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Yorodumi- PDB-3wnk: Crystal Structure of Bacillus circulans T-3040 cycloisomaltooligo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wnk | ||||||
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Title | Crystal Structure of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase | ||||||
Components | Cycloisomaltooligosaccharide glucanotransferase | ||||||
Keywords | TRANSFERASE / C2 type immunoglobulin fold / (beta/alpha)8-barrel / beta-jelly roll / Greek key / Glycoside Hydrolase / alpha-1 / 6-glucan | ||||||
Function / homology | Function and homology information cycloisomaltooligosaccharide glucanotransferase / glycosyltransferase activity / carbohydrate binding Similarity search - Function | ||||||
Biological species | Bacillus circulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Suzuki, N. / Fujimoto, Z. / Kim, Y.M. / Momma, M. / Kishine, N. / Suzuki, R. / Kobayashi, M. / Kimura, A. / Funane, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural elucidation of the cyclization mechanism of alpha-1,6-glucan by Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase. Authors: Suzuki, N. / Fujimoto, Z. / Kim, Y.M. / Momma, M. / Kishine, N. / Suzuki, R. / Suzuki, S. / Kitamura, S. / Kobayashi, M. / Kimura, A. / Funane, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Crystallization and preliminary X-ray crystallographic analysis of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040. Authors: Suzuki, N. / Kim, Y.M. / Momma, M. / Fujimoto, Z. / Kobayashi, M. / Kimura, A. / Funane, K. #2: Journal: Biochim.Biophys.Acta / Year: 2011 Title: Deletion analysis of regions at the C-terminal part of cycloisomaltooligosaccharide glucanotransferase from Bacillus circulans T-3040. Authors: Funane, K. / Kawabata, Y. / Suzuki, R. / Kim, Y.M. / Kang, H.K. / Suzuki, N. / Fujimoto, Z. / Kimura, A. / Kobayashi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wnk.cif.gz | 172 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wnk.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wnk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/3wnk ftp://data.pdbj.org/pub/pdb/validation_reports/wn/3wnk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 80221.305 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-738 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: T-3040 / Gene: cit / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P94286, cycloisomaltooligosaccharide glucanotransferase |
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-Non-polymers , 6 types, 567 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE DEPOSITORS |
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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: 3.27 Å3/Da / Density % sol: 62.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.0M sodium acetate trihydrate, 0.1M HEPES, 0.05M cadmium sulfate hydrate, 12%(v/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97800, 0.97885, 0.97931, 0.98319, 0.96408 | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: May 23, 2007 / Details: 1m long bent plane mirror of fused quartz | ||||||||||||||||||
Radiation | Monochromator: Triangular Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→44.34 Å / Num. all: 47422 / Num. obs: 47410 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.6 % / Biso Wilson estimate: 29.9 Å2 / Rsym value: 0.079 / Net I/σ(I): 47.1 | ||||||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 16.7 % / Mean I/σ(I) obs: 10.6 / Num. unique all: 4667 / Rsym value: 0.423 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→44.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.473 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.707 Å2
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Refine analyze | Luzzati coordinate error obs: 0.109 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→44.34 Å
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Refine LS restraints |
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