+Open data
-Basic information
Entry | Database: PDB / ID: 8i0d | ||||||
---|---|---|---|---|---|---|---|
Title | Sb3GT1 375S/Q377H mutant complex with UDP-Glc | ||||||
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-GLUCOSE / Glycosyltransferase Function and homology information | ||||||
Biological species | Scutellaria baicalensis (Baikal skullcap) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Wang, H.T. / Wang, Z.L. / Ye, M. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8i0d.cif.gz | 201.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8i0d.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 8i0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/8i0d ftp://data.pdbj.org/pub/pdb/validation_reports/i0/8i0d | HTTPS FTP |
---|
-Related structure data
Related structure data | 8hzzC 8i0eC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50409.512 Da / Num. of mol.: 1 / Mutation: Q376E 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 |
---|---|
#2: Chemical | ChemComp-UPG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.64 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.05 M Citric acid, 0.05 M BIS-TRIS propane / pH 5.0), 16% w/v Polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 17, 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: 1.43→47.47 Å / Num. obs: 85370 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.43→1.45 Å / Num. unique obs: 4352 / CC1/2: 0.78 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→44.59 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.318 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.568 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.43→44.59 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|