+Open data
-Basic information
Entry | Database: PDB / ID: 3vhg | ||||||
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Title | Recombinant thaumatin I at PH 8.0 | ||||||
Components | Thaumatin I | ||||||
Keywords | PLANT PROTEIN / THAUMATIN / SWEET-TASTING PROTEIN / thaumatin family / mainly beta / taste protein / sweet receptor / aril | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1 Å | ||||||
Authors | Masuda, T. / Mikami, B. / Kitabatake, N. / Tani, F. | ||||||
Citation | Journal: To be Published Title: Recombinat thaumatin I at pH 8.0 Authors: Masuda, T. / Mikami, B. / Tani, F. / Kitabatake, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vhg.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vhg.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/3vhg ftp://data.pdbj.org/pub/pdb/validation_reports/vh/3vhg | HTTPS FTP |
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-Related structure data
Related structure data | 3vhfS S: Starting model for refinement |
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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 genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Plasmid: pPIC6-preTH / Production host: Pichia pastoris (fungus) / Strain (production host): X33, SMD1168H / References: UniProt: Q8RVT0, UniProt: P02883*PLUS | ||
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#2: Chemical | #3: 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: 2.24 Å3/Da / Density % sol: 45.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50mM Tris-HCl buffer, 15% PEG3350, pH 8.0, 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: BL44XU / Wavelength: 0.9 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 107219 / % possible obs: 98.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 46.7486 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.115 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: 3VHF Resolution: 1→10 Å / Num. parameters: 19410 / Num. restraintsaints: 24492 / 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: 28 / Occupancy sum hydrogen: 1418.4 / Occupancy sum non hydrogen: 1982.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.05 Å
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