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Yorodumi- PDB-1ukt: Crystal structure of Y100L mutant cyclodextrin glucanotransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ukt | |||||||||
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Title | Crystal structure of Y100L mutant cyclodextrin glucanotransferase compexed with an acarbose | |||||||||
Components | Cyclomaltodextrin glucanotransferase | |||||||||
Keywords | TRANSFERASE / CGTASE / ACARBOSE / CARBOHYDRATE/PROTEIN INTERACTION | |||||||||
Function / homology | Function and homology information cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Haga, K. / Kanai, R. / Sakamoto, O. / Harata, K. / Yamane, K. | |||||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2003 Title: Effects of Essential Carbohydrate/Aromatic Stacking Interaction with Tyr100 and Phe259 on Substrate Binding of Cyclodextrin Glycosyltransferase from Alkalophilic Bacillus sp. 1011 Authors: Haga, K. / Kanai, R. / Sakamoto, O. / Aoyagi, M. / Harata, K. / Yamane, K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: X-ray Structure of Cyclodextrin Glucano-transferase from Alkalophilic Bacillus sp.1011. Comparison of Two Independent Molecules at 1.8 Angstrom Resolution Authors: Harata, K. / Haga, K. / Nakamura, A. / Aoyagi, M. / Yamane, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ukt.cif.gz | 278.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ukt.ent.gz | 222.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ukt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ukt_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1ukt_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1ukt_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 1ukt_validation.cif.gz | 72.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/1ukt ftp://data.pdbj.org/pub/pdb/validation_reports/uk/1ukt | HTTPS FTP |
-Related structure data
Related structure data | 1ukqC 1uksC 1pamS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 75180.070 Da / Num. of mol.: 2 / Mutation: Y100L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: 1011 / Plasmid: pTUE254 / Production host: Escherichia coli (E. coli) / Strain (production host): ME8417 References: UniProt: P05618, cyclomaltodextrin glucanotransferase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
Crystal grow | *PLUS Method: unknown / Details: Harata, K., (1996) Acta Cryst., D52, 1136. |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 22, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→76.77 Å / Num. all: 85791 / Num. obs: 68926 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2.01→2.05 Å / Rmerge(I) obs: 0.371 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PAM Resolution: 2.2→10 Å / Isotropic thermal model: ISOTROPIC / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→10 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: 6
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