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Crystal structure of the catalytic domain of XynA1 from Paenibacillus sp. JDR-2

X-ray diffraction
1.34Å resolution
PDB entry 3ro8 coloured by chain, front view.
PDB entry 3ro8 coloured by chain, side view.
PDB entry 3ro8 coloured by chain, top view.
Source organism: Paenibacillus sp. JDR-2
Assembly composition:
monomeric (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1
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Assembly Name: Endo-1,4-beta-xylanase A
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Multimeric state: monomeric
Accessible surface area: 13855.39 Å2
Buried surface area: 329.33 Å2
Dissociation area: 48.74 Å2
Dissociation energy (ΔGdiss): 8.59 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111558
Assembly 2
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Assembly Name: Endo-1,4-beta-xylanase A
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Multimeric state: monomeric
Accessible surface area: 13838.42 Å2
Buried surface area: 334.52 Å2
Dissociation area: 50.66 Å2
Dissociation energy (ΔGdiss): 8.36 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111558
Assembly 3 (preferred)
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Assembly Name: Endo-1,4-beta-xylanase A
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Multimeric state: monomeric
Accessible surface area: 13623.6 Å2
Buried surface area: 218.71 Å2
Dissociation area: 41.63 Å2
Dissociation energy (ΔGdiss): 7.1 kcal/mol
Dissociation entropy (TΔSdiss): -1.47 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111558
Assembly 4
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Assembly Name: Endo-1,4-beta-xylanase A
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Multimeric state: monomeric
Accessible surface area: 13473.67 Å2
Buried surface area: 230.99 Å2
Dissociation area: 47.6 Å2
Dissociation energy (ΔGdiss): 8.81 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111558
Assembly 5
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Assembly Name: Endo-1,4-beta-xylanase A
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Multimeric state: monomeric
Accessible surface area: 13562.5 Å2
Buried surface area: 463.17 Å2
Dissociation area: 52.12 Å2
Dissociation energy (ΔGdiss): 8.73 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111558
Assembly 6
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Assembly Name: Endo-1,4-beta-xylanase A
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Multimeric state: monomeric
Accessible surface area: 13755.89 Å2
Buried surface area: 235.6 Å2
Dissociation area: 48.94 Å2
Dissociation energy (ΔGdiss): 9.01 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111558
Assembly 7
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Assembly Name: Endo-1,4-beta-xylanase A
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Multimeric state: monomeric
Accessible surface area: 13939.2 Å2
Buried surface area: 232.2 Å2
Dissociation area: 48.09 Å2
Dissociation energy (ΔGdiss): 8.86 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111558
Assembly 8
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Assembly Name: Endo-1,4-beta-xylanase A
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Multimeric state: monomeric
Accessible surface area: 13939.65 Å2
Buried surface area: 233.94 Å2
Dissociation area: 48.61 Å2
Dissociation energy (ΔGdiss): 8.88 kcal/mol
Dissociation entropy (TΔSdiss): -1.46 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-111558

Macromolecules

Endo-1,4-beta-xylanase A
Chains: A, B, C, D, E, F, G, H
Length: 341 amino acids
Theoretical weight: 38.4 KDa
Source organism: Paenibacillus sp. JDR-2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C6CRV0 (Residues: 518-851; Coverage: 23%)
Gene names: Pjdr2_0221, xynA, xynA1
Pfam: Glycosyl hydrolase family 10
InterPro:
CATH: Glycosidases
Endo-1,4-beta-xylanase A in PDB entry 3ro8, assembly 3, front view.
Endo-1,4-beta-xylanase A in PDB entry 3ro8, assembly 3, side view.
Endo-1,4-beta-xylanase A in PDB entry 3ro8, assembly 3, top view.
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