› 3or3

X-ray diffraction
1.95Å resolution

Restriction endonuclease HPY188I in complex with product DNA

Released:
DOI: 10.2210/pdb3or3/pdb
PDB entry 3or3 coloured by chain, front view.
PDB entry 3or3 coloured by chain, side view.
PDB entry 3or3 coloured by chain, top view.
Source organism: Helicobacter pylori 118
Primary publication:
Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
Sokolowska M, Czapinska H, Bochtler M
Nucleic Acids Res 39 1554-64 (2011)
PMID: 20935048

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116665 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Restriction endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 180 amino acids
Theoretical weight: 21.13 KDa
Source organism: Helicobacter pylori 118
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KJ88 (Residues: 1-170; Coverage: 100%)
Gene names: DDP42_05685, EDC13_06450, EPC71_02780, F7195_05565, hpy188IR
Structure domains: GIY-YIG endonuclease
5'-D(*GP*AP*TP*CP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 5 nucleotides
Theoretical weight: 1.5 KDa
Source organism: Helicobacter pylori 118
Expression system: Not provided
5'-D(*GP*TP*TP*CP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 5 nucleotides
Theoretical weight: 1.5 KDa
Source organism: Helicobacter pylori 118
Expression system: Not provided
5'-D(P*GP*AP*AP*C)-3' Chain: E
Molecule details ›
Chain: E
Length: 4 nucleotides
Theoretical weight: 1.2 KDa
Source organism: Helicobacter pylori 118
Expression system: Not provided
5'-D(P*GP*AP*TP*C)-3' Chain: F
Molecule details ›
Chain: F
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: Helicobacter pylori 118
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 3 x CA
Ligand CL 4 x CL
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P41212
Unit cell:
a: 65.395Å b: 65.395Å c: 221.783Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.201
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Type II restriction endonucleases--a historical perspective and more.
Pingoud et al. (2014)
5 more

2 mentions without citation

Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
Sokolowska et al. (2011)
1 more