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- PDB-1ded: CRYSTAL STRUCTURE OF ALKALOPHILIC ASPARAGINE 233-REPLACED CYCLODE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ded | |||||||||
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Title | CRYSTAL STRUCTURE OF ALKALOPHILIC ASPARAGINE 233-REPLACED CYCLODEXTRIN GLUCANOTRANSFERASE COMPLEXED WITH AN INHIBITOR, ACARBOSE, AT 2.0 A RESOLUTION | |||||||||
![]() | CYCLODEXTRIN GLUCANOTRANSFERASE | |||||||||
![]() | TRANSFERASE / CYCLODEXTRIN GLUCANOTRANSFERASE / CGTASE / ACARBOSE | |||||||||
Function / homology | ![]() cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Ishii, N. / Haga, K. / Yamane, K. / Harata, K. | |||||||||
![]() | ![]() Title: Crystal structure of alkalophilic asparagine 233-replaced cyclodextrin glucanotransferase complexed with an inhibitor, acarbose, at 2.0 A resolution. Authors: Ishii, N. / Haga, K. / Yamane, K. / Harata, 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 | ![]() | 369.5 KB | Display | ![]() |
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PDB format | ![]() | 310.9 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 | ![]() | 59 KB | Display | |
Data in CIF | ![]() | 85.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | TWO INDEPENDENT MOLECULES IN AN ASYMMETRIC UNIT, BEING RELATED BY PSEUDO TWO-FOLD SYMMETRY. THE BIOLOGICAL ASSEMBLY IS UNKNOWN IF THE ENZYME WORKS AS A DIMER. |
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Components
#1: Protein | Mass: 75206.039 Da / Num. of mol.: 2 / Fragment: CYCLODEXTRIN GLUCANOTRANSFERASE (CGTASE) / Mutation: H233N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P05618, cyclomaltodextrin glucanotransferase #2: Polysaccharide | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.44 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 3000, ISO-PROPANOL, SODIUM CITRATE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20.5 Å / Num. all: 95583 / Num. obs: 95583 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.16 / % possible all: 79.97 |
Reflection | *PLUS |
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Processing
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Refinement | Resolution: 2→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |