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Crystal Structure of a Nudix Protein from Pyrobaculum aerophilum Reveals a Dimer with Intertwined Beta Sheets

X-ray diffraction
2.4Å resolution
PDB entry 1jrk coloured by chain, front view.
PDB entry 1jrk coloured by chain, side view.
PDB entry 1jrk coloured by chain, top view.
Source organism: Pyrobaculum aerophilum
Assemblies composition:
homo dimer (preferred)
homo tetramer
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Nudix hydrolase domain-containing protein
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Multimeric state: homo dimer
Accessible surface area: 14627.83 Å2
Buried surface area: 4152.62 Å2
Dissociation area: 1,626.09 Å2
Dissociation energy (ΔGdiss): 25.67 kcal/mol
Dissociation entropy (TΔSdiss): 12.33 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-187402
Assembly 2
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Assembly Name: Nudix hydrolase domain-containing protein
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Multimeric state: homo dimer
Accessible surface area: 14964.9 Å2
Buried surface area: 4235.12 Å2
Dissociation area: 1,641.09 Å2
Dissociation energy (ΔGdiss): 25.65 kcal/mol
Dissociation entropy (TΔSdiss): 12.38 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-187402
Assembly 3
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Assembly Name: Nudix hydrolase domain-containing protein
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Multimeric state: homo tetramer
Accessible surface area: 26863.3 Å2
Buried surface area: 11117.17 Å2
Dissociation area: 1,374.75 Å2
Dissociation energy (ΔGdiss): 20.49 kcal/mol
Dissociation entropy (TΔSdiss): 13.3 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-187403

Macromolecules

Nudix hydrolase domain-containing protein
Chains: A, B, C, D
Length: 156 amino acids
Theoretical weight: 17.81 KDa
Source organism: Pyrobaculum aerophilum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8ZTD8 (Residues: 6-146; Coverage: 97%)
Gene name: PAE3301
Pfam: NUDIX domain
InterPro:
CATH: Nucleoside Triphosphate Pyrophosphohydrolase
SCOP: MutT-like
Nudix hydrolase domain-containing protein in PDB entry 1jrk, assembly 1, front view.
Nudix hydrolase domain-containing protein in PDB entry 1jrk, assembly 1, side view.
Nudix hydrolase domain-containing protein in PDB entry 1jrk, assembly 1, top view.
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