› 3waz

X-ray diffraction
3Å resolution

Crystal structure of a restriction enzyme PabI in complex with DNA

Released:
DOI: 10.2210/pdb3waz/pdb
PDB entry 3waz coloured by chain, front view.
PDB entry 3waz coloured by chain, side view.
PDB entry 3waz coloured by chain, top view.
Source organisms:
Primary publication:
A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi.
Miyazono K, Furuta Y, Watanabe-Matsui M, Miyakawa T, Ito T, Kobayashi I, Tanokura M
Nat Commun 5 3178 (2014)
PMID: 24458096

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117077 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Restriction endonuclease type II Pab1 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 220 amino acids
Theoretical weight: 25.34 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9V2B6 (Residues: 8-226; Coverage: 97%)
Gene name: PAB0105
Sequence domains: R.Pab1 restriction endonuclease
DNA (5'-D(*GP*CP*AP*TP*AP*GP*CP*TP*GP*TP*(ORP)P*CP*AP*GP*CP*TP*AP*TP*GP*C)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 20 nucleotides
Theoretical weight: 6.02 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ADE 2 x ADE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: I222
Unit cell:
a: 104.508Å b: 151.402Å c: 187.697Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.194
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

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

6 mentions without citation

Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway.
Mullins et al. (2019)
5 more