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- PDB-7vco: Frischella perrara beta-fructofuranosidase -

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Basic information

Entry
Database: PDB / ID: 7vco
TitleFrischella perrara beta-fructofuranosidase
ComponentsSucrose-6-phosphate hydrolase
KeywordsHYDROLASE / GH32 / fructooligosaccharide
Function / homology
Function and homology information


beta-fructofuranosidase activity / sucrose metabolic process / beta-fructofuranosidase / cytoplasm
Similarity search - Function
Sucrose-6-phosphate hydrolase / 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Sucrose-6-phosphate hydrolase
Similarity search - Component
Biological speciesFrischella perrara (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTonozuka, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05956 Japan
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2022
Title: Enzymatic and structural characterization of beta-fructofuranosidase from the honeybee gut bacterium Frischella perrara.
Authors: Kubota, A. / Kawai, R. / Li, D. / Kozono, T. / Sasaki, N. / Nishikawa, A. / Fujii, T. / Tochio, T. / Tonozuka, T.
History
DepositionSep 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Apr 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sucrose-6-phosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1493
Polymers55,8931
Non-polymers2562
Water4,702261
1
A: Sucrose-6-phosphate hydrolase
hetero molecules

A: Sucrose-6-phosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2996
Polymers111,7862
Non-polymers5134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)66.402, 66.402, 465.263
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

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Components

#1: Protein Sucrose-6-phosphate hydrolase / beta-fructofuranosidase / Invertase


Mass: 55892.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frischella perrara (bacteria) / Gene: FPB0191_01269 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A7S0J1, beta-fructofuranosidase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe sequence data was deposited in the DDBJ under accession number LC639952. The gene was directly ...The sequence data was deposited in the DDBJ under accession number LC639952. The gene was directly obtained from the gut of honeybees, and residues I107V, P259A, V352A were considered to be naturally occurred.

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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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2-propanol, PEG 600, PEG 3350, ammonium acetate, HEPES-NaOH

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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 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→48.9 Å / Num. obs: 82441 / % possible obs: 100 % / Redundancy: 17.6 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.02 / Net I/σ(I): 19.9
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 11732 / Rpim(I) all: 0.143 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PIG

3pig


Resolution: 1.6→48.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.884 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22559 3951 4.8 %RANDOM
Rwork0.20002 ---
obs0.20123 78311 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.224 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 17 261 4219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134081
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173752
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6325545
X-RAY DIFFRACTIONr_angle_other_deg1.361.588627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2335495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65623.304224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0315668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9051519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02988
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8782.6121965
X-RAY DIFFRACTIONr_mcbond_other1.8752.6111963
X-RAY DIFFRACTIONr_mcangle_it2.6323.9162456
X-RAY DIFFRACTIONr_mcangle_other2.6293.9162456
X-RAY DIFFRACTIONr_scbond_it2.6362.8642116
X-RAY DIFFRACTIONr_scbond_other2.6362.8642117
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9114.1833087
X-RAY DIFFRACTIONr_long_range_B_refined4.86329.9714453
X-RAY DIFFRACTIONr_long_range_B_other4.85829.8164412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 267 -
Rwork0.26 5667 -
obs--100 %

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