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Yorodumi- PDB-3x3r: Recombinant thaumatin in the presence of 1.0M PST and soaked 1 hr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x3r | ||||||
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Title | Recombinant thaumatin in the presence of 1.0M PST and soaked 1 hr at 293K | ||||||
Components | thaumatin I | ||||||
Keywords | PLANT PROTEIN / thaumatin / sweet-tasting protein / sweet receptor / mainly beta / taste protein / sweet taste receptor / aril | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Masuda, T. / Okubo, K. / Mikami, B. | ||||||
Citation | Journal: To be Published Title: Structure of the recombinant thaumatin in the presence of PST at room temperature Authors: Masuda, T. / Okubo, K. / Mikami, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x3r.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x3r.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 3x3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/3x3r ftp://data.pdbj.org/pub/pdb/validation_reports/x3/3x3r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22228.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Plasmid: pPIC6-pre-TH / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: A1IIJ1, UniProt: P02883*PLUS |
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#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.05M ADA, 1.0M K-Na TARTRATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. obs: 41467 / % possible obs: 99.9 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 67.22 |
Reflection shell | Resolution: 1.52→1.55 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 6.88 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→28.687 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 9.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.05 Å2 / Biso mean: 21.4712 Å2 / Biso min: 9.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→28.687 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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