› 1dq3

X-ray diffraction
2.1Å resolution

CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI

Released:
DOI: 10.2210/pdb1dq3/pdb
PDB entry 1dq3 coloured by chain, front view.
PDB entry 1dq3 coloured by chain, side view.
PDB entry 1dq3 coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.
Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K
J Mol Biol 300 889-901 (2000)
PMID: 10891276

Function and Biology Details

Reaction catalysed: 
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123094 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endonuclease PI-PfuI Chain: A
Molecule details ›
Chain: A
Length: 454 amino acids
Theoretical weight: 53.16 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E7FHX6 (Residues: 302-755; Coverage: 26%)
Gene names: PF0440, rnr
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P21
Unit cell:
a: 56.55Å b: 85.28Å c: 65.41Å
α: 90° β: 112.94° γ: 90°
R-values:
R R work R free
0.192 0.192 0.232
Expression system: Escherichia coli BL21(DE3)

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Citations

6 review citations

Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.
Chevalier et al. (2001)
5 more

16 mentions without citation

Protein domain identification methods and online resources.
Wang et al. (2021)
15 more