› 2o6m

X-ray diffraction
2.3Å resolution

H98Q mutant of the homing endonuclease I-PPOI complexed with DNA

Released:
DOI: 10.2210/pdb2o6m/pdb
PDB entry 2o6m coloured by chain, front view.
PDB entry 2o6m coloured by chain, side view.
PDB entry 2o6m coloured by chain, top view.
Source organism: Physarum polycephalum
Primary publication:
Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.
Eastberg JH, Eklund J, Monnat R, Stoddard BL
Biochemistry 46 7215-25 (2007)
PMID: 17516660

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115710 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Intron-encoded endonuclease I-PpoI Chains: A, B
Molecule details ›
Chains: A, B
Length: 163 amino acids
Theoretical weight: 17.8 KDa
Source organism: Physarum polycephalum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q94702 (Residues: 1-163; Coverage: 100%)
Sequence domains: Zinc-binding loop region of homing endonuclease
Structure domains: Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A
5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DA)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 21 nucleotides
Theoretical weight: 6.44 KDa
Source organism: Physarum polycephalum
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P3121
Unit cell:
a: 113.85Å b: 113.85Å c: 88.88Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.211 0.244
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

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