› 4unc

X-ray diffraction
2.3Å resolution

THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 8 DAYS INCUBATION IN 5MM MN (STATE 6)

Released:
DOI: 10.2210/pdb4unc/pdb
PDB entry 4unc coloured by chain, front view.
PDB entry 4unc coloured by chain, side view.
PDB entry 4unc coloured by chain, top view.
Source organisms:
Primary publication:
Visualizing phosphodiester-bond hydrolysis by an endonuclease.
Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G
Nat Struct Mol Biol 22 65-72 (2015)
PMID: 25486305

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118209 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Homing endonuclease I-DmoI Chains: A, D, G
Molecule details ›
Chains: A, D, G
Length: 199 amino acids
Theoretical weight: 23.27 KDa
Source organism: Desulfurococcus mucosus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21505 (Residues: 2-188; Coverage: 96%)
Sequence domains: LAGLIDADG-like domain
Structure domains: Homing endonucleases
5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP*GP*TP*AP*A)-3' Chains: B, E, H
Molecule details ›
Chains: B, E, H
Length: 14 nucleotides
Theoretical weight: 4.3 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*CP*GP*CP*GP*CP*CP*GP*GP*AP*AP*CP*TP*TP*AP*C)-3' Chains: C, F, I
Molecule details ›
Chains: C, F, I
Length: 15 nucleotides
Theoretical weight: 4.55 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*GP*TP*TP*CP*CP*GP*GP*CP*GP*CP*G)-3' Chains: J, L, N
Molecule details ›
Chains: J, L, N
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*CP*CP*GP*GP*CP*AP*AP*GP*GP*C)-3' Chains: K, M, O
Molecule details ›
Chains: K, M, O
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MN 9 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 106.803Å b: 70.409Å c: 107.172Å
α: 90° β: 119.77° γ: 90°
R-values:
R R work R free
0.186 0.185 0.224
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Class 2 CRISPR-Cas RNA-guided endonucleases: Swiss Army knives of genome editing.
Stella et al. (2017)
1 more