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- PDB-3wou: Crystal Structure of The Recombinant Thaumatin II at 0.99 A -

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Basic information

Entry
Database: PDB / ID: 3wou
TitleCrystal Structure of The Recombinant Thaumatin II at 0.99 A
ComponentsThaumatin-2
KeywordsPLANT PROTEIN / Osmotin / thaumatin-like protein / Sweet-tasting protein / Sweet receptors
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 II
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.99 Å
AuthorsMasuda, T. / Mikami, B. / Tani, F.
CitationJournal: Biochimie / Year: 2014
Title: Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues
Authors: Masuda, T. / Mikami, B. / Tani, F.
History
DepositionDec 30, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thaumatin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7975
Polymers22,3121
Non-polymers4844
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.685, 57.685, 150.011
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-2 / Thaumatin II


Mass: 22312.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Plasmid: pPIC6-preTHII / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P02884
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.797 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M ADA, 0.75M TARTRATE, 12.5% GLYCEROL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jul 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.99→50 Å / Num. obs: 141082 / % possible obs: 99.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 64.34
Reflection shellResolution: 0.99→1.01 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 6.26 / % possible all: 100

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.99→10 Å / Num. parameters: 20908 / Num. restraintsaints: 28815 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1185 7044 -RANDOM
Rwork0.097 ---
all-133756 --
obs-133756 100 %-
Refine analyzeNum. disordered residues: 89 / Occupancy sum hydrogen: 1412.46 / Occupancy sum non hydrogen: 1964.84
Refinement stepCycle: LAST / Resolution: 0.99→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 32 441 2030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0182
X-RAY DIFFRACTIONs_angle_d0.0389
X-RAY DIFFRACTIONs_zero_chiral_vol0.1108
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1171
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0343
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0067
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0517
X-RAY DIFFRACTIONs_approx_iso_adps0.1733
X-RAY DIFFRACTIONs_similar_dist0
LS refinement shellResolution: 0.99→1.01 Å
RfactorNum. reflection% reflection
Rwork0.176 --
obs-7886 99.77 %

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