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- PDB-5wr8: Thaumatin structure determined by SACLA at 1.55 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5wr8
TitleThaumatin structure determined by SACLA at 1.55 Angstrom
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Sweet-tasting protein / Sweet receptor
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 / Resolution: 1.55 Å
AuthorsMasuda, T. / Suzuki, M. / Inoue, S. / Sugahara, M.
CitationJournal: Sci Rep / Year: 2017
Title: Hydroxyethyl cellulose matrix applied to serial crystallography
Authors: Sugahara, M. / Nakane, T. / Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Tanaka, R. / Nakatsu, T. / Mizohata, E. / Yumoto, F. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / ...Authors: Sugahara, M. / Nakane, T. / Masuda, T. / Suzuki, M. / Inoue, S. / Song, C. / Tanaka, R. / Nakatsu, T. / Mizohata, E. / Yumoto, F. / Tono, K. / Joti, Y. / Kameshima, T. / Hatsui, T. / Yabashi, M. / Nureki, O. / Numata, K. / Nango, E. / Iwata, S.
History
DepositionDec 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint0 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.459, 58.459, 151.639
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 / Sweet-tasting protein


Mass: 22228.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: Q8RVT0, 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.: 126 / 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: 57.79 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 7.3
Details: 20 mM N-(2-acetamido) iminodiacetic acid, 2.0 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 39121 / % possible obs: 100 % / Redundancy: 647.6 % / CC1/2: 0.988 / Net I/σ(I): 7.7
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 668.5 % / Mean I/σ(I) obs: 2 / CC1/2: 0.76 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementResolution: 1.55→29.229 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.2
RfactorNum. reflection% reflection
Rfree0.1505 1937 4.95 %
Rwork0.1272 --
obs0.1284 39121 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→29.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 10 126 1687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061770
X-RAY DIFFRACTIONf_angle_d0.9842412
X-RAY DIFFRACTIONf_dihedral_angle_d11.526654
X-RAY DIFFRACTIONf_chiral_restr0.039255
X-RAY DIFFRACTIONf_plane_restr0.004331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58880.28941410.22132608X-RAY DIFFRACTION100
1.5888-1.63170.2661270.18242603X-RAY DIFFRACTION100
1.6317-1.67970.18891340.14532613X-RAY DIFFRACTION100
1.6797-1.7340.18141230.1322614X-RAY DIFFRACTION100
1.734-1.79590.1731190.11542630X-RAY DIFFRACTION100
1.7959-1.86780.16741260.11242640X-RAY DIFFRACTION100
1.8678-1.95280.16261360.10412626X-RAY DIFFRACTION100
1.9528-2.05570.13841510.0982610X-RAY DIFFRACTION100
2.0557-2.18450.15341270.10742652X-RAY DIFFRACTION100
2.1845-2.35310.14661540.11682642X-RAY DIFFRACTION100
2.3531-2.58980.1461350.13192667X-RAY DIFFRACTION100
2.5898-2.96420.17531570.14292684X-RAY DIFFRACTION100
2.9642-3.73340.15511550.13092715X-RAY DIFFRACTION100
3.7334-29.23470.12681520.12542880X-RAY DIFFRACTION99

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