PDBe 1k3w

X-ray diffraction
1.42Å resolution

Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease 8 Chain: A
Molecule details ›
Chain: A
Length: 262 amino acids
Theoretical weight: 29.81 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P50465 (Residues: 2-263; Coverage: 100%)
Gene names: JW0704, b0714, nei
Sequence domains:
Structure domains:
5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.96 KDa
Source organism: Escherichia coli
Expression system: Not provided
5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.86 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P4322
Unit cell:
a: 76.03Å b: 76.03Å c: 164.933Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.165 0.203
Expression systems:
  • Escherichia coli
  • Not provided