› 2ezv

X-ray diffraction
2.4Å resolution

Crystal structure of tetrameric restriction endonuclease SfiI bound to cognate DNA.

Released:
DOI: 10.2210/pdb2ezv/pdb
PDB entry 2ezv coloured by chain, front view.
PDB entry 2ezv coloured by chain, side view.
PDB entry 2ezv coloured by chain, 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 octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115231 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II restriction enzyme SfiI Chains: A, B
Molecule details ›
Chains: A, B
Length: 269 amino acids
Theoretical weight: 31.09 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:
5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3' Chain: F
Molecule details ›
Chain: F
Length: 21 nucleotides
Theoretical weight: 6.45 KDa
Source organism: Streptomyces fimbriatus
Expression system: Not provided
5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3' Chain: G
Molecule details ›
Chain: G
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
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P3221
Unit cell:
a: 85.6Å b: 85.6Å c: 202.4Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.224 0.265
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

4 mentions without citation

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