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- PDB-8i2r: Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i2r | ||||||
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Title | Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y in complex with fructose | ||||||
![]() | Beta-fructosyltransferase | ||||||
![]() | TRANSFERASE / Beta-fructosyltransferase / HYDROLASE | ||||||
Function / homology | beta-D-fructopyranose / beta-D-fructofuranose![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tonozuka, T. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.3 KB | Display | ![]() |
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PDB format | ![]() | 90.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 37.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i2qC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 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.) ![]() Strain: NBRC 3744 / Production host: ![]() ![]() | ||||||||
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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Refine LS restraints |
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