+Open data
-Basic information
Entry | Database: PDB / ID: 5sw0 | ||||||
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Title | Thaumatin Structure at pH 4.0 | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / Sweet-tasting protein / sweet receptor / acidic pH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.269 Å | ||||||
Authors | Masuda, T. / Okubo, K. / Suzuki, M. / Mikami, B. | ||||||
Citation | Journal: To Be Published Title: Thaumatin Structure at pH 4.0 Authors: Masuda, T. / Okubo, K. / Suzuki, M. / Mikami, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sw0.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sw0.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 5sw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/5sw0 ftp://data.pdbj.org/pub/pdb/validation_reports/sw/5sw0 | HTTPS FTP |
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-Related structure data
Related structure data | 3vhgS S: Starting model for refinement |
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Similar 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: pPIC6alpha / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q8RVT0, UniProt: P02883*PLUS |
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#2: Chemical | ChemComp-PO4 / |
#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: 2.13 Å3/Da / Density % sol: 42.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG8000, 50 mM sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.269→50 Å / Num. obs: 50840 / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 64.11 |
Reflection shell | Resolution: 1.269→1.29 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 5.61 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3vhg Resolution: 1.269→24.425 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.269→24.425 Å
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Refine LS restraints |
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LS refinement shell |
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