4b5j

X-ray diffraction
2.1Å resolution

Neisseria AP endonuclease bound to the substrate with an orphan Adenine base

Released:

Function and Biology Details

Reaction catalysed:
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Exodeoxyribonuclease III Chain: A
Molecule details ›
Chain: A
Length: 259 amino acids
Theoretical weight: 29.7 KDa
Source organism: Neisseria meningitidis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7DD47 (Residues: 1-259; Coverage: 100%)
Gene names: NMB2082, exoA
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3' Chain: U
Molecule details ›
Chain: U
Length: 11 nucleotides
Theoretical weight: 3.19 KDa
Source organism: Neisseria meningitidis
Expression system: Not provided
5'-D(*CP*GP*AP*TP*GP*AP*GP*TP*AP*GP*CP)-3' Chain: V
Molecule details ›
Chain: V
Length: 11 nucleotides
Theoretical weight: 3.4 KDa
Source organism: Neisseria meningitidis
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P43212
Unit cell:
a: 69.88Å b: 69.88Å c: 122.27Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.208 0.258
Expression systems:
  • Escherichia coli
  • Not provided