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- PDB-3x3r: Recombinant thaumatin in the presence of 1.0M PST and soaked 1 hr... -

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Basic information

Entry
Database: PDB / ID: 3x3r
TitleRecombinant thaumatin in the presence of 1.0M PST and soaked 1 hr at 293K
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: 1.52 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 1.1Oct 30, 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
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.429, 58.429, 151.650
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.: 159 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M ADA, 1.0M K-Na TARTRATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 41467 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 67.22
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 6.88 / % possible all: 99.8

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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: 1.52→28.687 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 9.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1288 2069 5 %
Rwork0.0996 --
obs0.101 41377 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.05 Å2 / Biso mean: 21.4712 Å2 / Biso min: 9.75 Å2
Refinement stepCycle: LAST / Resolution: 1.52→28.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 10 159 1720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071826
X-RAY DIFFRACTIONf_angle_d1.112493
X-RAY DIFFRACTIONf_chiral_restr0.046257
X-RAY DIFFRACTIONf_plane_restr0.005346
X-RAY DIFFRACTIONf_dihedral_angle_d12.209684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5201-1.55550.13891360.09512570270699
1.5555-1.59430.1331340.088525562690100
1.5943-1.63750.11661350.078125622697100
1.6375-1.68560.10651350.073725732708100
1.6856-1.740.12211360.069525782714100
1.74-1.80220.12151360.07725862722100
1.8022-1.87440.13091360.076825792715100
1.8744-1.95960.11831370.069826102747100
1.9596-2.06290.09851370.076125942731100
2.0629-2.19210.12581370.089226082745100
2.1921-2.36130.12741380.10426352773100
2.3613-2.59880.14031380.119426262764100
2.5988-2.97450.15111410.128326632804100
2.9745-3.74630.12841420.110826982840100
3.7463-28.69210.12971510.103628703021100

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