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- PDB-3wxs: Thaumatin structure determined by SPring-8 Angstrom Compact free ... -

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Basic information

Entry
Database: PDB / ID: 3wxs
TitleThaumatin structure determined by SPring-8 Angstrom Compact free electron Laser (SACLA)
Componentsthaumatin I
KeywordsPLANT PROTEIN / thaumatin / sweet-tasting protein / thaumatin family / sweet receptor / mainly beta / taste protein / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMasuda, T. / Nango, E. / Sugahara, M. / Mizohata, E. / Tanaka, T. / Tanaka, R. / Suzuki, M. / Mikami, B. / Iwata, S.
CitationJournal: Nat. Methods / Year: 2015
Title: Grease matrix as a versatile carrier of proteins for serial crystallography
Authors: Sugahara, M. / Mizohata, E. / Nango, E. / Suzuki, M. / Tanaka, T. / Masuda, T. / Tanaka, R. / Shimamura, T. / Tanaka, Y. / Suno, C. / Ihara, K. / Pan, D. / Kakinouchi, K. / Sugiyama, S. / ...Authors: Sugahara, M. / Mizohata, E. / Nango, E. / Suzuki, M. / Tanaka, T. / Masuda, T. / Tanaka, R. / Shimamura, T. / Tanaka, Y. / Suno, C. / Ihara, K. / Pan, D. / Kakinouchi, K. / Sugiyama, S. / Murata, M. / Inoue, T. / Tono, K. / Song, C. / Park, J. / Kameshima, T. / Hatsui, T. / Joti, Y. / Yabashi, M. / Iwata, S.
History
DepositionAug 7, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.699, 57.699, 149.776
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 natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / 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.: 166 / 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: 8856

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293 K / Method: batch method / pH: 7.2
Details: 0.1M ADA, 1.0M K/Na tartrate, pH 7.2, batch method, temperature 293K

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.23 Å
DetectorType: MPCCD octal / Detector: CCD / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 22712 / % possible obs: 99.9 % / Biso Wilson estimate: 18.59 Å2
Reflection shellResolution: 2→2.04 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3al7

3al7


Resolution: 2→28.849 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 921 5.15 %
Rwork0.1568 --
obs0.1591 17889 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.63 Å2 / Biso mean: 20.0307 Å2 / Biso min: 5.8 Å2
Refinement stepCycle: LAST / Resolution: 2→28.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 10 166 1727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081710
X-RAY DIFFRACTIONf_angle_d1.1322319
X-RAY DIFFRACTIONf_chiral_restr0.042244
X-RAY DIFFRACTIONf_plane_restr0.004314
X-RAY DIFFRACTIONf_dihedral_angle_d13.106623
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.10550.22421230.157323632486
2.1055-2.23730.18941210.147923712492
2.2373-2.410.19941370.146823882525
2.41-2.65240.2151290.155723782507
2.6524-3.03580.191360.155524242560
3.0358-3.82340.20031350.146924382573
3.8234-28.85250.19721400.174126062746

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