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- PDB-8yk6: Magnetic effects of thaumatin crystals; observation of the crysta... -

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Basic information

Entry
Database: PDB / ID: 8yk6
TitleMagnetic effects of thaumatin crystals; observation of the crystal growth of magneto-Archimedes levitation and magnetic orientation
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Sweet-Tasting Protein Magneto-Archimedes Levitation
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsNakabayashi, M. / Inaka, K. / Fujiwara, M. / Hagiwara, M. / Maki, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos One / Year: 2025
Title: Magnetic effects of thaumatin crystals; observation of crystal growth by magneto-Archimedes levitation and magnetic orientation.
Authors: Maki, S. / Fujiwara, M. / Fujiwara, Y. / Nakabayashi, M. / Morimoto, S. / Tanaka, S. / Fujiwara, S. / Hagiwara, M. / Inaka, K.
History
DepositionMar 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3782
Polymers22,2281
Non-polymers1501
Water6,251347
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.083, 58.083, 150.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22228.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.87 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5
Details: 84 mM ADA pH 6.5, 42 mM GdCl3, 0.51 M NaK-tartrate, 0.017 % NaN3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 0.99→45.98 Å / Num. obs: 145471 / % possible obs: 99 % / Redundancy: 8.2 % / Biso Wilson estimate: 8.176 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.026 / Net I/σ(I): 20.6
Reflection shellResolution: 0.99→1 Å / Redundancy: 8 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 7116 / CC1/2: 0.93 / Rpim(I) all: 0.314 / % 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: 0.99→37.99 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.39 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13382 7248 5 %RANDOM
Rwork0.12598 ---
obs0.12639 138147 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å2-0 Å2
2---0.17 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 0.99→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1545 0 10 347 1902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131922
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181708
X-RAY DIFFRACTIONr_angle_refined_deg1.921.6622631
X-RAY DIFFRACTIONr_angle_other_deg1.5961.5893972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78721.32798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70615299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4831515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022272
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02466
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_it0.930.994986
X-RAY DIFFRACTIONr_mcbond_other0.9260.992985
X-RAY DIFFRACTIONr_mcangle_it1.3541.5071244
X-RAY DIFFRACTIONr_mcangle_other1.3541.5081245
X-RAY DIFFRACTIONr_scbond_it1.2391.187936
X-RAY DIFFRACTIONr_scbond_other1.2391.187935
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5871.6961378
X-RAY DIFFRACTIONr_long_range_B_refined2.69913.7232196
X-RAY DIFFRACTIONr_long_range_B_other2.11512.3872072
X-RAY DIFFRACTIONr_rigid_bond_restr2.12233630
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.99→1.011 Å
RfactorNum. reflection% reflection
Rfree0.189 518 -
Rwork0.193 10046 -
obs--99.96 %

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