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- PDB-7wxt: Thaumatin protected by polyacrylamide gel -

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Basic information

Entry
Database: PDB / ID: 7wxt
TitleThaumatin protected by polyacrylamide gel
ComponentsThaumatin I
KeywordsHYDROLASE / Hydrogel / polyacrylamide gel / PLANT PROTEIN
Function / homology
Function and homology information


defense response / cytoplasmic vesicle / extracellular region
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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMuroyama, H. / Tomoike, F. / Nagae, T. / Okada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K15713 Japan
CitationJournal: To Be Published
Title: Post-crystallization protection of protein crystals by polyacrylamide
Authors: Muroyama, H. / Kato, S. / Itabashi, T. / Nagae, T. / Okada, T. / Tomoike, F.
History
DepositionFeb 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,7336
Polymers22,1571
Non-polymers5765
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.013, 58.013, 150.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 22156.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M potassium sodium tartrate, 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.7→45.95 Å / Num. obs: 29190 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 16.24 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.204 / Rrim(I) all: 0.211 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.7613.21.1512.228500.7511.197100
1.76-1.830.919328460.8360.953
1.83-1.910.7164.428560.8560.743
1.91-2.026.10.4986.128850.9380.517100
2.02-2.140.4158.428790.9490.43
2.14-2.310.31511.928870.960.327
2.31-2.5414.30.2481629120.9770.257100
2.54-2.910.17722.929360.9830.184
2.91-3.6614.10.1214629740.9930.125100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ald

3ald


Resolution: 1.7→45.94 Å / SU ML: 0.1874 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6399
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2147 1366 4.68 %
Rwork0.1832 27818 -
obs0.1846 29184 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.81 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 0 159 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561637
X-RAY DIFFRACTIONf_angle_d0.7892216
X-RAY DIFFRACTIONf_chiral_restr0.0505236
X-RAY DIFFRACTIONf_plane_restr0.0048293
X-RAY DIFFRACTIONf_dihedral_angle_d21.4949236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.3231400.24952708X-RAY DIFFRACTION99.93
1.76-1.830.23621350.21452711X-RAY DIFFRACTION100
1.83-1.910.23241350.18752721X-RAY DIFFRACTION100
1.91-2.020.20551280.18252756X-RAY DIFFRACTION99.97
2.02-2.140.2091540.17852725X-RAY DIFFRACTION100
2.14-2.310.2761260.17972761X-RAY DIFFRACTION100
2.31-2.540.23681440.18242768X-RAY DIFFRACTION100
2.54-2.910.21121190.18822817X-RAY DIFFRACTION100
2.91-3.660.18561450.16392829X-RAY DIFFRACTION100
3.66-45.940.18941400.18233022X-RAY DIFFRACTION99.91

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