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- PDB-6m0e: Beijerinckia indica beta-fructosyltransferase complexed with fructose -

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Basic information

Entry
Database: PDB / ID: 6m0e
TitleBeijerinckia indica beta-fructosyltransferase complexed with fructose
ComponentsLevansucrase
KeywordsHYDROLASE / GH68 / fructooligosaccharide
Function / homologylevansucrase / levansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / beta-D-fructopyranose / beta-D-fructofuranose / Levansucrase
Function and homology information
Biological speciesBeijerinckia indica subsp. indica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsTonozuka, T.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2020
Title: Crystal structure of a glycoside hydrolase family 68 beta-fructosyltransferase from Beijerinckia indica subsp. indica in complex with fructose.
Authors: Tonozuka, T. / Kitamura, J. / Nagaya, M. / Kawai, R. / Nishikawa, A. / Hirano, K. / Tamura, K. / Fujii, T. / Tochio, T.
History
DepositionFeb 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 14, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Levansucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9789
Polymers57,0051
Non-polymers9748
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-6 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.377, 81.521, 99.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Levansucrase /


Mass: 57004.793 Da / Num. of mol.: 1 / Mutation: 198-202, 522-534 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIB 8712) (bacteria)
Strain: ATCC 9039 / DSM 1715 / NCIB 8712 / Gene: Bind_2021 / Production host: Escherichia coli (E. coli) / References: UniProt: B2IF78, levansucrase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / 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 / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
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 / Water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe gene was cloned using B. indica subsp. indica strain NBRC 3744, and DNA primers for the PCR ...The gene was cloned using B. indica subsp. indica strain NBRC 3744, and DNA primers for the PCR amplification was designed using the sequence of Bind_2021 of B. indica subsp. indica strain ATCC 9039. Two amino acid residues are different between the strain NBRC 3744 (Pro479 and Gly495) and the strain ATCC 9039 (Thr479 and Arg495). Sequence DDBJ accession number LC522529.

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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: 1.93 Å3/Da / Density % sol: 36.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% (w/v) polyethylene glycol 10000, 0.2 M MgCl2, 0.1 M Na K 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: 1.35→45.2 Å / Num. obs: 96105 / % possible obs: 98.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Net I/σ(I): 19.4
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 13691 / Rpim(I) all: 0.19 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0D

6m0d


Resolution: 1.35→45.2 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1663 4663 4.856 %
Rwork0.1499 --
all0.151 --
obs-96024 98.683 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.306 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0.001 Å20 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.35→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3701 0 63 583 4347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133884
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173338
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6555323
X-RAY DIFFRACTIONr_angle_other_deg2.311.5757780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2725477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46222.981208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64815526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9771519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024423
X-RAY DIFFRACTIONr_gen_planes_other0.010.02830
X-RAY DIFFRACTIONr_nbd_refined0.1960.2673
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.23182
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21902
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2373
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0630.28
X-RAY DIFFRACTIONr_nbd_other0.2320.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.239
X-RAY DIFFRACTIONr_mcbond_it1.0821.4531908
X-RAY DIFFRACTIONr_mcbond_other1.0671.4521907
X-RAY DIFFRACTIONr_mcangle_it1.7352.1822382
X-RAY DIFFRACTIONr_mcangle_other1.7382.1832383
X-RAY DIFFRACTIONr_scbond_it1.4991.6121976
X-RAY DIFFRACTIONr_scbond_other1.4981.6121977
X-RAY DIFFRACTIONr_scangle_it2.3452.3672940
X-RAY DIFFRACTIONr_scangle_other2.3452.3672941
X-RAY DIFFRACTIONr_lrange_it4.31618.8534399
X-RAY DIFFRACTIONr_lrange_other3.98117.9264256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.2253500.2056592X-RAY DIFFRACTION97.4042
1.385-1.4230.2053340.1946419X-RAY DIFFRACTION97.6855
1.423-1.4640.1753300.1816291X-RAY DIFFRACTION97.828
1.464-1.5090.2013120.1726140X-RAY DIFFRACTION98.0547
1.509-1.5590.1753410.1615897X-RAY DIFFRACTION98.4377
1.559-1.6130.1692790.1585786X-RAY DIFFRACTION98.5378
1.613-1.6740.1812800.1555557X-RAY DIFFRACTION98.5647
1.674-1.7420.1792740.1485424X-RAY DIFFRACTION98.8893
1.742-1.820.172540.155178X-RAY DIFFRACTION98.7277
1.82-1.9080.1652540.1454983X-RAY DIFFRACTION99.3927
1.908-2.0120.1732530.1484707X-RAY DIFFRACTION98.9625
2.012-2.1330.1832280.1424497X-RAY DIFFRACTION99.4946
2.133-2.280.1682150.1444256X-RAY DIFFRACTION99.2673
2.28-2.4630.1782060.143952X-RAY DIFFRACTION99.7122
2.463-2.6970.1521790.1463675X-RAY DIFFRACTION99.6896
2.697-3.0140.161560.1433314X-RAY DIFFRACTION98.5236
3.014-3.4780.1451330.1392966X-RAY DIFFRACTION99.4544
3.478-4.2550.1481370.1392534X-RAY DIFFRACTION99.8505
4.255-5.9950.151950.1392004X-RAY DIFFRACTION99.8098
5.995-45.20.146530.191189X-RAY DIFFRACTION99.1221

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