› 8vnk

X-ray diffraction
1.61Å resolution

Homing endonuclease I-PpoI-DNA complex:reaction at pH6.0 (K+ MES) with 500 uM Mn2+ for 160s

Released:
DOI: 10.2210/pdb8vnk/pdb
PDB entry 8vnk coloured by chain, front view.
PDB entry 8vnk coloured by chain, side view.
PDB entry 8vnk coloured by chain, top view.
Source organisms:
Entry authors: Chang C, Gao Y

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-246852 (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: 162 amino acids
Theoretical weight: 17.68 KDa
Source organism: Physarum polycephalum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q94702 (Residues: 2-163; Coverage: 99%)
Sequence domains: Zinc-binding loop region of homing endonuclease
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: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MN 2 x MN
Ligand NA 2 x NA
Ligand GOL 5 x GOL
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P3121
Unit cell:
a: 114.06Å b: 114.06Å c: 88.02Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.182 0.194
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links