+Open data
-Basic information
Entry | Database: PDB / ID: 8i0e | ||||||
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Title | Sb3GT1 complex with UDP | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase / PLANT PROTEIN | ||||||
Function / homology | UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / hexosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase Function and homology information | ||||||
Biological species | Scutellaria baicalensis (Baikal skullcap) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wang, H.T. / Wang, Z.L. / Ye, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants. Authors: Wang, H.T. / Wang, Z.L. / Chen, K. / Yao, M.J. / Zhang, M. / Wang, R.S. / Zhang, J.H. / Agren, H. / Li, F.D. / Li, J. / Qiao, X. / Ye, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i0e.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i0e.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 8i0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/8i0e ftp://data.pdbj.org/pub/pdb/validation_reports/i0/8i0e | HTTPS FTP |
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-Related structure data
Related structure data | 8hzzC 8i0dC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 50312.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scutellaria baicalensis (Baikal skullcap) Gene: UGT78B4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A482AQV3, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-UDP / |
#3: 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: 2.12 Å3/Da / Density % sol: 42.11 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium malonate pH 4.0, 20% PEG 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.71 Å / Num. obs: 34695 / % possible obs: 99 % / Redundancy: 13 % / CC1/2: 0.99 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 1706 / CC1/2: 0.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.993 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.151 / 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: 33.517 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→45.75 Å
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Refine LS restraints |
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