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Crystal structure of VapBC15 complex from Mycobacterium tuberculosis

X-ray diffraction
2.1Å resolution
PDB entry 4chg coloured by chain, front view.
PDB entry 4chg coloured by chain, side view.
PDB entry 4chg coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Assemblies composition:
hetero tetramer
hetero trimer (preferred)
Entry contents: 2 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: Ribonuclease VapC15 and Antitoxin VapB15
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Multimeric state: hetero tetramer
Accessible surface area: 12205.06 Å2
Buried surface area: 8905.71 Å2
Dissociation area: 1,743.19 Å2
Dissociation energy (ΔGdiss): 22.3 kcal/mol
Dissociation entropy (TΔSdiss): 12.35 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-161403
Assembly 2 (preferred)
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Assembly Name: Ribonuclease VapC15 and Antitoxin VapB15
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Multimeric state: hetero trimer
Accessible surface area: 12243.09 Å2
Buried surface area: 6619.78 Å2
Dissociation area: 1,813.04 Å2
Dissociation energy (ΔGdiss): 23.99 kcal/mol
Dissociation entropy (TΔSdiss): 11.86 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-161402
Assembly 3
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Assembly Name: Ribonuclease VapC15 and Antitoxin VapB15
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Multimeric state: hetero trimer
Accessible surface area: 12026.73 Å2
Buried surface area: 6556.74 Å2
Dissociation area: 1,750.29 Å2
Dissociation energy (ΔGdiss): 22.98 kcal/mol
Dissociation entropy (TΔSdiss): 11.83 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-161402

Macromolecules

Ribonuclease VapC15
Chains: A, B, C, D, E, F
Length: 133 amino acids
Theoretical weight: 15.01 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WF97 (Residues: 1-132; Coverage: 100%)
Gene names: MTCY39.07c, Rv2010, vapC15
Pfam: PIN domain
InterPro:
CATH: 5'-nuclease
Ribonuclease VapC15 in PDB entry 4chg, assembly 2, front view.
Ribonuclease VapC15 in PDB entry 4chg, assembly 2, side view.
Ribonuclease VapC15 in PDB entry 4chg, assembly 2, top view.
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Antitoxin VapB15
Chains: G, H, I, J
Length: 88 amino acids
Theoretical weight: 9.96 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WLM7 (Residues: 1-80; Coverage: 100%)
Gene names: MTCY39.08c, Rv2009, vapB15
Pfam: Bacterial antitoxin of type II TA system, VapB
InterPro: Bacterial antitoxin of type II TA system, VapB
Antitoxin VapB15 in PDB entry 4chg, assembly 2, front view.
Antitoxin VapB15 in PDB entry 4chg, assembly 2, side view.
Antitoxin VapB15 in PDB entry 4chg, assembly 2, top view.
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