+Open data
-Basic information
Entry | Database: PDB / ID: 5yyp | ||||||
---|---|---|---|---|---|---|---|
Title | Structure K137A thaumatin | ||||||
Components | Preprothaumatin I | ||||||
Keywords | PLANT PROTEIN / Sweet-tasting protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å | ||||||
Authors | Masuda, T. / Kigo, S. / Mitsumoto, M. / Ohta, K. / Suzuki, M. / Mikami, B. / Kitabatake, N. / Tani, F. | ||||||
Citation | Journal: Front Mol Biosci / Year: 2018 Title: Positive Charges on the Surface of Thaumatin Are Crucial for the Multi-Point Interaction with the Sweet Receptor. Authors: Masuda, T. / Kigo, S. / Mitsumoto, M. / Ohta, K. / Suzuki, M. / Mikami, B. / Kitabatake, N. / Tani, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yyp.cif.gz | 149 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yyp.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yyp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5yyp_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5yyp_validation.xml.gz | 15 KB | Display | |
Data in CIF | 5yyp_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/5yyp ftp://data.pdbj.org/pub/pdb/validation_reports/yy/5yyp | HTTPS FTP |
-Related structure data
Related structure data | 5yyqC 5yyrC 3al7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22169.941 Da / Num. of mol.: 1 / Mutation: K137A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Komagataella pastoris (fungus) / References: UniProt: A1IIJ1, UniProt: P02883*PLUS | ||
---|---|---|---|
#2: Chemical | ChemComp-TLA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M ADA, 0.75M potassium sodium tartrate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.01→50 Å / Num. obs: 133031 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 44.07 |
Reflection shell | Resolution: 1.01→1.03 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.94 / Num. measured obs: 6523 / CC1/2: 0.924 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3al7 Resolution: 1.01→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY
| ||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 43 / Occupancy sum hydrogen: 1421 / Occupancy sum non hydrogen: 1919.3 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.01→20 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
|