› 3fc3

X-ray diffraction
1.75Å resolution

Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I

Released:
DOI: 10.2210/pdb3fc3/pdb
PDB entry 3fc3 coloured by chain, front view.
PDB entry 3fc3 coloured by chain, side view.
PDB entry 3fc3 coloured by chain, top view.
Source organism: Helicobacter pylori J99
Primary publication:
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
Sokolowska M, Czapinska H, Bochtler M
Nucleic Acids Res 37 3799-810 (2009)
PMID: 19380375

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116244 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 200 amino acids
Theoretical weight: 22.77 KDa
Source organism: Helicobacter pylori J99
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9ZL26 (Residues: 1-190; Coverage: 100%)
Gene name: jhp_0755
Sequence domains:
Structure domains:
5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3' Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: Helicobacter pylori J99
Expression system: Not provided
5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3' Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: Helicobacter pylori J99
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand NA 3 x NA
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: R32
Unit cell:
a: 90.089Å b: 90.089Å c: 334.254Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.181 0.205
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
6 more

6 mentions without citation

Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
Sokolowska et al. (2009)
5 more