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- PDB-6m0d: Beijerinckia indica beta-fructosyltransferase -

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Basic information

Entry
Database: PDB / ID: 6m0d
TitleBeijerinckia indica beta-fructosyltransferase
ComponentsLevansucrase
KeywordsHYDROLASE / GH68 / fructooligosaccharide
Function / homologylevansucrase / levansucrase activity / Glycoside hydrolase, family 68 / Levansucrase/Invertase / carbohydrate utilization / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Levansucrase
Function and homology information
Biological speciesBeijerinckia indica subsp. indica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)57,0533
Polymers57,0051
Non-polymers492
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.891, 80.900, 92.661
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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.74 Å3/Da / Density % sol: 29.26 %
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: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→46.3 Å / Num. obs: 20772 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.054 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.23 Å / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 1750 / CC1/2: 0.935 / Rpim(I) all: 0.14 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W18

1w18


Resolution: 2.2→44.3 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.261
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2657 1011 4.894 %
Rwork0.2217 --
all0.224 --
obs-20660 99.298 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.338 Å2
Baniso -1Baniso -2Baniso -3
1--0.006 Å20 Å20 Å2
2--0.014 Å2-0 Å2
3----0.008 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 2 66 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133813
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173285
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.6485217
X-RAY DIFFRACTIONr_angle_other_deg2.411.577647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0585475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73422.947207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2691519
X-RAY DIFFRACTIONr_chiral_restr0.0690.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024412
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02829
X-RAY DIFFRACTIONr_nbd_refined0.2020.2768
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.23293
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21810
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.24
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2860.226
X-RAY DIFFRACTIONr_nbd_other0.2710.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.27
X-RAY DIFFRACTIONr_mcbond_it2.2332.9751906
X-RAY DIFFRACTIONr_mcbond_other2.2312.9741905
X-RAY DIFFRACTIONr_mcangle_it3.2694.4552379
X-RAY DIFFRACTIONr_mcangle_other3.2694.4562380
X-RAY DIFFRACTIONr_scbond_it2.6013.1631907
X-RAY DIFFRACTIONr_scbond_other2.6013.1631907
X-RAY DIFFRACTIONr_scangle_it3.8154.6712838
X-RAY DIFFRACTIONr_scangle_other3.8144.6712838
X-RAY DIFFRACTIONr_lrange_it5.29334.7774161
X-RAY DIFFRACTIONr_lrange_other5.28834.7834159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.323530.2411419X-RAY DIFFRACTION99.3923
2.257-2.3180.28640.2351406X-RAY DIFFRACTION99.5935
2.318-2.3860.351700.2351366X-RAY DIFFRACTION100
2.386-2.4590.315540.2261323X-RAY DIFFRACTION99.5662
2.459-2.5390.246770.2131283X-RAY DIFFRACTION99.7799
2.539-2.6280.294730.2271228X-RAY DIFFRACTION99.7699
2.628-2.7270.306580.2321206X-RAY DIFFRACTION99.842
2.727-2.8380.354650.2181148X-RAY DIFFRACTION99.9176
2.838-2.9630.282590.2211121X-RAY DIFFRACTION99.9153
2.963-3.1070.269650.2291074X-RAY DIFFRACTION99.5629
3.107-3.2750.308500.248981X-RAY DIFFRACTION98.6603
3.275-3.4720.264460.214964X-RAY DIFFRACTION99.5074
3.472-3.7110.242550.214915X-RAY DIFFRACTION98.4772
3.711-4.0060.271500.193813X-RAY DIFFRACTION97.4041
4.006-4.3850.204460.194790X-RAY DIFFRACTION99.4055
4.385-4.8970.254370.203697X-RAY DIFFRACTION96.9617
4.897-5.6440.199260.216652X-RAY DIFFRACTION99.2679
5.644-6.8870.262210.247550X-RAY DIFFRACTION98.4483
6.887-9.6340.184280.222440X-RAY DIFFRACTION99.1525
9.634-44.30.275140.297273X-RAY DIFFRACTION97.9522

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