› 3c0x

X-ray diffraction
2.3Å resolution

I-SceI in complex with a top nicked DNA substrate

Released:
DOI: 10.2210/pdb3c0x/pdb
PDB entry 3c0x coloured by chain, front view.
PDB entry 3c0x coloured by chain, side view.
PDB entry 3c0x coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway.
Moure CM, Gimble FS, Quiocho FA
Nucleic Acids Res 36 3287-96 (2008)
PMID: 18424798

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116114 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Intron-encoded endonuclease I-SceI Chain: A
Molecule details ›
Chain: A
Length: 235 amino acids
Theoretical weight: 27.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P03882 (Residues: 1-235; Coverage: 100%)
Gene names: OMEGA, Q0160, SCEI, SECY
Sequence domains: LAGLIDADG DNA endonuclease family
Structure domains: Homing endonucleases
DNA (5'-D(*DC*DAP*DCP*DGP*DCP*DTP*DAP*DGP*DGP*DGP*DAP*DTP*DAP*DA)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(P*DCP*DAP*DGP*DGP*DGP*DTP*DAP*DAP*DTP*DAP*DC)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.38 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(*DG*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DAP*DTP*DCP*DCP*DCP*DTP*DAP*DGP*DCP*DGP*DT)-3') Chain: D
Molecule details ›
Chain: D
Length: 25 nucleotides
Theoretical weight: 7.62 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 3 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P41212
Unit cell:
a: 80.68Å b: 80.68Å c: 128.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.255 0.255 0.288
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
5 more