› 2f03

X-ray diffraction
3.05Å resolution

Crystal structure of tetrameric restriction endonuclease SfiI in complex with cognate DNA (partial bound form)

Released:
DOI: 10.2210/pdb2f03/pdb
PDB entry 2f03 coloured by chain, ensemble of 2 models, front view.
PDB entry 2f03 coloured by chain, ensemble of 2 models, side view.
PDB entry 2f03 coloured by chain, ensemble of 2 models, top view.
Source organism: Streptomyces fimbriatus
Primary publication:
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
Vanamee ES, Viadiu H, Kucera R, Dorner L, Picone S, Schildkraut I, Aggarwal AK
EMBO J 24 4198-208 (2005)
PMID: 16308566

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

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115232 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II restriction enzyme SfiI Chains: A, C
Molecule details ›
Chains: A, C
Length: 269 amino acids
Theoretical weight: 31.27 KDa
Source organism: Streptomyces fimbriatus
Expression system: Not provided
UniProt:
  • Canonical: O52512 (Residues: 1-269; Coverage: 100%)
Gene name: sfiIR
Sequence domains: Type II restriction enzyme SfiI
Structure domains:
DNA (5'-D(*AP*TP*G*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*TP*AP*TP*T)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 21 nucleotides
Theoretical weight: 6.45 KDa
Source organism: Streptomyces fimbriatus
Expression system: Not provided
DNA (5'-D(*AP*AP*TP*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*AP*CP*AP*T)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 21 nucleotides
Theoretical weight: 6.44 KDa
Source organism: Streptomyces fimbriatus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P6122
Unit cell:
a: 85.6Å b: 85.6Å c: 418.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.241 0.241 0.293
Expression system: Not provided

Quick links

Citations

2 review citations

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

1 mention without citation

A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
Vanamee et al. (2005)