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Yorodumi- PDB-1kcl: Bacillus ciruclans strain 251 Cyclodextrin glycosyl transferase m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kcl | |||||||||
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Title | Bacillus ciruclans strain 251 Cyclodextrin glycosyl transferase mutant G179L | |||||||||
Components | Cyclodextrin glycosyltransferase | |||||||||
Keywords | TRANSFERASE / glycosyltransferase / cyclodextrin | |||||||||
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: 1.94 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 | 1kcl.cif.gz | 173.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kcl.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kcl_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1kcl_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1kcl_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 1kcl_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kcl ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kcl | HTTPS FTP |
-Related structure data
Related structure data | 1kckC 1d3cS 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: 74631.594 Da / Num. of mol.: 1 / Mutation: G179L 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, UniProt: P43379*PLUS, cyclomaltodextrin glucanotransferase |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(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-(1-4)-beta-D-glucopyranose / beta-maltotriose | ||
#4: Polysaccharide | #6: Sugar | ChemComp-GLC / | |
-Non-polymers , 3 types, 1026 molecules
#5: Chemical | #7: Chemical | ChemComp-MPD / ( | #8: Water | ChemComp-HOH / | |
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-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: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 1, 2001 / Details: Franks' mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→39.5 Å / Num. all: 62081 / Num. obs: 60480 / % possible obs: 97.5 % / Redundancy: 4 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.372 / % possible all: 96.6 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 96.6 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1D3C Resolution: 1.94→39.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2118442.21 / 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: 76.6 Å2 / ksol: 0.367011 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→39.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.06 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.152 / Rfactor Rfree: 0.186 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.2 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.267 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.229 |