› 3a4k

X-ray diffraction
2.17Å resolution

Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution

Released:
DOI: 10.2210/pdb3a4k/pdb
PDB entry 3a4k coloured by chain, front view.
PDB entry 3a4k coloured by chain, side view.
PDB entry 3a4k 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 hexamer (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-116056 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Type II restriction enzyme HindIII Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 301 amino acids
Theoretical weight: 35.14 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(*GP*CP*CP*A)-3') Chains: E, G, I, K
Molecule details ›
Chains: E, G, I, K
Length: 4 nucleotides
Theoretical weight: 1.18 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Not provided
DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3') Chains: F, H, J, L
Molecule details ›
Chains: F, H, J, L
Length: 8 nucleotides
Theoretical weight: 2.44 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Not provided
DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3') Chains: M, N
Molecule details ›
Chains: M, N
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P21
Unit cell:
a: 83.46Å b: 132.211Å c: 94.07Å
α: 90° β: 111.03° γ: 90°
R-values:
R R work R free
0.18 0.178 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 citation in other articles

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

3 mentions without citation

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