› 3c25

X-ray diffraction
2.5Å resolution

Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA

Released:
DOI: 10.2210/pdb3c25/pdb
PDB entry 3c25 coloured by chain, front view.
PDB entry 3c25 coloured by chain, side view.
PDB entry 3c25 coloured by chain, top view.
Source organism: Nocardia otitidiscaviarum
Primary publication:
Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.
Lambert AR, Sussman D, Shen B, Maunus R, Nix J, Samuelson J, Xu SY, Stoddard BL
Structure 16 558-69 (2008)
PMID: 18400177

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116117 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
NotI restriction endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 383 amino acids
Theoretical weight: 42.47 KDa
Source organism: Nocardia otitidiscaviarum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q2I6W2 (Residues: 1-383; Coverage: 100%)
Gene names: FOH10_30205, notIR
DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3') Chain: C
Molecule details ›
Chain: C
Length: 22 nucleotides
Theoretical weight: 6.78 KDa
Source organism: Nocardia otitidiscaviarum
Expression system: Not provided
DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3') Chain: D
Molecule details ›
Chain: D
Length: 22 nucleotides
Theoretical weight: 6.73 KDa
Source organism: Nocardia otitidiscaviarum
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand FE 2 x FE
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P21
Unit cell:
a: 73.89Å b: 81.712Å c: 73.583Å
α: 90° β: 99.51° γ: 90°
R-values:
R R work R free
0.226 0.223 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

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

3 mentions without citation

Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
Chen et al. (2011)
2 more