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Yorodumi- PDB-3wq6: beta-Primeverosidase in complex with disaccharide substrate-analo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wq6 | |||||||||
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Title | beta-Primeverosidase in complex with disaccharide substrate-analog N-beta-primeverosylamidine, artificial aglycone derivative | |||||||||
Components | beta-primeverosidase | |||||||||
Keywords | HYDROLASE / DIGLYCOSIDASE / DIGLYCOSIDE / DISACCHARIDE / GLYCOSIDE HYDROLASE FAMILY 1 (GH1) / (BETA/ALPHA)8 BARREL / SPECIFIC HYDROLYSIS OF BETA-PRIMEVEROSIDES / AROMA FORMATION / OOLONG TEA / BLACK TEA | |||||||||
Function / homology | Function and homology information beta-primeverosidase / beta-primeverosidase activity / 2-phenylethyl 6-O-beta-D-xylopyranosyl-beta-D-glucopyranoside glucosidase (Yabukita) activity / linalyl 6-O-alpha-L-arabinopyranosyl-beta-D-glucopyranoside glucosidase (Yabukita) activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Camellia sinensis (black tea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Saino, H. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal structures of beta-primeverosidase in complex with disaccharide amidine inhibitors. Authors: Saino, H. / Shimizu, T. / Hiratake, J. / Nakatsu, T. / Kato, H. / Sakata, K. / Mizutani, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wq6.cif.gz | 252 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wq6.ent.gz | 194.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/3wq6 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/3wq6 | HTTPS FTP |
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-Related structure data
Related structure data | 3wq4C 3wq5C 1cbgS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57104.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camellia sinensis (black tea) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-TN-5B1-4 / References: UniProt: Q7X9A9, beta-primeverosidase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar |
-Non-polymers , 2 types, 1783 molecules
#4: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10mg/mL protein, 0.01% TritonX-100, 21% PEG 4000, 0.3M ammonium acetate, 0.1M sodium citrate (pH 5.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 2006 |
Radiation | Monochromator: Confocal, Multilayer Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 97485 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.6 / Num. unique all: 14038 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CBG Resolution: 1.8→39.37 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 15.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→39.37 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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