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Yorodumi- PDB-1kck: Bacillus circulans strain 251 Cyclodextrin glycosyl transferase m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kck | ||||||||||||
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Title | Bacillus circulans strain 251 Cyclodextrin glycosyl transferase mutant N193G | ||||||||||||
Components | CYCLODEXTRIN GLYCOSYLTRANSFERASE | ||||||||||||
Keywords | TRANSFERASE / glycosyl transferase / cylcodextrin / acarbose | ||||||||||||
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 circulans (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.43 Å | ||||||||||||
Authors | Rozeboom, H.J. / Uitdehaag, J.C.M. / Dijkstra, B.W. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: The remote substrate binding subsite -6 in cyclodextrin-glycosyltransferase controls the transferase activity of the enzyme via an induced-fit mechanism. Authors: Leemhuis, H. / Uitdehaag, J.C. / Rozeboom, H.J. / Dijkstra, B.W. / Dijkhuizen, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kck.cif.gz | 158.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kck.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kck_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1kck_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1kck_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 1kck_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kck ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kck | HTTPS FTP |
-Related structure data
Related structure data | 1kclC 2cxgS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74518.430 Da / Num. of mol.: 1 / Mutation: N193G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 251 / Plasmid: pDp66k- / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 References: UniProt: P43379, cyclomaltodextrin glucanotransferase |
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-Sugars , 5 types, 5 molecules
#2: Polysaccharide | alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
#5: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltotriose |
#7: Sugar | ChemComp-GLC / |
-Non-polymers , 3 types, 436 molecules
#6: Chemical | ChemComp-ADH / | ||
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#8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.7 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD. Ca, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Lawson, C.L., (1994) J.Mol.Biol., 236, 590. / pH: 7.55 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→26.64 Å / Num. all: 34166 / Num. obs: 31710 / % possible obs: 92.9 % / Biso Wilson estimate: 17.7 Å2 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 92.1 % |
Reflection shell | *PLUS % possible obs: 70.2 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2CXG Resolution: 2.43→26.64 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 451525.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.79 Å2 / ksol: 0.317506 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.43→26.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.43→2.52 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5.2 % / Rfactor obs: 0.153 / Rfactor Rfree: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.278 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.23 |