+Open data
-Basic information
Entry | Database: PDB / ID: 6kvk | |||||||||||||||||||||||||||
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Title | Crystal structure of UDP-Sm-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: 2.397 Å | |||||||||||||||||||||||||||
Authors | Li, J.X. / Liu, Z.F. / Wang, Y. / Zhang, P. | |||||||||||||||||||||||||||
Funding support | China, 8items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kvk.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kvk.ent.gz | 81.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kvk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6kvk_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6kvk_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 6kvk_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/6kvk ftp://data.pdbj.org/pub/pdb/validation_reports/kv/6kvk | HTTPS FTP |
-Related structure data
Related structure data | 6kviC 6kvjC 6kvlC 2vceS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 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 |
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#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-DX0 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 24% (vol/vol) 2-propanol, 0.1 M 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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 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: 2.397→33.051 Å / Num. obs: 19809 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 0.986 / Rrim(I) all: 0.142 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.397→2.483 Å / Num. unique obs: 1864 / CC1/2: 0.803 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VCE Resolution: 2.397→33.051 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.88 / Stereochemistry target values: ML
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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 max: 123.83 Å2 / Biso mean: 44.4119 Å2 / Biso min: 16.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.397→33.051 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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