› 3w52

X-ray diffraction
1.76Å resolution

Zinc-dependent bifunctional nuclease

Released:
DOI: 10.2210/pdb3w52/pdb
PDB entry 3w52 coloured by chain, front view.
PDB entry 3w52 coloured by chain, side view.
PDB entry 3w52 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Mechanistic insights to catalysis by a zinc-dependent bi-functional nuclease from Arabidopsis thaliana
Chou TL, Ko TP, Ko CY, Lin TY, Guo RT, Yu TF, Chan HC, Shaw JF, Wang AHJ
Biocatal Agric Biotechnol (2013)

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189937 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Endonuclease 2 Chain: A
Molecule details ›
Chain: A
Length: 269 amino acids
Theoretical weight: 30.61 KDa
Source organism: Arabidopsis thaliana
Expression system: Agrobacterium tumefaciens
UniProt:
  • Canonical: Q9C9G4 (Residues: 28-290; Coverage: 100%)
Gene names: At1g68290, ENDO2, T22E19.8
Sequence domains: S1/P1 Nuclease
Structure domains: P1 Nuclease

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand ADE 1 x ADE
Ligand ZN 3 x ZN
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P212121
Unit cell:
a: 54.254Å b: 66.727Å c: 99.487Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.167 0.196
Expression system: Agrobacterium tumefaciens

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