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- PDB-3wq5: beta-Primeverosidase in complex with disaccharide substrate-analo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wq5 | |||||||||
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Title | beta-Primeverosidase in complex with disaccharide substrate-analog N-beta-primeverosylamidine, natural aglycone derivative | |||||||||
![]() | Beta-primeverosidase | |||||||||
![]() | 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 | ![]() beta-primeverosidase / beta-primeverosidase activity / : / : / beta-glucosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Saino, H. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 240.4 KB | Display | ![]() |
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PDB format | ![]() | 186.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 49.1 KB | Display | |
Data in CIF | ![]() | 76.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wq4C ![]() 3wq6C ![]() 1cbgS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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 | ChemComp-NAG / |
-Non-polymers , 2 types, 1393 molecules ![](data/chem/img/VPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.68 % |
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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, 0.1 M 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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 5, 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: 93522 / % possible obs: 96.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 4.7 / Num. unique all: 13124 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CBG Resolution: 1.8→32.748 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 19.16 / 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→32.748 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
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