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Yorodumi- PDB-3cgt: STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH ITS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cgt | |||||||||
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Title | STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE COMPLEXED WITH ITS MAIN PRODUCT BETA-CYCLODEXTRIN | |||||||||
Components | CYCLODEXTRIN GLYCOSYLTRANSFERASE | |||||||||
Keywords | GLYCOSYLTRANSFERASE / STARCH DEGRADATION / 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 / DIFFERENCE FOURIER / Resolution: 2.4 Å | |||||||||
Authors | Schmidt, A.K. / Schulz, G.E. | |||||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin. Authors: Schmidt, A.K. / Cottaz, S. / Driguez, H. / Schulz, G.E. #1: Journal: Biochemistry / Year: 1992 Title: Catalytic Center of Cyclodextrin Glycosyltransferase Derived from X-Ray Structure Analysis Combined with Site-Directed Mutagenesis Authors: Klein, C. / Hollender, J. / Bender, H. / Schulz, G.E. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of Cyclodextrin Glycosyltransferase Refined at 2.0 A Resolution Authors: Klein, C. / Schulz, G.E. #3: Journal: Appl.Microbiol.Biotechnol. / Year: 1990 Title: Molecular Cloning, Nucleotide Sequence and Expression in Escherichia Coli of the Beta-Cyclodextrin Glycosyltransferase Gene from Bacillus Circulans Strain No. 8 Authors: Nitschke, L. / Heeger, K. / Bender, H. / Schulz, G.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cgt.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cgt.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cgt_validation.pdf.gz | 927.3 KB | Display | wwPDB validaton report |
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Full document | 3cgt_full_validation.pdf.gz | 934.4 KB | Display | |
Data in XML | 3cgt_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 3cgt_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/3cgt ftp://data.pdbj.org/pub/pdb/validation_reports/cg/3cgt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 74507.008 Da / Num. of mol.: 1 / Mutation: E257A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 8 / Cellular location: EXTRACELLULAR / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 References: UniProt: P30920, cyclomaltodextrin glucanotransferase | ||
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#2: Polysaccharide | Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin | ||
#3: Chemical | #4: 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: 3.79 Å3/Da / Density % sol: 67.53 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.9 / Details: pH 6.9 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→29.24 Å / Num. obs: 42278 / % possible obs: 89.1 % / Redundancy: 4.3 % / Rsym value: 0.096 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.41→2.48 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.266 / % possible all: 71.5 |
Reflection | *PLUS Num. measured all: 183009 / Rmerge(I) obs: 0.096 |
Reflection shell | *PLUS % possible obs: 71.5 % / Rmerge(I) obs: 0.266 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 25.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.288 |