› 3dvo

X-ray diffraction
1.89Å resolution

SgrAI with cognate DNA and calcium bound

Released:
DOI: 10.2210/pdb3dvo/pdb
PDB entry 3dvo coloured by chain, front view.
PDB entry 3dvo coloured by chain, side view.
PDB entry 3dvo coloured by chain, top view.
Source organisms:
Primary publication:
The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, Hough D, Bitinaite J, Horton NC
Nucleic Acids Res 36 5405-16 (2008)
PMID: 18701646

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116186 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
SgraIR restriction enzyme Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 338 amino acids
Theoretical weight: 37.94 KDa
Source organism: Streptomyces griseus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9F6L0 (Residues: 2-339; Coverage: 100%)
Gene name: sgraIR
Sequence domains: Cfr10I/Bse634I restriction endonuclease
Structure domains: Restriction Endonuclease
DNA (5'-D(*DGP*DAP*DGP*DTP*DCP*DCP*DAP*DCP*DCP*DGP*DGP*DTP*DGP*DGP*DAP*DCP*DTP*DC)-3') Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 18 nucleotides
Theoretical weight: 5.52 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 8 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P21
Unit cell:
a: 59.136Å b: 119.248Å c: 123.799Å
α: 90° β: 95.62° γ: 90°
R-values:
R R work R free
0.221 0.22 0.273
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation.
Park et al. (2019)
17 other articles

9 mentions without citation

The structure of SgrAI bound to DNA; recognition of an 8 base pair target.
Dunten et al. (2008)
8 more