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- PDB-5gqp: Thaumatin Structure at pH 8.0, orthorhombic type1 -

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Basic information

Entry
Database: PDB / ID: 5gqp
TitleThaumatin Structure at pH 8.0, orthorhombic type1
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
Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.296 Å
AuthorsMasuda, T. / Sano, A. / Murata, K. / Okubo, K. / Suzuki, M. / Mikami, B.
CitationJournal: To Be Published
Title: Thaumatin Structure at pH 8.0, orthorhombic type1
Authors: Masuda, T. / Sano, A. / Murata, K. / Okubo, K. / Suzuki, M. / Mikami, B.
History
DepositionAug 8, 2016Deposition site: PDBJ / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thaumatin I


Theoretical massNumber of molelcules
Total (without water)22,2281
Polymers22,2281
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9710 Å2
Unit cell
Length a, b, c (Å)50.964, 53.372, 71.135
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3350, 50 mM Tris buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.296→50 Å / Num. obs: 47852 / % possible obs: 98.1 % / Redundancy: 7.1 % / Net I/σ(I): 52.33
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.67 / % possible all: 96.4

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Processing

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

3vhg


Resolution: 1.296→22.435 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.59
RfactorNum. reflection% reflection
Rfree0.1693 2334 4.88 %
Rwork0.1428 --
obs0.1441 47797 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.296→22.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 0 317 1868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061658
X-RAY DIFFRACTIONf_angle_d1.0782245
X-RAY DIFFRACTIONf_dihedral_angle_d11.943601
X-RAY DIFFRACTIONf_chiral_restr0.044237
X-RAY DIFFRACTIONf_plane_restr0.005302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2959-1.32240.17761140.17012440X-RAY DIFFRACTION90
1.3224-1.35110.20741400.1622605X-RAY DIFFRACTION97
1.3511-1.38250.19011250.15592609X-RAY DIFFRACTION97
1.3825-1.41710.18551040.14482644X-RAY DIFFRACTION97
1.4171-1.45540.19991320.13442647X-RAY DIFFRACTION97
1.4554-1.49820.15871470.13092625X-RAY DIFFRACTION98
1.4982-1.54660.16341300.12762650X-RAY DIFFRACTION98
1.5466-1.60190.18131260.12412675X-RAY DIFFRACTION98
1.6019-1.6660.15731340.12362676X-RAY DIFFRACTION99
1.666-1.74180.17241370.12922695X-RAY DIFFRACTION99
1.7418-1.83360.18321500.13112670X-RAY DIFFRACTION98
1.8336-1.94840.16581580.13592689X-RAY DIFFRACTION99
1.9484-2.09870.15341480.13422713X-RAY DIFFRACTION99
2.0987-2.30970.16181660.1382711X-RAY DIFFRACTION99
2.3097-2.64350.19681350.15512766X-RAY DIFFRACTION100
2.6435-3.32880.16491500.15382786X-RAY DIFFRACTION100
3.3288-22.43790.1621380.14572862X-RAY DIFFRACTION97

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