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Structure of E. coli RppH bound to RNA and three magnesium ions

X-ray diffraction
1.6Å resolution
PDB entry 4s2y coloured by chain, front view.
PDB entry 4s2y coloured by chain, side view.
PDB entry 4s2y coloured by chain, top view.
Source organism: Escherichia coli K-12
Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Entry contents: 1 distinct polypeptide molecule
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: RNA pyrophosphohydrolase and RNA
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Multimeric state: hetero dimer
Accessible surface area: 7919.84 Å2
Buried surface area: 1801.48 Å2
Dissociation area: 560.44 Å2
Dissociation energy (ΔGdiss): 22.26 kcal/mol
Dissociation entropy (TΔSdiss): 6.18 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-141546
Assembly 2
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Assembly Name: RNA pyrophosphohydrolase and RNA
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Multimeric state: hetero tetramer
Accessible surface area: 14509.81 Å2
Buried surface area: 4929.65 Å2
Dissociation area: 671.22 Å2
Dissociation energy (ΔGdiss): 3.81 kcal/mol
Dissociation entropy (TΔSdiss): 11.51 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-141548

Macromolecules

RNA pyrophosphohydrolase
Chain: A
Length: 161 amino acids
Theoretical weight: 18.97 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A776 (Residues: 1-160; Coverage: 91%)
Gene names: JW2798, b2830, nudH, rppH, ygdP
Pfam: NUDIX domain
InterPro:
CATH: Nucleoside Triphosphate Pyrophosphohydrolase
RNA pyrophosphohydrolase in PDB entry 4s2y, assembly 1, front view.
RNA pyrophosphohydrolase in PDB entry 4s2y, assembly 1, side view.
RNA pyrophosphohydrolase in PDB entry 4s2y, assembly 1, top view.
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RNA chain B
Name: RNA (5'-R(*(APC)*GP*U)-3')
Representative chains: B
Source organism: Escherichia coli K-12 [83333]
Expression system: Not provided
Length: 3 nucleotides
Theoretical weight: 1.09 KDa
RNA (5'-R(*(APC)*GP*U)-3') in PDB entry 4s2y, assembly 1, front view.
RNA (5'-R(*(APC)*GP*U)-3') in PDB entry 4s2y, assembly 1, side view.
RNA (5'-R(*(APC)*GP*U)-3') in PDB entry 4s2y, assembly 1, top view.
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