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- PDB-7dcg: Alpha-glucosidase from Weissella cibaria BBK-1 bound with maltotriose -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dcg | ||||||
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Title | Alpha-glucosidase from Weissella cibaria BBK-1 bound with maltotriose | ||||||
![]() | Alpha-glycosidase | ||||||
![]() | HYDROLASE / glycoside hydrolase / maltooligosaccharides / carbohydrate metabolism / alpha-glucosidase | ||||||
Function / homology | alpha-maltotriose![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krusong, K. / Wangpaiboon, K. / Kim, S. / Mori, T. / Hakoshima, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A GH13 alpha-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides. Authors: Wangpaiboon, K. / Laohawuttichai, P. / Kim, S.Y. / Mori, T. / Nakapong, S. / Pichyangkura, R. / Pongsawasdi, P. / Hakoshima, T. / Krusong, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 329.4 KB | Display | ![]() |
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PDB format | ![]() | 220.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d9bSC ![]() 7d9cC ![]() 7dchC ![]() 7ehhC ![]() 7ehiC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 68398.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
-Non-polymers , 5 types, 573 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MG_256496 FOR THE PROTEIN. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, dioxane, MES |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 109716 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.92 Å2 / Rpim(I) all: 0.045 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 6.5 % / Num. unique obs: 10808 / Rpim(I) all: 0.602 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D9B Resolution: 1.53→26.02 Å / SU ML: 0.1168 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.5091 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→26.02 Å
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Refine LS restraints |
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LS refinement shell |
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