› 5e5o

X-ray diffraction
2.36Å resolution

I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions

Released:
DOI: 10.2210/pdb5e5o/pdb
PDB entry 5e5o coloured by chain, front view.
PDB entry 5e5o coloured by chain, side view.
PDB entry 5e5o coloured by chain, top view.
Source organisms:
Primary publication:
The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.
Shen BW, Lambert A, Walker BC, Stoddard BL, Kaiser BK
J Mol Biol 428 206-220 (2016)
PMID: 26705195

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118612 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Homing endonuclease LAGLIDADG domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.16 KDa
Source organism: Sordaria macrospora k-hell
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: F7WD42 (Residues: 114-415; Coverage: 70%)
Gene name: SMAC_12671
Sequence domains: LAGLIDADG endonuclease
Structure domains: Homing endonucleases
DNA (25-MER) Chain: B
Molecule details ›
Chain: B
Length: 25 nucleotides
Theoretical weight: 7.69 KDa
Source organism: synthetic construct
Expression system: Not provided
Top strand DNA (25-MER) Chain: C
Molecule details ›
Chain: C
Length: 25 nucleotides
Theoretical weight: 7.66 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 3 x CA
Ligand EDO 7 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 61.327Å b: 67.993Å c: 97.743Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.188 0.274
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 citation in other articles

Characterization of homing endonuclease binding and cleavage specificities using yeast surface display SELEX (YSD-SELEX).
Jacoby et al. (2017)
1 more

2 mentions without citation

Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.
Lambert et al. (2016)
1 more