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- PDB-7vcg: Thaumatin protected by alginate gel -

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Basic information

Entry
Database: PDB / ID: 7vcg
TitleThaumatin protected by alginate gel
ComponentsThaumatin I
KeywordsPLANT PROTEIN / Hydrogel Alginate gel
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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMuroyama, H. / Tomoike, F. / Nagae, T. / Okada, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Post-crystallization protection of protein crystals
Authors: Morita, S. / Muroyama, H. / Itabashi, T. / Nagae, T. / Takeuchi, S. / Okada, T. / Tomoike, F.
History
DepositionSep 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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)22,4914
Polymers22,1571
Non-polymers3343
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.945, 57.945, 150.235
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.: 1 / 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.: 234 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7.5 / Details: 1 M sodium tartrate, 0.1 M HEPES

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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: Jul 21, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.25→45.91 Å / Num. obs: 71712 / % possible obs: 100 % / Redundancy: 13.9 % / Biso Wilson estimate: 9.17 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.064 / Rrim(I) all: 0.24 / Net I/σ(I): 21.5
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.937 / Num. unique obs: 7048 / CC1/2: 0.785 / Rpim(I) all: 0.262 / Rrim(I) all: 0.973 / % possible all: 100

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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: 1.25→28.97 Å / SU ML: 0.0953 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.1683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1616 2000 2.79 %
Rwork0.1481 69712 -
obs0.1485 71712 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.13 Å2
Refinement stepCycle: LAST / Resolution: 1.25→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 22 234 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471637
X-RAY DIFFRACTIONf_angle_d0.81812222
X-RAY DIFFRACTIONf_chiral_restr0.0787236
X-RAY DIFFRACTIONf_plane_restr0.0052294
X-RAY DIFFRACTIONf_dihedral_angle_d27.9005664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.24991400.18434906X-RAY DIFFRACTION100
1.28-1.320.20681410.16724900X-RAY DIFFRACTION100
1.32-1.350.18721400.15444889X-RAY DIFFRACTION100
1.35-1.40.15831410.15014897X-RAY DIFFRACTION99.98
1.4-1.450.1781420.14074933X-RAY DIFFRACTION99.98
1.45-1.510.16671400.13174898X-RAY DIFFRACTION99.98
1.51-1.570.15651420.12644939X-RAY DIFFRACTION100
1.57-1.660.13571420.12414952X-RAY DIFFRACTION99.98
1.66-1.760.1491410.12544943X-RAY DIFFRACTION100
1.76-1.90.17741430.13924966X-RAY DIFFRACTION100
1.9-2.090.14081430.1355002X-RAY DIFFRACTION100
2.09-2.390.15181440.1495021X-RAY DIFFRACTION100
2.39-3.010.17171470.16335108X-RAY DIFFRACTION100
3.01-28.970.15321540.1595358X-RAY DIFFRACTION99.86

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