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- PDB-8jz8: Subatomic structure of orthorhombic thaumatin at 0.89 Angstroms -

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Basic information

Entry
Database: PDB / ID: 8jz8
TitleSubatomic structure of orthorhombic thaumatin at 0.89 Angstroms
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Thaumatin / Sweet-tasting protein
Function / homology
Function and homology information


cytoplasmic vesicle
Similarity search - Function
Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 Å
AuthorsMasuda, T. / Suzuki, M. / Yamasaki, M. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05875 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Subatomic structure of orthorhombic thaumatin at 0.89 angstrom reveals that highly flexible conformations are crucial for thaumatin sweetness.
Authors: Masuda, T. / Suzuki, M. / Yamasaki, M. / Mikami, B.
History
DepositionJul 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)22,5464
Polymers22,2281
Non-polymers3183
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.706, 63.665, 71.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22228.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: P02883
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M N-(2-acetanido) iminodiacetic acid, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.89→50 Å / Num. obs: 153640 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Rrim(I) all: 0.062 / Net I/σ(I): 49.55
Reflection shellResolution: 0.89→0.91 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.81 / Num. unique obs: 7590 / CC1/2: 0.861 / Rpim(I) all: 0.219 / Rrim(I) all: 0.546 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXLrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VJQ

3vjq


Resolution: 0.89→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.131 7677 5 %Random selection
Rwork0.113 ---
obs-153516 99.9 %-
Displacement parametersBiso max: 93.63 Å2 / Biso mean: 12.1813 Å2 / Biso min: 3.66 Å2
Refinement stepCycle: LAST / Resolution: 0.89→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 21 411 1983
LS refinement shellResolution: 0.89→0.91 Å
RfactorNum. reflection% reflection
Rfree0.123 -5 %
Rwork0.105 7590 -
obs--100 %

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