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

X-ray diffraction
1.98Å resolution
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
Assembly composition:
hetero pentamer (preferred)
Entry contents: 1 distinct polypeptide molecule
4 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Homing endonuclease LAGLIDADG domain-containing protein and DNA
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Multimeric state: hetero pentamer
Accessible surface area: 18181.2 Å2
Buried surface area: 9182.47 Å2
Dissociation area: 1,227.5 Å2
Dissociation energy (ΔGdiss): 23.79 kcal/mol
Dissociation entropy (TΔSdiss): 10.01 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117794

Macromolecules

Homing endonuclease LAGLIDADG domain-containing protein
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
Pfam: LAGLIDADG endonuclease
InterPro:
CATH: Homing endonucleases
Homing endonuclease LAGLIDADG domain-containing protein in PDB entry 4lox, assembly 1, front view.
Homing endonuclease LAGLIDADG domain-containing protein in PDB entry 4lox, assembly 1, side view.
Homing endonuclease LAGLIDADG domain-containing protein in PDB entry 4lox, assembly 1, top view.
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DNA chain B
Name: DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A)-3')
Representative chains: B
Source organism: Sordaria macrospora k-hell [771870]
Expression system: Not provided
Length: 14 nucleotides
Theoretical weight: 4.25 KDa
DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A)-3') in PDB entry 4lox, assembly 1, front view.
DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A)-3') in PDB entry 4lox, assembly 1, side view.
DNA (5'-D(*CP*GP*TP*AP*CP*AP*CP*CP*TP*GP*AP*TP*AP*A)-3') in PDB entry 4lox, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(P*TP*GP*GP*AP*GP*GP*AP*TP*AP*CP*C)-3')
Representative chains: C
Source organism: Sordaria macrospora k-hell [771870]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.4 KDa
DNA (5'-D(P*TP*GP*GP*AP*GP*GP*AP*TP*AP*CP*C)-3') in PDB entry 4lox, assembly 1, front view.
DNA (5'-D(P*TP*GP*GP*AP*GP*GP*AP*TP*AP*CP*C)-3') in PDB entry 4lox, assembly 1, side view.
DNA (5'-D(P*TP*GP*GP*AP*GP*GP*AP*TP*AP*CP*C)-3') in PDB entry 4lox, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(*GP*GP*TP*AP*TP*CP*CP*TP*CP*CP*AP*TP*TP*AP*T)-3')
Representative chains: D
Source organism: Sordaria macrospora k-hell [771870]
Expression system: Not provided
Length: 15 nucleotides
Theoretical weight: 4.53 KDa
DNA (5'-D(*GP*GP*TP*AP*TP*CP*CP*TP*CP*CP*AP*TP*TP*AP*T)-3') in PDB entry 4lox, assembly 1, front view.
DNA (5'-D(*GP*GP*TP*AP*TP*CP*CP*TP*CP*CP*AP*TP*TP*AP*T)-3') in PDB entry 4lox, assembly 1, side view.
DNA (5'-D(*GP*GP*TP*AP*TP*CP*CP*TP*CP*CP*AP*TP*TP*AP*T)-3') in PDB entry 4lox, assembly 1, top view.
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DNA chain E
Name: DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3')
Representative chains: E
Source organism: Sordaria macrospora k-hell [771870]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3') in PDB entry 4lox, assembly 1, front view.
DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3') in PDB entry 4lox, assembly 1, side view.
DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3') in PDB entry 4lox, assembly 1, top view.
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