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- PDB-5sw1: Thaumatin Structure at pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 5sw1
TitleThaumatin Structure at pH 6.0
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Sweet-tasting protein / sweet receptor / 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
(CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMasuda, T. / Sano, A. / Murata, K. / Okubo, K. / Suzuki, M. / Mikami, B.
CitationJournal: To Be Published
Title: Thaumatin Structure at pH 6.0
Authors: Masuda, T. / Sano, A. / Murata, K. / 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

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Assembly

Deposited unit
A: Thaumatin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4182
Polymers22,2281
Non-polymers1901
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-1 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.368, 52.527, 71.026
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: pPIC6 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q8RVT0, UniProt: P02883*PLUS
#2: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG8000, 50 mM ADA buffer

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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: Nov 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 80097 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 49.8
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 6 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 5.64 / % possible all: 100

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Processing

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

3vhg


Resolution: 1.1→21.116 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.93
RfactorNum. reflection% reflectionSelection details
Rfree0.1448 4013 5.02 %Random
Rwork0.1307 ---
obs0.1314 80019 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→21.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 13 381 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061739
X-RAY DIFFRACTIONf_angle_d1.1832366
X-RAY DIFFRACTIONf_dihedral_angle_d10.955640
X-RAY DIFFRACTIONf_chiral_restr0.046248
X-RAY DIFFRACTIONf_plane_restr0.006324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1001-1.1130.20931270.17442536X-RAY DIFFRACTION97
1.113-1.12660.16971380.1492586X-RAY DIFFRACTION100
1.1266-1.14090.15981370.14162606X-RAY DIFFRACTION100
1.1409-1.15590.1531390.13192537X-RAY DIFFRACTION100
1.1559-1.17170.1571400.13052619X-RAY DIFFRACTION100
1.1717-1.18850.1461360.12442584X-RAY DIFFRACTION100
1.1885-1.20620.14621520.12332584X-RAY DIFFRACTION100
1.2062-1.2250.13811240.12322630X-RAY DIFFRACTION100
1.225-1.24510.13861270.11912613X-RAY DIFFRACTION100
1.2451-1.26660.12011160.11782583X-RAY DIFFRACTION100
1.2666-1.28960.13251530.11622587X-RAY DIFFRACTION100
1.2896-1.31440.14651250.11782641X-RAY DIFFRACTION100
1.3144-1.34120.12791430.11182584X-RAY DIFFRACTION100
1.3412-1.37040.12581330.10692611X-RAY DIFFRACTION100
1.3704-1.40230.14231360.10632604X-RAY DIFFRACTION100
1.4023-1.43730.13171290.10912582X-RAY DIFFRACTION100
1.4373-1.47620.13011430.10472641X-RAY DIFFRACTION100
1.4762-1.51960.12231400.10592596X-RAY DIFFRACTION100
1.5196-1.56870.11571390.1052613X-RAY DIFFRACTION100
1.5687-1.62470.1311390.11282631X-RAY DIFFRACTION100
1.6247-1.68970.13471430.11982655X-RAY DIFFRACTION100
1.6897-1.76660.14241300.12542624X-RAY DIFFRACTION100
1.7666-1.85970.14881510.13142619X-RAY DIFFRACTION100
1.8597-1.97610.14691670.13532593X-RAY DIFFRACTION100
1.9761-2.12860.14521470.13152645X-RAY DIFFRACTION100
2.1286-2.34250.1411500.13912648X-RAY DIFFRACTION100
2.3425-2.68090.15951370.14562689X-RAY DIFFRACTION100
2.6809-3.37540.1751360.1452722X-RAY DIFFRACTION100
3.3754-21.12020.13431360.13782843X-RAY DIFFRACTION100

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