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- PDB-7vky: The complex structure of beta-1,2-glucosyltransferase from Ignavi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vky | ||||||
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Title | The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophorose | ||||||
![]() | beta-1,2-glucosyltransferase | ||||||
![]() | TRANSFERASE / beta-1 / 2-glucosyltransferase Glycoside / hydrolase family 35 / HYDROLASE | ||||||
Function / homology | ![]() vacuole / beta-galactosidase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kobayashi, K. / Shimizu, H. / Tanaka, N. / Kuramochi, K. / Nakai, H. / Nakajima, M. / Taguchi, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages. Authors: Kobayashi, K. / Shimizu, H. / Tanaka, N. / Kuramochi, K. / Nakai, H. / Nakajima, M. / Taguchi, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 319.3 KB | Display | ![]() |
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PDB format | ![]() | 246.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 52.7 KB | Display | |
Data in CIF | ![]() | 77.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vkwC ![]() 7vkxC ![]() 7vkzC ![]() 7vl0C ![]() 7vl1C ![]() 7vl2C ![]() 7vl3C ![]() 7vl4C ![]() 7vl5C ![]() 7vl6C ![]() 7vl7C ![]() 7x87C C: citing same article ( |
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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
#1: Protein | Mass: 83165.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 19864 / JCM 16511 / NBRC 101810 / Mat9-16 / Gene: IALB_1185 / Plasmid: pET30a / Production host: ![]() ![]() #2: Polysaccharide | beta-D-glucopyranose-(1-2)-beta-D-glucopyranose | #3: Polysaccharide | beta-D-glucopyranose-(1-2)-alpha-D-glucopyranose | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-HCl (pH 7.5), 0.2M calcium acetate, 20%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→57.14 Å / Num. obs: 307557 / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.386 / Num. unique obs: 4817 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.008 Å2
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Refinement step | Cycle: LAST / Resolution: 2→55.312 Å
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Refine LS restraints |
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LS refinement shell |
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