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- PDB-3wpz: Microbacterium saccharophilum K-1 beta-fructofuranosidase mutant ... -

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Basic information

Entry
Database: PDB / ID: 3wpz
TitleMicrobacterium saccharophilum K-1 beta-fructofuranosidase mutant T47S/S200T/F447P/F470Y/P500S
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: 2.27 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 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
C: Beta-fructofuranosidase


Theoretical massNumber of molelcules
Total (without water)178,1323
Polymers178,1323
Non-polymers00
Water12,088671
1
A: Beta-fructofuranosidase


Theoretical massNumber of molelcules
Total (without water)59,3771
Polymers59,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-fructofuranosidase


Theoretical massNumber of molelcules
Total (without water)59,3771
Polymers59,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-fructofuranosidase


Theoretical massNumber of molelcules
Total (without water)59,3771
Polymers59,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.941, 86.261, 85.923
Angle α, β, γ (deg.)63.23, 86.27, 86.68
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-fructofuranosidase


Mass: 59377.191 Da / Num. of mol.: 3 / Fragment: UNP residues 37-578 / Mutation: T47S/S200T/F447P/F470Y/P500S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
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: Feb 13, 2011
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: 2.27→50 Å / Num. obs: 65821 / % possible obs: 97.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.6
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.3 / % possible all: 95.4

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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: 3WPU

3wpu


Resolution: 2.27→42.98 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.98 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21124 3361 5.1 %RANDOM
Rwork0.15819 ---
obs0.16087 63098 97.06 %-
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: 30.295 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.27→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12519 0 0 671 13190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912867
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211559
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.93717505
X-RAY DIFFRACTIONr_angle_other_deg0.78326634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66551611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85524.698645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85151917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3311560
X-RAY DIFFRACTIONr_chiral_restr0.0820.21812
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023114
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: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 237 -
Rwork0.2 4362 -
obs--90.25 %

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