+Open data
-Basic information
Entry | Database: PDB / ID: 8hw3 | ||||||
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Title | Limosilactobacillus reuteri N1 GtfB-acarbose | ||||||
Components | dextransucrase | ||||||
Keywords | TRANSFERASE / glucanotransferase / carbohydrate-active enzyme | ||||||
Function / homology | Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / Glycoside hydrolase superfamily / hydrolase activity / beta-acarbose / dextransucrase Function and homology information | ||||||
Biological species | Limosilactobacillus reuteri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | ||||||
Authors | Dong, J.J. / Bai, Y.X. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2024 Title: Insights into the Structure-Function Relationship of GH70 GtfB alpha-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized ...Title: Insights into the Structure-Function Relationship of GH70 GtfB alpha-Glucanotransferases from the Crystal Structure and Molecular Dynamic Simulation of a Newly Characterized Limosilactobacillus reuteri N1 GtfB Enzyme. Authors: Dong, J. / Bai, Y. / Wang, Q. / Chen, Q. / Li, X. / Wang, Y. / Ji, H. / Meng, X. / Pijning, T. / Svensson, B. / Dijkhuizen, L. / Abou Hachem, M. / Jin, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hw3.cif.gz | 333.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hw3.ent.gz | 268 KB | Display | PDB format |
PDBx/mmJSON format | 8hw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/8hw3 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/8hw3 | HTTPS FTP |
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-Related structure data
Related structure data | 8hu4C 8hwkC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 92394.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Limosilactobacillus reuteri (bacteria) / Gene: FOL80_07450 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A848PDI7, dextransucrase #2: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.83 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 4% v/v MPD, 0.1 M Citric acid pH 3.5, 20% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Aug 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→47.11 Å / Num. obs: 58618 / % possible obs: 99 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.66→2.73 Å / Rmerge(I) obs: 0.501 / Num. unique obs: 4439 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→47.11 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.194 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 1.26 / ESU R Free: 0.347 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.109 Å2
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Refinement step | Cycle: 1 / Resolution: 2.66→47.11 Å
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Refine LS restraints |
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