› 4cxv

X-ray diffraction
2Å resolution

Structure of bifunctional endonuclease (AtBFN2) in complex with phosphate.

Released:
DOI: 10.2210/pdb4cxv/pdb
PDB entry 4cxv coloured by chain, front view.
PDB entry 4cxv coloured by chain, side view.
PDB entry 4cxv coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structural insights of the ssDNA binding site in the multifunctional endonuclease AtBFN2 from Arabidopsis thaliana.
Yu TF, Maestre-Reyna M, Ko CY, Ko TP, Sun YJ, Lin TY, Shaw JF, Wang AH
OpenAccess logo PLoS One 9 e105821 (2014)
PMID: 25157844

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 (5 distinct):
Endonuclease 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 269 amino acids
Theoretical weight: 30.61 KDa
Source organism: Arabidopsis thaliana
Expression system: Arabidopsis thaliana
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, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
3 bound ligands:
Ligand NAG 1 x NAG
Ligand PO4 2 x PO4
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P1
Unit cell:
a: 45.524Å b: 52.87Å c: 60.841Å
α: 71.34° β: 78.63° γ: 76.62°
R-values:
R R work R free
0.204 0.202 0.249
Expression system: Arabidopsis thaliana

Quick links

Citations

1 review citation

Carbohydrate structure: the rocky road to automation.
Agirre et al. (2017)
1 other article

3 mentions without citation

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
Kovaľ et al. (2016)
2 more