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- PDB-7vkz: 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: 7vkz | ||||||
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Title | The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with 1-Deoxynojirimycin | ||||||
![]() | 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 | ![]() | 313.8 KB | Display | ![]() |
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PDB format | ![]() | 243.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 51.6 KB | Display | |
Data in CIF | ![]() | 74.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vkwC ![]() 7vkxC ![]() 7vkyC ![]() 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: 84774.727 Da / Num. of mol.: 2 / Mutation: E343G 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: Chemical | #3: Chemical | #4: 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: 2.14 Å3/Da / Density % sol: 42.41 % |
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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: May 7, 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→47.58 Å / Num. obs: 96821 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 4809 / % possible all: 100 |
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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: 23.007 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.106 Å
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Refine LS restraints |
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LS refinement shell |
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