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- PDB-3x3o: Recombinant thaumatin in the presence of 0.5M PST at 298K -

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Basic information

Entry
Database: PDB / ID: 3x3o
TitleRecombinant thaumatin in the presence of 0.5M PST at 298K
Componentsthaumatin I
KeywordsPLANT PROTEIN / thaumatin / sweet-tasting protein / sweet receptor / mainly beta / taste protein / sweet taste receptor / aril
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMasuda, T. / Okubo, K. / Mikami, B.
CitationJournal: To be Published
Title: Structure of the recombinant thaumatin in the presence of PST at room temperature
Authors: Masuda, T. / Okubo, K. / Mikami, B.
History
DepositionJan 26, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.603, 58.603, 151.551
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


Mass: 22228.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Plasmid: pPIC6-pre-TH / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: A1IIJ1, UniProt: P02883*PLUS
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M ADA, 0.5M K-Na TARTRATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 45055 / % possible obs: 99.9 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 64.72
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.96 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→32.039 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 10.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.134 2223 4.94 %
Rwork0.1111 --
obs0.1123 44961 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.74 Å2 / Biso mean: 20.4019 Å2 / Biso min: 8.82 Å2
Refinement stepCycle: LAST / Resolution: 1.48→32.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 10 168 1729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061823
X-RAY DIFFRACTIONf_angle_d1.0732489
X-RAY DIFFRACTIONf_chiral_restr0.043258
X-RAY DIFFRACTIONf_plane_restr0.005345
X-RAY DIFFRACTIONf_dihedral_angle_d12.01680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4801-1.51230.16551290.132596272599
1.5123-1.54750.14021370.109626232760100
1.5475-1.58620.1331470.096926352782100
1.5862-1.62910.12931340.091526312765100
1.6291-1.6770.13071370.086426282765100
1.677-1.73120.11681450.083326002745100
1.7312-1.7930.12711100.086226672777100
1.793-1.86480.12821350.088226272762100
1.8648-1.94970.11311500.086626502800100
1.9497-2.05240.1291330.090726532786100
2.0524-2.1810.13891370.102526892826100
2.181-2.34940.12641440.111426712815100
2.3494-2.58570.14691490.130426802829100
2.5857-2.95960.13791310.139627222853100
2.9596-3.72790.14491580.125927402898100
3.7279-32.04610.12721470.110429263073100

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