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Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA

Solution NMR
PDB entry 2h3a coloured by chain, ensemble of 20 models, front view.
PDB entry 2h3a coloured by chain, ensemble of 20 models, side view.
PDB entry 2h3a coloured by chain, ensemble of 20 models, top view.
Source organism: Escherichia coli
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Antitoxin CcdA and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 14953.75 Å2
Buried surface area: 7875.77 Å2
Dissociation area: 1,553.25 Å2
Dissociation energy (ΔGdiss): 16.26 kcal/mol
Dissociation entropy (TΔSdiss): 10.5 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-115324

Macromolecules

Antitoxin CcdA
Chains: A, B
Length: 72 amino acids
Theoretical weight: 8.41 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P62552 (Residues: 1-72; Coverage: 100%)
Gene names: ECOK12F042, H, ccdA, letA
Pfam: Post-segregation antitoxin CcdA
InterPro: Post-segregation antitoxin CcdA
CATH: Arc Repressor Mutant
Antitoxin CcdA in PDB entry 2h3a, assembly 1, front view.
Antitoxin CcdA in PDB entry 2h3a, assembly 1, side view.
Antitoxin CcdA in PDB entry 2h3a, assembly 1, top view.
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DNA chain C
Name: 5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3'
Representative chains: C
Source organism: Escherichia coli [562]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3' in PDB entry 2h3a, assembly 1, front view.
5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3' in PDB entry 2h3a, assembly 1, side view.
5'-D(P*AP*TP*AP*TP*GP*TP*AP*TP*AP*CP*CP*CP*G)-3' in PDB entry 2h3a, assembly 1, top view.
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DNA chain D
Name: 5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3'
Representative chains: D
Source organism: Escherichia coli [562]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.99 KDa
5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3' in PDB entry 2h3a, assembly 1, front view.
5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3' in PDB entry 2h3a, assembly 1, side view.
5'-D(P*TP*CP*GP*GP*GP*TP*AP*TP*AP*CP*AP*TP*A)-3' in PDB entry 2h3a, assembly 1, top view.
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