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- PDB-6c6w: Structure of a Complex Between Thaumatin and Thioflavin T -

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Basic information

Entry
Database: PDB / ID: 6c6w
TitleStructure of a Complex Between Thaumatin and Thioflavin T
ComponentsThaumatin I
KeywordsPROTEIN BINDING / SWEET TASTING PROTEIN / dye binding / amyloid staining / dimer / UNKNOWN FUNCTION
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
Chem-TFX / L(+)-TARTARIC ACID / Thaumatin I / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Investigation into the binding of dyes within protein crystals.
Authors: McPherson, A. / Larson, S.B.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6773
Polymers22,2431
Non-polymers4332
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint1 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.475, 58.475, 151.710
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 I


Mass: 22243.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: Q8RVT0, UniProt: P02883*PLUS
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-TFX / 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium / Thioflavin T


Mass: 283.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.93 Å3/Da / Density % sol: 58 % / Description: tetragonal bipyramids
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop composed of equal parts 40 mg/ml protein in H20 and 1.0 M sodium-potassium tartrate at pH 6.5. Crystals grew in 24 to 48 hours at room temperature
PH range: 6.0 8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→54.56 Å / Num. obs: 12192 / % possible obs: 88.1 % / Redundancy: 9.5 % / Biso Wilson estimate: 24.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.021 / Rrim(I) all: 0.071 / Rsym value: 0.061 / Net I/av σ(I): 23.1 / Net I/σ(I): 23.1
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 247 / CC1/2: 0.887 / Rpim(I) all: 0.159 / Rrim(I) all: 0.247 / Rsym value: 0.18 / % possible all: 20.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→54.56 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.538 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1669 600 4.9 %RANDOM
Rwork0.12975 ---
obs0.13166 11534 89.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.041 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.23→54.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 30 119 1701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021627
X-RAY DIFFRACTIONr_bond_other_d0.0010.021434
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9722211
X-RAY DIFFRACTIONr_angle_other_deg0.70733332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37622.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34415244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2631512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211841
X-RAY DIFFRACTIONr_gen_planes_other00.02354
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2562.16827
X-RAY DIFFRACTIONr_mcbond_other2.2432.153826
X-RAY DIFFRACTIONr_mcangle_it3.5063.2261032
X-RAY DIFFRACTIONr_mcangle_other3.5083.2341033
X-RAY DIFFRACTIONr_scbond_it4.2352.75800
X-RAY DIFFRACTIONr_scbond_other4.2342.755801
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4893.9171180
X-RAY DIFFRACTIONr_long_range_B_refined8.23541.4676697
X-RAY DIFFRACTIONr_long_range_B_other8.17541.2496648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.232→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.126 9 -
Rwork0.19 223 -
obs--24.02 %
Refinement TLS params.Method: refined / Origin x: 12.202 Å / Origin y: 24.5066 Å / Origin z: 33.0032 Å
111213212223313233
T0.0546 Å20.006 Å2-0.0093 Å2-0.0081 Å2-0.0114 Å2--0.0184 Å2
L0.1716 °20.091 °20.0892 °2-0.5078 °20.5524 °2--1.2244 °2
S0.0762 Å °-0.0112 Å °0.0184 Å °0.0254 Å °-0.0049 Å °-0.0067 Å °0.1141 Å °0.0224 Å °-0.0712 Å °

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