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Open data
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Basic information
Entry | Database: PDB / ID: 6e0d | |||||||||
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Title | X-ray structure of a complex of thaumatin with xylene cyanol | |||||||||
![]() | Thaumatin I | |||||||||
![]() | PLANT PROTEIN/ANTIBIOTIC / SWEET TASTING PROTEIN / disulfides / dye binding / xylene cyanol / PLANT PROTEIN / PLANT PROTEIN-ANTIBIOTIC complex | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | McPherson, A. | |||||||||
![]() | ![]() Title: Investigation into the binding of dyes within protein crystals. Authors: McPherson, A. / Larson, S.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.2 KB | Display | ![]() |
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PDB format | ![]() | 39.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799.6 KB | Display | ![]() |
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Full document | ![]() | 801 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25478.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-TLA / |
#3: Sugar | ChemComp-XXX / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.92 % / Description: tetragonal bipyramids |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: CCD / Date: Apr 15, 2015 |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.694 Å2
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Refinement step | Cycle: 1 / Resolution: 2.24→52 Å
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