+Open data
-Basic information
Entry | Database: PDB / ID: 3wou | ||||||
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Title | Crystal Structure of The Recombinant Thaumatin II at 0.99 A | ||||||
Components | Thaumatin-2 | ||||||
Keywords | PLANT PROTEIN / Osmotin / thaumatin-like protein / Sweet-tasting protein / Sweet receptors | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.99 Å | ||||||
Authors | Masuda, T. / Mikami, B. / Tani, F. | ||||||
Citation | Journal: Biochimie / Year: 2014 Title: Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues Authors: Masuda, T. / Mikami, B. / Tani, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wou.cif.gz | 155.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wou.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/3wou ftp://data.pdbj.org/pub/pdb/validation_reports/wo/3wou | HTTPS FTP |
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-Related structure data
Related structure data | 3wox |
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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: 22312.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Plasmid: pPIC6-preTHII / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P02884 | ||||
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#2: Chemical | #3: Chemical | #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: 2.797 Å3/Da / Density % sol: 56.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M ADA, 0.75M TARTRATE, 12.5% GLYCEROL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: 0.99→50 Å / Num. obs: 141082 / % possible obs: 99.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 64.34 |
Reflection shell | Resolution: 0.99→1.01 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 6.26 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.99→10 Å / Num. parameters: 20908 / Num. restraintsaints: 28815 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 89 / Occupancy sum hydrogen: 1412.46 / Occupancy sum non hydrogen: 1964.84 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.99→1.01 Å
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