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Open data
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Basic information
Entry | Database: PDB / ID: 8wp5 | ||||||
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Title | Crystal structure of LbUGT1 in complex with UDP | ||||||
![]() | Glycosyltransferase | ||||||
![]() | TRANSFERASE / Lycibarbarspermidines / Biosynthesis / Glycosyltransferase | ||||||
Function / homology | URIDINE-5'-DIPHOSPHATE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hu, D. / Wang, G.Q. | ||||||
Funding support | 1items
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![]() | ![]() Title: Functional and structural dissection of glycosyltransferases underlying the glycodiversity of wolfberry-derived bioactive ingredients lycibarbarspermidines. Authors: Li, S.Y. / Wang, G.Q. / Long, L. / Gao, J.L. / Zhou, Z.Q. / Wang, Y.H. / Lv, J.M. / Chen, G.D. / Hu, D. / Abe, I. / Gao, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 81.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 771.3 KB | Display | ![]() |
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Full document | ![]() | 782.8 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8w53C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 54972.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.59 % |
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Crystal grow | Temperature: 292.2 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES sodium hydroxide, 200 mM Ammonium sulfate, 10% 2-propanol, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→48.902 Å / Num. obs: 20277 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 60.6546327524 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.57→2.64 Å / Num. unique obs: 1468 / CC1/2: 0.794 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.7668723766 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57005953651→48.901758191 Å
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Refine LS restraints |
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LS refinement shell |
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