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- PDB-6e0d: X-ray structure of a complex of thaumatin with xylene cyanol -

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Basic information

Entry
Database: PDB / ID: 6e0d
TitleX-ray structure of a complex of thaumatin with xylene cyanol
ComponentsThaumatin I
KeywordsPLANT PROTEIN/ANTIBIOTIC / SWEET TASTING PROTEIN / disulfides / dye binding / xylene cyanol / PLANT PROTEIN / PLANT PROTEIN-ANTIBIOTIC complex
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 / Chem-XXX / Thaumatin I
Similarity search - Component
Biological speciesThaumatococcus daniellii (katemfe)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 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
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,9513
Polymers25,4791
Non-polymers4722
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint2 kcal/mol
Surface area9830 Å2
Unit cell
Length a, b, c (Å)58.654, 58.654, 151.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-502-

XXX

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Components

#1: Protein Thaumatin I / Thaumatin-1


Mass: 25478.957 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: Sugar ChemComp-XXX / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside / (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL / NEOMYCIN A / NEAMINE / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside


Type: D-saccharide / Mass: 322.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.56 Å3/Da / Density % sol: 51.92 % / Description: tetragonal bipyramids
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop at room temperature with 0.6 ml reservoirs composed of 0.6 M to 1.0 M sodium tartrate titrated to pH 6.5. Drops composed of equal volumes of 50 mg/ml lyophilized thaumatin in ...Details: Sitting drop at room temperature with 0.6 ml reservoirs composed of 0.6 M to 1.0 M sodium tartrate titrated to pH 6.5. Drops composed of equal volumes of 50 mg/ml lyophilized thaumatin in water with the reservoir solution. Crystals appear after 12 hours and grow to full size over three days
PH range: 6.0 - 8.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å
DetectorType: RIGAKU / Detector: CCD / Date: Apr 15, 2015
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.23→52 Å / Num. obs: 12161 / % possible obs: 88.5 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Rsym value: 0.048 / Net I/av σ(I): 32.1 / Net I/σ(I): 32.1
Reflection shellResolution: 2.23→2.3 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.069 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 238 / CC1/2: 0.933 / Rpim(I) all: 0.067 / Rrim(I) all: 0.096 / Rsym value: 0.069 / % possible all: 20.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→52 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.148 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16405 609 5 %RANDOM
Rwork0.12515 ---
obs0.12716 11496 89.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.694 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.24→52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 32 109 1687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021636
X-RAY DIFFRACTIONr_bond_other_d0.0010.021435
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9722226
X-RAY DIFFRACTIONr_angle_other_deg0.7133352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75423.13467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5181512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211828
X-RAY DIFFRACTIONr_gen_planes_other00.02348
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_it2.5111.982827
X-RAY DIFFRACTIONr_mcbond_other2.5061.98826
X-RAY DIFFRACTIONr_mcangle_it3.3912.9621033
X-RAY DIFFRACTIONr_mcangle_other3.392.9651034
X-RAY DIFFRACTIONr_scbond_it5.4052.713806
X-RAY DIFFRACTIONr_scbond_other5.3982.713806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8563.7851185
X-RAY DIFFRACTIONr_long_range_B_refined15.28426.0361793
X-RAY DIFFRACTIONr_long_range_B_other15.28126.0081792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.237→2.295 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 12 -
Rwork0.12 199 -
obs--21.66 %

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