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- PDB-3vsr: Microbacterium saccharophilum K-1 beta-fructofuranosidase catalyt... -

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Basic information

Entry
Database: PDB / ID: 3vsr
TitleMicrobacterium saccharophilum K-1 beta-fructofuranosidase catalytic domain
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 Å
AuthorsTonozuka, T. / Tamaki, A. / Yokoi, G. / Miyazaki, T. / Ichikawa, M. / Nishikawa, A. / Ohta, Y. / Hidaka, Y. / Katayama, K. / Hatada, Y. ...Tonozuka, T. / Tamaki, A. / Yokoi, G. / Miyazaki, T. / Ichikawa, M. / Nishikawa, A. / Ohta, Y. / Hidaka, Y. / Katayama, K. / Hatada, Y. / Ito, T. / Fujita, K.
CitationJournal: Enzyme.Microb.Technol. / Year: 2012
Title: Crystal structure of a lactosucrose-producing enzyme, Arthrobacter sp. K-1 beta-fructofuranosidase
Authors: Tonozuka, T. / Tamaki, A. / Yokoi, G. / Miyazaki, T. / Ichikawa, M. / Nishikawa, A. / Ohta, Y. / Hidaka, Y. / Katayama, K. / Hatada, Y. / Ito, T. / Fujita, K.
History
DepositionMay 8, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Mar 12, 2014Group: Structure summary
Revision 1.4Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-fructofuranosidase


Theoretical massNumber of molelcules
Total (without water)54,5401
Polymers54,5401
Non-polymers00
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.723, 72.391, 58.709
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-fructofuranosidase


Mass: 54539.672 Da / Num. of mol.: 1 / Fragment: UNP residues 37-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter (bacteria) / Strain: K-1 / Gene: bff / Production host: Bacillus subtilis (bacteria) / Strain (production host): ISW1214 / References: UniProt: Q8VW87, beta-fructofuranosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM sodium acetate pH 5.5, 22.5% polyethylene glycol 8000, 300mM glycine, 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: Mar 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 31999 / % possible obs: 98.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 36.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 9 / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PT2

1pt2


Resolution: 2→27.11 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24095 1608 5 %RANDOM
Rwork0.19322 ---
obs0.19558 30364 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 0 400 4238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9325387
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4625494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93924.68203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45815575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0411518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213187
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5771.52446
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03323929
X-RAY DIFFRACTIONr_scbond_it1.55431509
X-RAY DIFFRACTIONr_scangle_it2.4014.51457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 122 -
Rwork0.291 2012 -
obs--89.85 %

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