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Yorodumi- PDB-8i2r: Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i2r | ||||||
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Title | Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y in complex with fructose | ||||||
Components | Beta-fructosyltransferase | ||||||
Keywords | TRANSFERASE / Beta-fructosyltransferase / HYDROLASE | ||||||
Function / homology | beta-D-fructopyranose / beta-D-fructofuranose Function and homology information | ||||||
Biological species | Beijerinckia indica subsp. indica NBRC 3744 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Tonozuka, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2023 Title: Characterization and alteration of product specificity of Beijerinckia indica subsp. indica beta-fructosyltransferase. Authors: Li, D. / Miyasaka, Y. / Kubota, A. / Kozono, T. / Kitano, Y. / Sasaki, N. / Fujii, T. / Tochio, T. / Kadota, Y. / Nishikawa, A. / Tonozuka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i2r.cif.gz | 124.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i2r.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 8i2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/8i2r ftp://data.pdbj.org/pub/pdb/validation_reports/i2/8i2r | HTTPS FTP |
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-Related structure data
Related structure data | 8i2qC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57039.840 Da / Num. of mol.: 1 / Mutation: variant H395R, F473Y Source method: isolated from a genetically manipulated source Details: DDBJ LC522529 Source: (gene. exp.) Beijerinckia indica subsp. indica NBRC 3744 (bacteria) Strain: NBRC 3744 / Production host: Escherichia coli (E. coli) / References: EC: 2.4.1.100 | ||||||||
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#2: Chemical | #3: Sugar | ChemComp-FRU / | #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% (w/v) polyethylene glycol 10000, 0.2 M magnesium chloride, 0.1 M potassium sodium tartrate, 0.1 M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→47.8 Å / Num. obs: 95951 / % possible obs: 99.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.36→1.43 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 13917 / Rpim(I) all: 0.201 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→37.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.055 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.745 Å2
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Refinement step | Cycle: 1 / Resolution: 1.36→37.82 Å
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