› 4lox

X-ray diffraction
1.98Å resolution

Crystal structure of the I-SmaMI LAGLIDADG homing endonuclease bound to cleaved DNA

Released:
DOI: 10.2210/pdb4lox/pdb
PDB entry 4lox coloured by chain, front view.
PDB entry 4lox coloured by chain, side view.
PDB entry 4lox coloured by chain, top view.
Source organism: Sordaria macrospora k-hell
Entry authors: Chik J, Shen B, Stoddard B

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117794 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Homing endonuclease LAGLIDADG domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.12 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 (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.25 KDa
Source organism: Sordaria macrospora k-hell
Expression system: Not provided
DNA (5'-D(P*TP*GP*GP*AP*GP*GP*AP*TP*AP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.4 KDa
Source organism: Sordaria macrospora k-hell
Expression system: Not provided
DNA (5'-D(*GP*GP*TP*AP*TP*CP*CP*TP*CP*CP*AP*TP*TP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.53 KDa
Source organism: Sordaria macrospora k-hell
Expression system: Not provided
DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3') Chain: E
Molecule details ›
Chain: E
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
Source organism: Sordaria macrospora k-hell
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 61.284Å b: 67.429Å c: 98.09Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.186 0.277
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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