+Open data
-Basic information
Entry | Database: PDB / ID: 5sw2 | ||||||
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Title | Thaumatin Structure at pH 6.0, orthorhombic type1 | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / Sweet-tasting protein / sweet receptor / pH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Masuda, T. / Sano, A. / Murata, K. / Okubo, K. / Suzuki, M. / Mikami, B. | ||||||
Citation | Journal: To Be Published Title: Thaumatin Structure at pH 6.0, orthorhombic type1 Authors: Masuda, T. / Sano, A. / Murata, K. / 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 | 5sw2.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sw2.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 5sw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/5sw2 ftp://data.pdbj.org/pub/pdb/validation_reports/sw/5sw2 | 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: pPIC6 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q8RVT0, UniProt: P02883*PLUS | ||
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#2: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG4000, 50 mM ADA |
-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: RAYONIX MX-225 / Detector: CCD / Date: Dec 18, 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: 1.2→23.9 Å / Num. obs: 61408 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VHG Resolution: 1.2→23.9 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→23.9 Å
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Refine LS restraints |
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LS refinement shell |
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