› 3ldy

X-ray diffraction
1.97Å resolution

An extraordinary mechanism of DNA perturbation exhibited by the rare-cutting HNH restriction endonuclease PacI

Released:
DOI: 10.2210/pdb3ldy/pdb
PDB entry 3ldy coloured by chain, front view.
PDB entry 3ldy coloured by chain, side view.
PDB entry 3ldy coloured by chain, top view.
Source organism: Pseudomonas alcaligenes
Primary publication:
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
Shen BW, Heiter DF, Chan SH, Wang H, Xu SY, Morgan RD, Wilson GG, Stoddard BL
Structure 18 734-43 (2010)
PMID: 20541511

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero hexamer
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Restriction endonuclease PacI Chain: A
Molecule details ›
Chain: A
Length: 142 amino acids
Theoretical weight: 15.78 KDa
Source organism: Pseudomonas alcaligenes
Expression system: Pseudomonas alcaligenes
UniProt:
  • Canonical: D5MNX7 (Residues: 1-142; Coverage: 100%)
Gene name: pacIR
Structure domains: Herpes Virus-1
DNA (5'-D(*GP*AP*GP*GP*CP*TP*TP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 8 nucleotides
Theoretical weight: 2.47 KDa
Source organism: Pseudomonas alcaligenes
Expression system: Not provided
DNA (5'-D(P*AP*TP*TP*AP*AP*GP*CP*CP*TP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3 KDa
Source organism: Pseudomonas alcaligenes
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1, RIGAKU MICROMAX-007 HF, ALS BEAMLINE 5.0.2
Spacegroup: C2221
Unit cell:
a: 36.908Å b: 115.788Å c: 114.689Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.217
Expression systems:
  • Pseudomonas alcaligenes
  • Not provided

Quick links

Citations

5 review citations

Diverse functions of restriction-modification systems in addition to cellular defense.
Vasu et al. (2013)
4 more

5 mentions without citation

Staphylococcal pathogenicity island DNA packaging system involving cos-site packaging and phage-encoded HNH endonucleases.
Quiles-Puchalt et al. (2014)
4 more