› 3zi5

X-ray diffraction
3.2Å resolution

Crystal STRUCTURE OF RESTRICTION ENDONUCLEASE BFII C-TERMINAL RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA

Released:
DOI: 10.2210/pdb3zi5/pdb
PDB entry 3zi5 coloured by chain, front view.
PDB entry 3zi5 coloured by chain, side view.
PDB entry 3zi5 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme.
Golovenko D, Manakova E, Zakrys L, Zaremba M, Sasnauskas G, Gražulis S, Siksnys V
Nucleic Acids Res 42 4113-22 (2014)
PMID: 24423868

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117117 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Restriction endonuclease Chains: A, D
Molecule details ›
Chains: A, D
Length: 166 amino acids
Theoretical weight: 18.7 KDa
Source organism: Cytobacillus firmus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9F4C9 (Residues: 193-358; Coverage: 46%)
Gene name: R
Sequence domains: Metal-independent restriction enzyme BfiI DNA binding domain
Structure domains: At1g16640 B3 domain
5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3' Chains: B, E
Molecule details ›
Chains: B, E
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3' Chains: C, F
Molecule details ›
Chains: C, F
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P65
Unit cell:
a: 175.18Å b: 175.18Å c: 35.789Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.176 0.226
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Type II restriction endonucleases--a historical perspective and more.
Pingoud et al. (2014)
1 more

3 mentions without citation

Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme.
Golovenko et al. (2014)
2 more