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Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

X-ray diffraction
1.67Å resolution
PDB entry 1k1e coloured by chain, front view.
PDB entry 1k1e coloured by chain, side view.
PDB entry 1k1e coloured by chain, top view.
Source organism: Haemophilus influenzae Rd KW20
Assemblies composition:
homo tetramer (preferred)
homo octamer
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1
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Assembly Name: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
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Multimeric state: homo tetramer
Accessible surface area: 23808.98 Å2
Buried surface area: 11740.81 Å2
Dissociation area: 4,750.49 Å2
Dissociation energy (ΔGdiss): 34.49 kcal/mol
Dissociation entropy (TΔSdiss): 38.4 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-155268
Assembly 2 (preferred)
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Assembly Name: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
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Multimeric state: homo tetramer
Accessible surface area: 23691.74 Å2
Buried surface area: 11487.78 Å2
Dissociation area: 4,711.98 Å2
Dissociation energy (ΔGdiss): 37.49 kcal/mol
Dissociation entropy (TΔSdiss): 38.35 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-155268
Assembly 3
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Assembly Name: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
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Multimeric state: homo tetramer
Accessible surface area: 23950.56 Å2
Buried surface area: 11876.17 Å2
Dissociation area: 4,716.79 Å2
Dissociation energy (ΔGdiss): 34.7 kcal/mol
Dissociation entropy (TΔSdiss): 38.39 kcal/mol
Symmetry number: 4
PDBe Complex ID: PDB-CPX-155268
Assembly 4
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Assembly Name: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
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Multimeric state: homo octamer
Accessible surface area: 44038.36 Å2
Buried surface area: 27615.14 Å2
Dissociation area: 1,933.2 Å2
Dissociation energy (ΔGdiss): 6.27 kcal/mol
Dissociation entropy (TΔSdiss): 14.97 kcal/mol
Symmetry number: 8
PDBe Complex ID: PDB-CPX-155269
Assembly 5
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Assembly Name: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
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Multimeric state: homo octamer
Accessible surface area: 43971.62 Å2
Buried surface area: 26757.69 Å2
Dissociation area: 1,764.55 Å2
Dissociation energy (ΔGdiss): 4.97 kcal/mol
Dissociation entropy (TΔSdiss): 14.93 kcal/mol
Symmetry number: 8
PDBe Complex ID: PDB-CPX-155269

Macromolecules

3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 180 amino acids
Theoretical weight: 19.46 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli
UniProt:
  • Canonical: P45314 (Residues: 1-180; Coverage: 100%)
Gene name: HI_1679
Pfam: haloacid dehalogenase-like hydrolase
InterPro:
CATH: HAD superfamily/HAD-like
SCOP: Probable phosphatase YrbI
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC in PDB entry 1k1e, assembly 2, front view.
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC in PDB entry 1k1e, assembly 2, side view.
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC in PDB entry 1k1e, assembly 2, top view.
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