAMLINE ESA
Spacegroup: P212121
Unit cell:
a: 72.47Å b: 115.91Å c: 169.24Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.238 0.252
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 citation in other articles

Influence of pump laser fluence on ultrafast myoglobin structural dynamics.
Barends et al. (2024)
1 more

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO