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- PDB-6yc5: RT structure of Thaumatin obtained at 1.35 A resolution from crys... -

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Basic information

Entry
Database: PDB / ID: 6yc5
TitleRT structure of Thaumatin obtained at 1.35 A resolution from crystal grown in a Kapton microchip.
ComponentsThaumatin-1
KeywordsPLANT PROTEIN / 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
L(+)-TARTARIC ACID / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2016-74875-P Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips.
Authors: Gavira, J.A. / Rodriguez-Ruiz, I. / Martinez-Rodriguez, S. / Basu, S. / Teychene, S. / McCarthy, A.A. / Mueller-Dieckman, C.
History
DepositionMar 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Thaumatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4003
Polymers22,2271
Non-polymers1732
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint1 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.390, 58.390, 151.447
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-1 / / Thaumatin I


Mass: 22227.059 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 / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293.5 K / Method: counter-diffusion / pH: 7 / Details: 20% w/v NaK Tartrate / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 293.5 K / Ambient temp details: Room Temperature / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2017
Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.35→54.48 Å / Num. obs: 52807 / % possible obs: 90.14 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.55 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.4
Reflection shellResolution: 1.35→1.4 Å / Num. unique obs: 3906 / CC1/2: 0.786

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
MxCuBEdata collection
XDSdata reduction
PHASERphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THW

1thw


Resolution: 1.35→54.48 Å / SU ML: 0.1135 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6331
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1483 2648 5.02 %
Rwork0.1268 50090 -
obs0.1279 52738 90.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.17 Å2
Refinement stepCycle: LAST / Resolution: 1.35→54.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 11 136 1698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01421884
X-RAY DIFFRACTIONf_angle_d1.31372589
X-RAY DIFFRACTIONf_chiral_restr0.1053269
X-RAY DIFFRACTIONf_plane_restr0.0095358
X-RAY DIFFRACTIONf_dihedral_angle_d6.13391252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.28771090.24381964X-RAY DIFFRACTION68.62
1.37-1.40.25521040.21762051X-RAY DIFFRACTION71.31
1.4-1.430.22711190.18322160X-RAY DIFFRACTION75.29
1.43-1.460.1941150.16162311X-RAY DIFFRACTION80.04
1.46-1.490.17021300.14092384X-RAY DIFFRACTION83.22
1.49-1.530.16861240.12552487X-RAY DIFFRACTION86.03
1.53-1.570.15691340.11592533X-RAY DIFFRACTION87.79
1.57-1.620.14181220.10712635X-RAY DIFFRACTION90.54
1.62-1.670.14461500.10432699X-RAY DIFFRACTION93.59
1.67-1.730.14791620.10422752X-RAY DIFFRACTION96.14
1.73-1.80.15111290.10552816X-RAY DIFFRACTION96.24
1.8-1.880.14311260.10812877X-RAY DIFFRACTION97.31
1.88-1.980.14561500.10552825X-RAY DIFFRACTION97.83
1.98-2.110.13521710.11112865X-RAY DIFFRACTION98.22
2.11-2.270.16071740.11292865X-RAY DIFFRACTION98.22
2.27-2.50.14881790.12642867X-RAY DIFFRACTION97.78
2.5-2.860.16861550.14522916X-RAY DIFFRACTION98.02
2.86-3.60.13861510.1342968X-RAY DIFFRACTION97.84
3.6-54.480.13181440.12973115X-RAY DIFFRACTION96.39

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