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Yorodumi- PDB-3wno: D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosacch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wno | |||||||||
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Title | D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with cycloisomaltooctaose | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 3wno.cif.gz | 327.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wno.ent.gz | 262 KB | Display | PDB format |
PDBx/mmJSON format | 3wno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/3wno ftp://data.pdbj.org/pub/pdb/validation_reports/wn/3wno | HTTPS FTP |
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-Related structure data
Related structure data | 3wnkSC 3wnlC 3wnmC 3wnnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 79134.141 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 39-738 / Mutation: D308A 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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-Sugars , 2 types, 5 molecules
#2: Polysaccharide | Cyclooctakis-(1-6)-(alpha-D-glucopyranose) Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 6 types, 1254 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-EDO / #8: Chemical | #9: 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: 2.87 Å3/Da / Density % sol: 57.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.6M ammonium sulfate, 0.1M MES, 10%(v/v) 1,4-dioxane, pH 6.5, 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: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 15, 2010 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35.7 Å / Num. all: 143858 / Num. obs: 143236 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.077 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.487 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WNK Resolution: 1.9→30.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.666 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 28.401 Å2
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Refine analyze | Luzzati coordinate error obs: 0.078 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30.47 Å
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Refine LS restraints |
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