+Open data
-Basic information
Entry | Database: PDB / ID: 3x3s | ||||||
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Title | Recombinant thaumatin in the presence of 1.5M PST 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: 1.46 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 | 3x3s.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x3s.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 3x3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x3s_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 3x3s_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 3x3s_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3x3s_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/3x3s ftp://data.pdbj.org/pub/pdb/validation_reports/x3/3x3s | HTTPS FTP |
-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: 2.92 Å3/Da / Density % sol: 57.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.05M ADA, 1.5 M 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: Oct 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. obs: 46801 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 73.99 |
Reflection shell | Resolution: 1.46→1.49 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 7.26 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→28.724 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 9.87 / 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: 76.21 Å2 / Biso mean: 20.8992 Å2 / Biso min: 9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→28.724 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 / % reflection obs: 100 %
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