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Yorodumi- PDB-7vkx: The complex structure of beta-1,2-glucosyltransferase from Ignavi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vkx | ||||||
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Title | The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with glucose | ||||||
Components | beta-1,2-glucosyltransferase | ||||||
Keywords | TRANSFERASE / beta-1 / 2-glucosyltransferase Glycoside / hydrolase family 35 / HYDROLASE | ||||||
Function / homology | Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Class I glutamine amidotransferase-like / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / beta-D-glucopyranose / Beta-galactosidase Function and homology information | ||||||
Biological species | Ignavibacterium album (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Kobayashi, K. / Shimizu, H. / Tanaka, N. / Kuramochi, K. / Nakai, H. / Nakajima, M. / Taguchi, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vkx.cif.gz | 317.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vkx.ent.gz | 253.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/7vkx ftp://data.pdbj.org/pub/pdb/validation_reports/vk/7vkx | HTTPS FTP |
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-Related structure data
Related structure data | 7vkwC 7vkyC 7vkzC 7vl0C 7vl1C 7vl2C 7vl3C 7vl4C 7vl5C 7vl6C 7vl7C 7x87C 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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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.) Ignavibacterium album (strain DSM 19864 / JCM 16511 / NBRC 101810 / Mat9-16) (bacteria) Strain: DSM 19864 / JCM 16511 / NBRC 101810 / Mat9-16 / Gene: IALB_1185 / Plasmid: pET30a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: I0AIT9 #2: Sugar | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.16 Å3/Da / Density % sol: 43.02 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→57.23 Å / Num. obs: 201492 / % possible obs: 95.6 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.56→1.58 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.559 / Num. unique obs: 10000 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→48.008 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.599 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.077 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: 13.501 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→48.008 Å
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Refine LS restraints |
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LS refinement shell |
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