› 4jdg

X-ray diffraction
2.74Å resolution

Structure of Tomato Bifunctional Nuclease TBN1, variant N211D

Released:
DOI: 10.2210/pdb4jdg/pdb
PDB entry 4jdg coloured by chain, front view.
PDB entry 4jdg coloured by chain, side view.
PDB entry 4jdg coloured by chain, top view.
Source organism: Solanum lycopersicum
Primary publication:
Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme.
Stránský J, Koval' T, Podzimek T, Týcová A, Lipovová P, Matoušek J, Kolenko P, Fejfarová K, Dušková J, Skálová T, Hašek J, Dohnálek J
Acta Crystallogr F Struct Biol Commun 71 1408-15 (2015)
PMID: 26527269

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-170983 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Aspergillus nuclease S1 Chain: A
Molecule details ›
Chain: A
Length: 277 amino acids
Theoretical weight: 31.65 KDa
Source organism: Solanum lycopersicum
Expression system: Nicotiana benthamiana
UniProt:
  • Canonical: Q0KFV0 (Residues: 26-302; Coverage: 100%)
Gene name: tbn1
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, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand ZN 3 x ZN
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: R3
Unit cell:
a: 115.944Å b: 115.944Å c: 74.713Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.194 0.264
Expression system: Nicotiana benthamiana

Quick links

Citations

2 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)
1 more