› 1dfm

X-ray diffraction
1.5Å resolution

Crystal structure of restriction endonuclease BGLII complexed with DNA 16-mer

Released:
DOI: 10.2210/pdb1dfm/pdb
PDB entry 1dfm coloured by chain, front view.
PDB entry 1dfm coloured by chain, side view.
PDB entry 1dfm coloured by chain, top view.
Source organism: Bacillus subtilis
Primary publication:
Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution.
Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK
Nat Struct Biol 7 134-40 (2000)
PMID: 10655616

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 domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113677 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Type II restriction enzyme BglII Chains: A, B
Molecule details ›
Chains: A, B
Length: 223 amino acids
Theoretical weight: 26.03 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q45488 (Residues: 1-223; Coverage: 100%)
Gene name: bglIIR
Structure domains: Restriction Endonuclease
DNA (5'-D(*TP*AP*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
Source organism: Bacillus subtilis
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 48.7Å b: 101.8Å c: 116.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.192 0.224
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.
Kobayashi I. (2001)
8 more

12 mentions without citation

Structure and function of type II restriction endonucleases.
Pingoud et al. (2001)
11 more