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- PDB-5sw0: Thaumatin Structure at pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 5sw0
TitleThaumatin Structure at pH 4.0
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Sweet-tasting protein / sweet receptor / acidic pH
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
PHOSPHATE ION / Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.269 Å
AuthorsMasuda, T. / Okubo, K. / Suzuki, M. / Mikami, B.
CitationJournal: To Be Published
Title: Thaumatin Structure at pH 4.0
Authors: Masuda, T. / Okubo, K. / Suzuki, M. / Mikami, B.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 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)22,3232
Polymers22,2281
Non-polymers951
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-4 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.641, 52.071, 70.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: pPIC6alpha / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q8RVT0, UniProt: P02883*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG8000, 50 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.269→50 Å / Num. obs: 50840 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 64.11
Reflection shellResolution: 1.269→1.29 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 5.61 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vhg

3vhg


Resolution: 1.269→24.425 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.24
RfactorNum. reflection% reflection
Rfree0.1658 2525 4.97 %
Rwork0.1424 --
obs0.1436 50757 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.269→24.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 5 210 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061701
X-RAY DIFFRACTIONf_angle_d1.0892310
X-RAY DIFFRACTIONf_dihedral_angle_d10.683621
X-RAY DIFFRACTIONf_chiral_restr0.042243
X-RAY DIFFRACTIONf_plane_restr0.005312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2694-1.29380.2173920.16622526X-RAY DIFFRACTION95
1.2938-1.32030.21891170.15972680X-RAY DIFFRACTION100
1.3203-1.3490.19951220.14612671X-RAY DIFFRACTION100
1.349-1.38030.18221330.13742661X-RAY DIFFRACTION100
1.3803-1.41490.17961600.1362643X-RAY DIFFRACTION100
1.4149-1.45310.16231340.12782651X-RAY DIFFRACTION100
1.4531-1.49590.13161460.11752668X-RAY DIFFRACTION100
1.4959-1.54410.13781780.11772603X-RAY DIFFRACTION100
1.5441-1.59930.15421300.11532673X-RAY DIFFRACTION100
1.5993-1.66330.15321540.11242676X-RAY DIFFRACTION100
1.6633-1.7390.15741480.1172663X-RAY DIFFRACTION100
1.739-1.83070.14861360.12822690X-RAY DIFFRACTION100
1.8307-1.94530.16511510.12872675X-RAY DIFFRACTION100
1.9453-2.09540.14141700.12622680X-RAY DIFFRACTION100
2.0954-2.30620.16121150.13682723X-RAY DIFFRACTION100
2.3062-2.63950.15821440.15412721X-RAY DIFFRACTION100
2.6395-3.32420.17571360.16182771X-RAY DIFFRACTION100
3.3242-24.42910.17761590.14932857X-RAY DIFFRACTION99

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