› 3bam

X-ray diffraction
1.8Å resolution

RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)

Released:
DOI: 10.2210/pdb3bam/pdb
PDB entry 3bam coloured by chain, front view.
PDB entry 3bam coloured by chain, side view.
PDB entry 3bam coloured by chain, top view.
Source organism: Bacillus amyloliquefaciens
Primary publication:
The role of metals in catalysis by the restriction endonuclease BamHI.
Viadiu H, Aggarwal AK
Nat Struct Biol 5 910-6 (1998)
PMID: 9783752

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 pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116088 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Type II restriction enzyme BamHI Chains: A, B
Molecule details ›
Chains: A, B
Length: 213 amino acids
Theoretical weight: 24.6 KDa
Source organism: Bacillus amyloliquefaciens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23940 (Residues: 1-213; Coverage: 100%)
Gene name: bamHIR
Sequence domains: Restriction endonuclease BamHI
Structure domains: Restriction Endonuclease
DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: Bacillus amyloliquefaciens
Expression system: Not provided
DNA (5'-D(*TP*AP*TP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.21 KDa
Source organism: Bacillus amyloliquefaciens
Expression system: Not provided
DNA (5'-D(P*GP*AP*TP*CP*CP*AP*TP*A)-3') Chain: E
Molecule details ›
Chain: E
Length: 8 nucleotides
Theoretical weight: 2.41 KDa
Source organism: Bacillus amyloliquefaciens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 106.4Å b: 79.6Å c: 67.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.226 0.268
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

15 review citations

Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
Yang et al. (2006)
14 more

12 mentions without citation

DNA conformations and their sequence preferences.
Svozil et al. (2008)
11 more