› 3n78

X-ray diffraction
2.95Å resolution

SgrAI bound to Secondary Site DNA and Mg(II)

Released:
DOI: 10.2210/pdb3n78/pdb
PDB entry 3n78 coloured by chain, front view.
PDB entry 3n78 coloured by chain, side view.
PDB entry 3n78 coloured by chain, top view.
Source organism: Streptomyces griseus
Primary publication:
New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA.
Little EJ, Dunten PW, Bitinaite J, Horton NC
Acta Crystallogr D Biol Crystallogr 67 67-74 (2011)
PMID: 21206063

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-116604 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
SgraIR restriction enzyme Chains: A, B
Molecule details ›
Chains: A, B
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(*AP*GP*TP*CP*CP*AP*CP*CP*GP*GP*GP*GP*GP*AP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.92 KDa
Source organism: Streptomyces griseus
Expression system: Not provided
DNA (5'-D(*AP*GP*TP*CP*CP*CP*CP*CP*GP*GP*TP*GP*GP*AP*CP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 16 nucleotides
Theoretical weight: 4.88 KDa
Source organism: Streptomyces griseus
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P21212
Unit cell:
a: 108.794Å b: 133.002Å c: 64.623Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.189 0.282
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)
8 other articles

1 mention without citation

New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA.
Little et al. (2011)