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Open data
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Basic information
Entry | Database: PDB / ID: 6kvj | |||||||||||||||||||||||||||
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Title | Crystal structure of UDPX-SrUGT76G1 | |||||||||||||||||||||||||||
![]() | UDP-glycosyltransferase 76G1 | |||||||||||||||||||||||||||
![]() | TRANSFERASE / glycosyltransferase / diterpenoid / Stevia rebaudiana / natural sweeteners / steviol glycosides (SGs) | |||||||||||||||||||||||||||
Function / homology | ![]() UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Li, J.X. / Liu, Z.F. / Wang, Y. / Zhang, P. | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights into the Catalytic Mechanism of a Plant Diterpene Glycosyltransferase SrUGT76G1. Authors: Liu, Z. / Li, J. / Sun, Y. / Zhang, P. / Wang, Y. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 105.9 KB | Display | ![]() |
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PDB format | ![]() | 78.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6kviC ![]() 6kvkC ![]() 6kvlC ![]() 2vceS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 52406.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6VAB4, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-UDX / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% (vol/vol) 2-propanol, 0.1M sodium citrate tribasic dihydrate, pH 5.9, 20% (wt/vol) pEG4000 |
-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: Nov 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.499→49.122 Å / Num. obs: 24046 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.998 / Rrim(I) all: 0.134 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.499→2.589 Å / Num. unique obs: 1378 / CC1/2: 0.716 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2vce Resolution: 2.499→49.122 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.68 Å2 / Biso mean: 51.2109 Å2 / Biso min: 20.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.499→49.122 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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