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- PDB-3wpu: Full-length beta-fructofuranosidase from Microbacterium saccharop... -

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Basic information

Entry
Database: PDB / ID: 3wpu
TitleFull-length beta-fructofuranosidase from Microbacterium saccharophilum K-1
ComponentsBeta-fructofuranosidase
KeywordsHYDROLASE / Glycoside hydrolase family 68 / Beta-propeller
Function / homology
Function and homology information


levansucrase activity / carbohydrate utilization / hydrolase activity / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 68 / Levansucrase/Invertase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
Beta-fructofuranosidase
Similarity search - Component
Biological speciesArthrobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYokoi, G. / Mori, M. / Sato, S. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2014
Title: Enhancing thermostability and the structural characterization of Microbacterium saccharophilum K-1 beta-fructofuranosidase
Authors: Ohta, Y. / Hatada, Y. / Hidaka, Y. / Shimane, Y. / Usui, K. / Ito, T. / Fujita, K. / Yokoi, G. / Mori, M. / Sato, S. / Miyazaki, T. / Nishikawa, A. / Tonozuka, T.
History
DepositionJan 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-fructofuranosidase
B: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2116
Polymers118,8432
Non-polymers3684
Water19,1501063
1
A: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6053
Polymers59,4211
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-fructofuranosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6053
Polymers59,4211
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.242, 62.791, 83.569
Angle α, β, γ (deg.)88.74, 82.37, 72.63
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-fructofuranosidase


Mass: 59421.285 Da / Num. of mol.: 2 / Fragment: UNP residues 37-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter (bacteria) / Strain: K-1 / Gene: bff / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VW87, beta-fructofuranosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1063 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM sodium acetate, 22.5% PEG 8000, 300mM Glycine, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 31, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 135214 / Num. obs: 135214 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.1 / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VSR

3vsr


Resolution: 1.6→39.12 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.562 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19005 6751 5 %RANDOM
Rwork0.15971 ---
obs0.16121 127911 96.04 %-
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: 16.556 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8354 0 24 1063 9441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198691
X-RAY DIFFRACTIONr_bond_other_d0.0020.027810
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.93811843
X-RAY DIFFRACTIONr_angle_other_deg0.779318021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33151108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18524.691437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.841151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6581541
X-RAY DIFFRACTIONr_chiral_restr0.0850.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022113
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 515 -
Rwork0.252 9187 -
obs--93.23 %

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