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- PDB-8yif: Crystal structure of GH13_30 alpha-glucosidase CmmB in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yif | ||||||
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Title | Crystal structure of GH13_30 alpha-glucosidase CmmB in complex with acarviosin | ||||||
![]() | Alpha-glucosidase | ||||||
![]() | HYDROLASE / alpha-glucosidase / inhibitor / complex | ||||||
Function / homology | ![]() glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / maltose catabolic process / maltose alpha-glucosidase activity / sucrose alpha-glucosidase activity / sucrose catabolic process / alpha-amylase activity / amino acid transport Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saburi, W. / Tagami, T. / Yu, J. / Ose, T. / Yao, M. / Mori, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Molecular mechanism for the substrate specificity of Arthrobacter globiformis M6 alpha-glucosidase CmmB, belonging to glycoside hydrolase family 13 subfamily 30 Authors: Saburi, W. / Tagami, T. / Usui, T. / Yu, J. / Ose, T. / Yao, M. / Mori, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789.8 KB | Display | ![]() |
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Full document | ![]() | 791.8 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8yieSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 64162.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: BAI67603.1 / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-A1L2I / Mass: 335.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C14H25NO8 / Feature type: SUBJECT OF INVESTIGATION |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5 mM acarviosin, 0.5 M lithium chloride, 10% (w/v) polyethylene glycol 6000, and 55 mM HEPES-NaOH buffer (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 9, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 70932 / % possible obs: 99.6 % / Redundancy: 6.61 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.089 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.6→1.7 Å / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 11229 / CC1/2: 0.873 / Rrim(I) all: 0.731 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8YIE Resolution: 1.6→42.13 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→42.13 Å
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Refine LS restraints |
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LS refinement shell |
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