+Open data
-Basic information
Entry | Database: PDB / ID: 6kvl | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of UDP-RebB-SrUGT76G1 | |||||||||||||||||||||||||||
Components | UDP-glycosyltransferase 76G1 | |||||||||||||||||||||||||||
Keywords | TRANSFERASE / glycosyltransferase / diterpenoid / Stevia rebaudiana / natural sweeteners / steviol glycosides (SGs). | |||||||||||||||||||||||||||
Function / homology | Function and homology information UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Stevia rebaudiana (plant) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å | |||||||||||||||||||||||||||
Authors | Li, J.X. / Liu, Z.F. / Wang, Y. / Zhang, P. | |||||||||||||||||||||||||||
Funding support | China, 8items
| |||||||||||||||||||||||||||
Citation | Journal: Plant Commun. / Year: 2020 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6kvl.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6kvl.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 6kvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/6kvl ftp://data.pdbj.org/pub/pdb/validation_reports/kv/6kvl | HTTPS FTP |
---|
-Related structure data
Related structure data | 6kviC 6kvjC 6kvkC 2vceS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 52406.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stevia rebaudiana (plant) / Gene: UGT76G1 / Production host: Escherichia coli (E. coli) References: UniProt: Q6VAB4, Transferases; Glycosyltransferases; Hexosyltransferases |
---|---|
#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-AUO / ( |
#4: 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: 2.43 Å3/Da / Density % sol: 49.38 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18% (vol/vol) 2-propanol, 0.1M sodium citrate tribasic dihydrate, pH 5.5, 18% (wt/vol) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 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: 1.998→39.674 Å / Num. obs: 53258 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.994 / Rrim(I) all: 0.153 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.998→2.07 Å / Num. unique obs: 3321 / CC1/2: 0.941 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VCE Resolution: 1.998→39.674 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.09 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.75 Å2 / Biso mean: 31.6381 Å2 / Biso min: 13.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.998→39.674 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|