› 1ipp

X-ray diffraction
2.2Å resolution

HOMING ENDONUCLEASE/DNA COMPLEX

Released:
DOI: 10.2210/pdb1ipp/pdb
PDB entry 1ipp coloured by chain, front view.
PDB entry 1ipp coloured by chain, side view.
PDB entry 1ipp coloured by chain, top view.
Source organism: Physarum polycephalum
Primary publication:
DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Flick KE, Jurica MS, Monnat RJ, Stoddard BL
Nature 394 96-101 (1998)
PMID: 9665136

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113977 (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: 17.81 KDa
Source organism: Physarum polycephalum
Expression system: Escherichia coli BL21(DE3)
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
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-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 CD 4 x CD
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P3121
Unit cell:
a: 113.9Å b: 113.9Å c: 88.5Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.212 0.316
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

15 review citations

Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
Yang et al. (2006)
14 more

2 mentions without citation

Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily.
Saravanan et al. (2004)
1 more