› 2flc

X-ray diffraction
2.59Å resolution

Post-Reactive Complex of Restriction Endonuclease HinP1I with Nicked Cognate DNA and Magnesium Ions

Released:
DOI: 10.2210/pdb2flc/pdb
PDB entry 2flc coloured by chain, front view.
PDB entry 2flc coloured by chain, side view.
PDB entry 2flc coloured by chain, top view.
Source organism: Haemophilus influenzae
Primary publication:
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X
Nucleic Acids Res 34 939-48 (2006)
PMID: 16473850

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115266 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
R.HinP1I restriction endonuclease Chain: A
Molecule details ›
Chain: A
Length: 247 amino acids
Theoretical weight: 28.79 KDa
Source organism: Haemophilus influenzae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5I6E6 (Residues: 1-247; Coverage: 100%)
Gene name: hinP1IR
Sequence domains: R.HinP1I restriction endonuclease
Structure domains: Trna Endonuclease; Chain: A, domain 1
5'-D(*CP*CP*AP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 4 nucleotides
Theoretical weight: 1.18 KDa
Source organism: Haemophilus influenzae
Expression system: Not provided
5'-D(P*CP*GP*CP*TP*GP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 6 nucleotides
Theoretical weight: 1.83 KDa
Source organism: Haemophilus influenzae
Expression system: Not provided
5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3' Chain: E
Molecule details ›
Chain: E
Length: 10 nucleotides
Theoretical weight: 3.05 KDa
Source organism: Haemophilus influenzae
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P6522
Unit cell:
a: 100.387Å b: 100.387Å c: 139.369Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.281 0.275 0.324
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

CRISPR-mediated adaptive immune systems in bacteria and archaea.
Sorek et al. (2013)
1 more

2 mentions without citation

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.
Kuznetsova et al. (2015)
1 more