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Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (hexagonal crystal form)

X-ray diffraction
1.9Å resolution
PDB entry 3kjj coloured by chain, front view.
PDB entry 3kjj coloured by chain, side view.
PDB entry 3kjj coloured by chain, top view.
Source organism: Neisseria meningitidis serogroup B
Assembly composition:
homo trimer (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: NMB1025 protein
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Multimeric state: homo trimer
Accessible surface area: 13579.49 Å2
Buried surface area: 7176.23 Å2
Dissociation area: 3,418.58 Å2
Dissociation energy (ΔGdiss): 37.32 kcal/mol
Dissociation entropy (TΔSdiss): 24.12 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-191710
Assembly 2
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Assembly Name: NMB1025 protein
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Multimeric state: homo trimer
Accessible surface area: 13245.7 Å2
Buried surface area: 6611.11 Å2
Dissociation area: 3,305.56 Å2
Dissociation energy (ΔGdiss): 38.81 kcal/mol
Dissociation entropy (TΔSdiss): 24 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-191710
Assembly 3
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Assembly Name: NMB1025 protein
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Multimeric state: homo trimer
Accessible surface area: 13200.08 Å2
Buried surface area: 6430.22 Å2
Dissociation area: 3,215.11 Å2
Dissociation energy (ΔGdiss): 37.03 kcal/mol
Dissociation entropy (TΔSdiss): 23.94 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-191710
Assembly 4
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Assembly Name: NMB1025 protein
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Multimeric state: homo trimer
Accessible surface area: 13716.19 Å2
Buried surface area: 7016.75 Å2
Dissociation area: 3,508.37 Å2
Dissociation energy (ΔGdiss): 39.71 kcal/mol
Dissociation entropy (TΔSdiss): 24.2 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-191710
Assembly 5
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Assembly Name: NMB1025 protein
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Multimeric state: homo trimer
Accessible surface area: 13679.45 Å2
Buried surface area: 6826.65 Å2
Dissociation area: 3,413.33 Å2
Dissociation energy (ΔGdiss): 43.63 kcal/mol
Dissociation entropy (TΔSdiss): 24.09 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-191710
Assembly 6
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Assembly Name: NMB1025 protein
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Multimeric state: homo trimer
Accessible surface area: 13012.92 Å2
Buried surface area: 6277.67 Å2
Dissociation area: 3,138.83 Å2
Dissociation energy (ΔGdiss): 32.29 kcal/mol
Dissociation entropy (TΔSdiss): 23.87 kcal/mol
Symmetry number: 3
PDBe Complex ID: PDB-CPX-191710

Macromolecules

NMB1025 protein
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Neisseria meningitidis serogroup B
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9JZJ4 (Residues: 1-120; Coverage: 100%)
Gene name: NMB1025
Pfam: Endoribonuclease L-PSP
InterPro:
CATH: RutC-like
Endoribonuclease L-PSP in PDB entry 3kjj, assembly 1, front view.
Endoribonuclease L-PSP in PDB entry 3kjj, assembly 1, side view.
Endoribonuclease L-PSP in PDB entry 3kjj, assembly 1, top view.
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