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- PDB-3wnm: D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosacch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wnm | |||||||||
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Title | D308A mutant of Bacillus circulans T-3040 cycloisomaltooligosaccharide glucanotransferase complexed with isomaltoheptaose | |||||||||
![]() | Cycloisomaltooligosaccharide glucanotransferase | |||||||||
![]() | TRANSFERASE / C2 type immunoglobulin fold / (beta/alpha)8-barrel / beta-jelly roll / Greek key / Glycoside Hydrolase / alpha-1 / 6-glucan | |||||||||
Function / homology | ![]() cycloisomaltooligosaccharide glucanotransferase / glycosyltransferase activity / carbohydrate binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Suzuki, N. / Fujimoto, Z. / Kim, Y.M. / Momma, M. / Kishine, N. / Suzuki, R. / Suzuki, S. / Kitamura, S. / Kobayashi, M. / Kimura, A. / Funane, K. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.8 KB | Display | ![]() |
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PDB format | ![]() | 127.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 43.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wnkC ![]() 3wnlSC ![]() 3wnnC ![]() 3wnoC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79134.141 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 39-738 / Mutation: D308A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P94286, cycloisomaltooligosaccharide glucanotransferase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#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 |
-Non-polymers , 5 types, 358 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / | ||||
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#5: Chemical | ChemComp-NA / | ||||
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-MES / | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | THE DEPOSITORS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.85 % |
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Crystal grow | Temperature: 302 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 302K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 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: 2.25→30.35 Å / Num. all: 44184 / Num. obs: 44028 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rsym value: 0.099 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.522 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WNL Resolution: 2.25→30.35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.914 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.179 / 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: 42.518 Å2
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Refine analyze | Luzzati coordinate error obs: 0.121 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→30.35 Å
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Refine LS restraints |
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