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- PDB-8i2r: Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y... -

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Basic information

Entry
Database: PDB / ID: 8i2r
TitleBeijerinckia indica beta-fructosyltransferase variant H395R/F473Y in complex with fructose
ComponentsBeta-fructosyltransferase
KeywordsTRANSFERASE / Beta-fructosyltransferase / HYDROLASE
Function / homologybeta-D-fructopyranose / beta-D-fructofuranose
Function and homology information
Biological speciesBeijerinckia indica subsp. indica NBRC 3744 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsTonozuka, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05956 Japan
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2023
Title: Characterization and alteration of product specificity of Beijerinckia indica subsp. indica beta-fructosyltransferase.
Authors: Li, D. / Miyasaka, Y. / Kubota, A. / Kozono, T. / Kitano, Y. / Sasaki, N. / Fujii, T. / Tochio, T. / Kadota, Y. / Nishikawa, A. / Tonozuka, T.
History
DepositionJan 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-fructosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6296
Polymers57,0401
Non-polymers5895
Water10,269570
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-3 kcal/mol
Surface area18130 Å2
Unit cell
Length a, b, c (Å)54.542, 81.697, 99.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-fructosyltransferase


Mass: 57039.840 Da / Num. of mol.: 1 / Mutation: variant H395R, F473Y
Source method: isolated from a genetically manipulated source
Details: DDBJ LC522529
Source: (gene. exp.) Beijerinckia indica subsp. indica NBRC 3744 (bacteria)
Strain: NBRC 3744 / Production host: Escherichia coli (E. coli) / References: EC: 2.4.1.100
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-BDF / beta-D-fructopyranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.95 Å3/Da / Density % sol: 36.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% (w/v) polyethylene glycol 10000, 0.2 M magnesium chloride, 0.1 M potassium sodium tartrate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.36→47.8 Å / Num. obs: 95951 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Net I/σ(I): 15.6
Reflection shellResolution: 1.36→1.43 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 13917 / Rpim(I) all: 0.201 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→37.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18156 4669 4.9 %RANDOM
Rwork0.16174 ---
obs0.1627 90892 99.35 %-
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: 17.745 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.36→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 38 570 4311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133863
X-RAY DIFFRACTIONr_bond_other_d0.0350.0153440
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.6555291
X-RAY DIFFRACTIONr_angle_other_deg2.3021.5827920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2885477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08122.905210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61315528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4251520
X-RAY DIFFRACTIONr_chiral_restr0.0720.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024520
X-RAY DIFFRACTIONr_gen_planes_other0.010.02944
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_it1.2211.6831908
X-RAY DIFFRACTIONr_mcbond_other1.2151.6821907
X-RAY DIFFRACTIONr_mcangle_it1.9322.5272382
X-RAY DIFFRACTIONr_mcangle_other1.9352.5282383
X-RAY DIFFRACTIONr_scbond_it1.6661.8621955
X-RAY DIFFRACTIONr_scbond_other1.6651.8621956
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5942.7392909
X-RAY DIFFRACTIONr_long_range_B_refined4.28121.4134319
X-RAY DIFFRACTIONr_long_range_B_other4.03820.5294177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.36→1.395 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 339 -
Rwork0.21 6709 -
obs--100 %

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