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Yorodumi- PDB-3wxs: Thaumatin structure determined by SPring-8 Angstrom Compact free ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wxs | ||||||
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Title | Thaumatin structure determined by SPring-8 Angstrom Compact free electron Laser (SACLA) | ||||||
Components | thaumatin I | ||||||
Keywords | PLANT PROTEIN / thaumatin / sweet-tasting protein / thaumatin family / sweet receptor / mainly beta / taste protein / aril | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Masuda, T. / Nango, E. / Sugahara, M. / Mizohata, E. / Tanaka, T. / Tanaka, R. / Suzuki, M. / Mikami, B. / Iwata, S. | ||||||
Citation | Journal: Nat. Methods / Year: 2015 Title: Grease matrix as a versatile carrier of proteins for serial crystallography Authors: Sugahara, M. / Mizohata, E. / Nango, E. / Suzuki, M. / Tanaka, T. / Masuda, T. / Tanaka, R. / Shimamura, T. / Tanaka, Y. / Suno, C. / Ihara, K. / Pan, D. / Kakinouchi, K. / Sugiyama, S. / ...Authors: Sugahara, M. / Mizohata, E. / Nango, E. / Suzuki, M. / Tanaka, T. / Masuda, T. / Tanaka, R. / Shimamura, T. / Tanaka, Y. / Suno, C. / Ihara, K. / Pan, D. / Kakinouchi, K. / Sugiyama, S. / Murata, M. / Inoue, T. / Tono, K. / Song, C. / Park, J. / Kameshima, T. / Hatsui, T. / Joti, Y. / Yabashi, M. / Iwata, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wxs.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wxs.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/3wxs ftp://data.pdbj.org/pub/pdb/validation_reports/wx/3wxs | HTTPS FTP |
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-Related structure data
Related structure data | 3wulC 3wumC 3wxqC 3wxtC 3wxuC 4w4qC 3al7S S: Starting model for refinement C: citing same article (ref.) |
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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 natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / 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: 8856 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 293 K / Method: batch method / pH: 7.2 Details: 0.1M ADA, 1.0M K/Na tartrate, pH 7.2, batch method, temperature 293K |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.23 Å |
Detector | Type: MPCCD octal / Detector: CCD / Date: Dec 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 22712 / % possible obs: 99.9 % / Biso Wilson estimate: 18.59 Å2 |
Reflection shell | Resolution: 2→2.04 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3al7 Resolution: 2→28.849 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.54 / 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: 78.63 Å2 / Biso mean: 20.0307 Å2 / Biso min: 5.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.849 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: 7 / % reflection obs: 100 %
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