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- PDB-5zcd: Crystal structure of Alpha-glucosidase in complex with maltotriose -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zcd | |||||||||
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Title | Crystal structure of Alpha-glucosidase in complex with maltotriose | |||||||||
![]() | Alpha-glucosidase | |||||||||
![]() | HYDROLASE / Alpha-glucosidase | |||||||||
Function / homology | ![]() oligosaccharide catabolic process / alpha-amylase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kato, K. / Saburi, W. / Yao, M. | |||||||||
![]() | ![]() Title: Function and structure of GH13_31 alpha-glucosidase with high alpha-(1→4)-glucosidic linkage specificity and transglucosylation activity. Authors: Auiewiriyanukul, W. / Saburi, W. / Kato, K. / 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 | ![]() | 146.8 KB | Display | ![]() |
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PDB format | ![]() | 110.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zcbC ![]() 5zccC ![]() 5zceC ![]() 2ze0S 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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Unit cell |
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Components
#1: Protein | Mass: 64928.445 Da / Num. of mol.: 1 / Mutation: E256Q 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 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350, Calcium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 66627 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.117 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.7→1.81 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2 / Num. unique obs: 10452 / Rrim(I) all: 0.743 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZE0 Resolution: 1.707→46.504 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.707→46.504 Å
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Refine LS restraints |
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LS refinement shell |
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