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Yorodumi- PDB-1d7f: CRYSTAL STRUCTURE OF ASPARAGINE 233-REPLACED CYCLODEXTRIN GLUCANO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d7f | ||||||
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Title | CRYSTAL STRUCTURE OF ASPARAGINE 233-REPLACED CYCLODEXTRIN GLUCANOTRANSFERASE FROM ALKALOPHILIC BACILLUS SP. 1011 DETERMINED AT 1.9 A RESOLUTION | ||||||
Components | CYCLODEXTRIN GLUCANOTRANSFERASE | ||||||
Keywords | TRANSFERASE / CYCLODEXTRIN GLUCANOTRANSFERASE / CGTASE | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Ishii, N. / Haga, K. / Yamane, K. / Harata, K. | ||||||
Citation | Journal: J.Mol.Recog. / Year: 2000 Title: Crystal structure of asparagine 233-replaced cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011 determined at 1.9 A resolution. Authors: Ishii, N. / Haga, K. / Yamane, K. / Harata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d7f.cif.gz | 285.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d7f.ent.gz | 235.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/1d7f ftp://data.pdbj.org/pub/pdb/validation_reports/d7/1d7f | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 75206.039 Da / Num. of mol.: 2 / Mutation: H233N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: 1011 / Plasmid: PTUE254 / Production host: Escherichia coli (E. coli) References: UniProt: P05618, cyclomaltodextrin glucanotransferase #2: Chemical | ChemComp-CA / #3: 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: 48.88 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: SODIUM CITRATE, PEG 3000, ISO-PROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal volume of enzyme and reservoir solutions | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
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→20.2 Å / Num. all: 103616 / Num. obs: 103616 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.215 / % possible all: 33 |
Reflection shell | *PLUS % possible obs: 33 % |
-Processing
Software |
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Refinement | Resolution: 1.9→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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