› 2dvy

X-ray diffraction
3Å resolution

Crystal structure of restriction endonucleases PabI

Released:
DOI: 10.2210/pdb2dvy/pdb
PDB entry 2dvy coloured by chain, front view.
PDB entry 2dvy coloured by chain, side view.
PDB entry 2dvy coloured by chain, top view.
Source organism: Pyrococcus abyssi
Primary publication:
Novel protein fold discovered in the PabI family of restriction enzymes.
Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I
OpenAccess logo Nucleic Acids Res 35 1908-18 (2007)
PMID: 17332011

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-577851 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Restriction endonuclease type II Pab1 domain-containing protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 226 amino acids
Theoretical weight: 26.05 KDa
Source organism: Pyrococcus abyssi
Expression system: Not provided
UniProt:
  • Canonical: Q9V2B6 (Residues: 1-226; Coverage: 100%)
Gene name: PAB0105
Sequence domains: R.Pab1 restriction endonuclease

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 84.57Å b: 113.956Å c: 89.173Å
α: 90° β: 116.23° γ: 90°
R-values:
R R work R free
0.247 0.247 0.318
Expression system: Not provided

Quick links

Citations

10 review citations

Protein production and purification.
Structural Genomics et al. (2008)
9 more

8 mentions without citation

Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology.
Fogeron et al. (2021)
7 more