6fk5

X-ray diffraction
2.02Å resolution

Structure of 3' phosphatase NExo (D146N) from Neisseria bound to DNA substrate in presence of magnesium ion

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 dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Exodeoxyribonuclease III Chain: A
Molecule details ›
Chain: A
Length: 258 amino acids
Theoretical weight: 29.32 KDa
Source organism: Neisseria meningitidis MC58
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9K100 (Residues: 1-256; Coverage: 100%)
Gene names: NMB0399, xthA
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
DNA (5'-D(P*CP*TP*AP*GP*CP*GP*AP*AP*GP*CP*TP*AP*GP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 18 nucleotides
Theoretical weight: 5.59 KDa
Source organism: other sequences
Expression system: synthetic construct

Ligands and Environments

2 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P43212
Unit cell:
a: 58.94Å b: 58.94Å c: 292.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.23 0.258
Expression systems:
  • Escherichia coli BL21(DE3)
  • synthetic construct