+Open data
-Basic information
Entry | Database: PDB / ID: 5yyq | ||||||
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Title | Structure K78A 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: 1.07 Å | ||||||
Authors | Masuda, T. / Kigo, S. / Mitsumoto, M. / Ohta, K. / Suzuki, M. / Mikami, B. / Kitabatake, N. / Tani, F. | ||||||
Funding support | Japan, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yyq.cif.gz | 146.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yyq.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yyq_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5yyq_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 5yyq_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 5yyq_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/5yyq ftp://data.pdbj.org/pub/pdb/validation_reports/yy/5yyq | HTTPS FTP |
-Related structure data
Related structure data | 5yypC 5yyrC 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: 22169.941 Da / Num. of mol.: 1 / Mutation: K78A 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 | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / #4: 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: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M ADA, 0.75M potassium sodium tartrate, pH 7.0 |
-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: Jul 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→50 Å / Num. obs: 112490 / % possible obs: 99.9 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 71.26 |
Reflection shell | Resolution: 1.07→1.09 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 8.2 / Num. measured obs: 5559 / CC1/2: 0.964 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3al7 Resolution: 1.07→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY
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Refine analyze | Num. disordered residues: 37 / Occupancy sum hydrogen: 1422 / Occupancy sum non hydrogen: 1844.1 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→20 Å
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Refine LS restraints |
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