› 2e52

X-ray diffraction
2Å resolution

Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA at 2.0 angstrom resolution

Released:
DOI: 10.2210/pdb2e52/pdb
PDB entry 2e52 coloured by chain, front view.
PDB entry 2e52 coloured by chain, side view.
PDB entry 2e52 coloured by chain, top view.
Source organism: Haemophilus influenzae Rd KW20
Primary publication:
Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations.
Watanabe N, Takasaki Y, Sato C, Ando S, Tanaka I
Acta Crystallogr D Biol Crystallogr 65 1326-33 (2009)
PMID: 19966419

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-115204 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Type II restriction enzyme HindIII Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 300 amino acids
Theoretical weight: 35 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P43870 (Residues: 1-300; Coverage: 100%)
Gene names: HI_1393, hindIIIR
Sequence domains: HindIII restriction endonuclease
Structure domains:
DNA (5'-D(*DGP*DCP*DCP*DAP*DAP*DGP*DCP*DTP*DTP*DGP*DGP*DC)-3') Chains: E, F, G, H, I, J
Molecule details ›
Chains: E, F, G, H, I, J
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand GOL 4 x GOL
Ligand ACT 3 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 83.125Å b: 131.532Å c: 93.718Å
α: 90° β: 111.2° γ: 90°
R-values:
R R work R free
0.177 0.175 0.217
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

Making the bend: DNA tertiary structure and protein-DNA interactions.
Harteis et al. (2014)
2 other articles

7 mentions without citation

Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease.
Horton et al. (2012)
6 more