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- PDB-7bwc: Bombyx mori GH32 beta-fructofuranosidase BmSUC1 mutant D63A in co... -

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Basic information

Entry
Database: PDB / ID: 7bwc
TitleBombyx mori GH32 beta-fructofuranosidase BmSUC1 mutant D63A in complex with sucrose
ComponentsBeta-fructofuranosidase
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / SUCROSE / BETA-PROPELLER / HORIZONTAL GENE TRANSFER
Function / homology
Function and homology information


beta-fructofuranosidase activity / beta-fructofuranosidase / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Sucrose-6-phosphate hydrolase / : / Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 ...Sucrose-6-phosphate hydrolase / : / Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
sucrose / Sucrose-6-phosphate hydrolase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMiyazaki, T. / Oba, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2020
Title: Structural insight into the substrate specificity of Bombyx mori beta-fructofuranosidase belonging to the glycoside hydrolase family 32.
Authors: Miyazaki, T. / Oba, N. / Park, E.Y.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3662
Polymers56,0231
Non-polymers3421
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint3 kcal/mol
Surface area17820 Å2
Unit cell
Length a, b, c (Å)96.522, 118.459, 101.285
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-638-

HOH

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Components

#1: Protein Beta-fructofuranosidase


Mass: 56023.266 Da / Num. of mol.: 1 / Mutation: D63A
Source method: isolated from a genetically manipulated source
Details: The sequence is registered GenBank with an accession code of BCD57653
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BmSuc1, Suc1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A6F8Z6Y2*PLUS, beta-fructofuranosidase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 13% PEG 3350, 40 mM citric acid, 60 mM Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 42574 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2.06 Å / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6137

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UYP

1uyp


Resolution: 1.95→41.975 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 11.908 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2469 2032 4.971 %
Rwork0.2159 --
all0.217 --
obs-40878 95.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.272 Å2
Baniso -1Baniso -2Baniso -3
1-5.133 Å2-0 Å2-0 Å2
2---3.174 Å2-0 Å2
3----1.959 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 23 144 3941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133929
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173419
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.6535356
X-RAY DIFFRACTIONr_angle_other_deg1.1491.587963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4245469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83723.045220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50915617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1031519
X-RAY DIFFRACTIONr_chiral_restr0.0470.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02879
X-RAY DIFFRACTIONr_nbd_refined0.1790.2691
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.23368
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21812
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2209
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.26
X-RAY DIFFRACTIONr_nbd_other0.1860.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1020.29
X-RAY DIFFRACTIONr_mcbond_it1.0853.6621861
X-RAY DIFFRACTIONr_mcbond_other1.0853.6621860
X-RAY DIFFRACTIONr_mcangle_it1.7845.492326
X-RAY DIFFRACTIONr_mcangle_other1.7845.492327
X-RAY DIFFRACTIONr_scbond_it1.1233.82068
X-RAY DIFFRACTIONr_scbond_other1.1233.82068
X-RAY DIFFRACTIONr_scangle_it1.8265.6593027
X-RAY DIFFRACTIONr_scangle_other1.8265.663028
X-RAY DIFFRACTIONr_lrange_it3.68941.5694363
X-RAY DIFFRACTIONr_lrange_other3.63741.3994333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3211380.3182761X-RAY DIFFRACTION93.2454
2.001-2.0550.3141510.3352872X-RAY DIFFRACTION99.9009
2.055-2.1150.3621330.3172842X-RAY DIFFRACTION99.9328
2.115-2.180.3491260.2942625X-RAY DIFFRACTION96.3235
2.18-2.2510.61130.5842126X-RAY DIFFRACTION80.5975
2.251-2.330.37960.3881913X-RAY DIFFRACTION74.9627
2.33-2.4180.2741380.2352441X-RAY DIFFRACTION98.888
2.418-2.5170.2931210.2132369X-RAY DIFFRACTION99.6399
2.517-2.6290.2771200.2152299X-RAY DIFFRACTION99.7937
2.629-2.7570.2561250.2222171X-RAY DIFFRACTION99.437
2.757-2.9060.2321030.2162075X-RAY DIFFRACTION99.4067
2.906-3.0820.2611020.2081965X-RAY DIFFRACTION99.375
3.082-3.2940.211030.2091846X-RAY DIFFRACTION99.3374
3.294-3.5570.22900.2031712X-RAY DIFFRACTION98.0414
3.557-3.8960.253900.2061594X-RAY DIFFRACTION98.8843
3.896-4.3540.187790.1521445X-RAY DIFFRACTION99.1542
4.354-5.0250.165740.1221291X-RAY DIFFRACTION99.635
5.025-6.1480.182590.1471099X-RAY DIFFRACTION99.8276
6.148-8.6650.178460.159888X-RAY DIFFRACTION100
8.665-41.9750.214250.18512X-RAY DIFFRACTION97.8142
Refinement TLS params.Method: refined / Origin x: 23.012 Å / Origin y: 18.847 Å / Origin z: 12.442 Å
111213212223313233
T0.1453 Å2-0.11 Å20.0837 Å2-0.1024 Å2-0.0806 Å2--0.1756 Å2
L0.6603 °20.0119 °2-0.9505 °2-0.7404 °20.0131 °2--1.3946 °2
S0.1563 Å °-0.1958 Å °0.1672 Å °-0.1148 Å °0.126 Å °0.0057 Å °-0.214 Å °0.2841 Å °-0.2824 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA25 - 488
2X-RAY DIFFRACTION1B1 - 2

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