[English] 日本語
Yorodumi- PDB-7vaa: Crystal structure of MiCGT(W93V/V124F/ F191A/R282H) in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vaa | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MiCGT(W93V/V124F/ F191A/R282H) in complex with UDPs | ||||||
Components | UDP-glycosyltransferase 13 | ||||||
Keywords | TRANSFERASE / MiCGT / Glycosyltransferase | ||||||
Function / homology | xylosyltransferase activity / UDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 13 Function and homology information | ||||||
Biological species | Mangifera indica (mango) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.10002756491 Å | ||||||
Authors | Zhong, L. / Zhang, Z.M. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Acs Catalysis / Year: 2021 Title: Directed Evolution of a Plant Glycosyltransferase for Chemo- and Regioselective Glycosylation of Pharmaceutically Significant Flavonoids Authors: Wen, Z. / Zhang, Z.M. / Zhong, L. / Fan, J. / Li, M. / Ma, Y. / Zhou, Y. / Zhang, W. / Guo, B. / Chen, B. / Wang, J.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7vaa.cif.gz | 225.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vaa.ent.gz | 145.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vaa_validation.pdf.gz | 1008.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7vaa_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7vaa_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 7vaa_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/7vaa ftp://data.pdbj.org/pub/pdb/validation_reports/va/7vaa | HTTPS FTP |
-Related structure data
Related structure data | 7va8C 2vceS S: Starting model for refinement 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: 52046.586 Da / Num. of mol.: 2 / Mutation: W93V, V124F, F191A, R282H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mangifera indica (mango) / Gene: CGT, UGT13 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0M4KE44, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% (v/v) PEG3350, 0.1 M Bis-Tris pH 7.0, 200 mM calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 19961 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.0425676209 Å2 / CC1/2: 0.896 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.1→3.15 Å / Num. unique obs: 1362 / CC1/2: 0.739 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VCE Resolution: 3.10002756491→48.4959484106 Å / SU ML: 0.433450366629 / Cross valid method: FREE R-VALUE / σ(F): 1.36306650605 / Phase error: 30.3573503523
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.5961658641 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.10002756491→48.4959484106 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|