[English] 日本語
![](img/lk-miru.gif)
- PDB-3wxs: Thaumatin structure determined by SPring-8 Angstrom Compact free ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3wxs | ||||||
---|---|---|---|---|---|---|---|
Title | Thaumatin structure determined by SPring-8 Angstrom Compact free electron Laser (SACLA) | ||||||
![]() | thaumatin I | ||||||
![]() | PLANT PROTEIN / thaumatin / sweet-tasting protein / thaumatin family / sweet receptor / mainly beta / taste protein / aril | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Masuda, T. / Nango, E. / Sugahara, M. / Mizohata, E. / Tanaka, T. / Tanaka, R. / Suzuki, M. / Mikami, B. / Iwata, S. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 41.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 439.4 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wulC ![]() 3wumC ![]() 3wxqC ![]() 3wxtC ![]() 3wxuC ![]() 4w4qC ![]() 3al7S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22228.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#2: Chemical | ChemComp-TLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3al7 Resolution: 2→28.849 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.54 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %
|