+Open data
-Basic information
Entry | Database: PDB / ID: 6l90 | ||||||
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Title | Crystal structure of ugt transferase enzyme | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information mogroside IE synthase / quercetin 7-O-glucosyltransferase activity / quercetin 3-O-glucosyltransferase activity / UDP-glucosyltransferase activity Similarity search - Function | ||||||
Biological species | Siraitia grosvenorii (arhat fruit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Li, J. / Shan, N. / Yang, J.G. / Liu, W.D. / Sun, Y.X. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Efficient O-Glycosylation of Triterpenes Enabled by Protein Engineering of Plant Glycosyltransferase UGT74AC1 Authors: Li, J. / Yang, J.G. / Mu, S. / Shang, N. / Liu, C. / Zhu, Y. / Cai, Y. / Liu, P. / Lin, J. / Liu, W.D. / Sun, Y.X. / Ma, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l90.cif.gz | 108.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l90.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 6l90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l90_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 6l90_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 6l90_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 6l90_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/6l90 ftp://data.pdbj.org/pub/pdb/validation_reports/l9/6l90 | HTTPS FTP |
-Related structure data
Related structure data | 6l8wC 6l8xC 6l8zC 2pq6S 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
#1: Protein | Mass: 51332.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Siraitia grosvenorii (arhat fruit) / Gene: UDPG1 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: K7NBW3, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-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: 49.87 % / Mosaicity: 1.041 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG8000, MgAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 20, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.02→25 Å / Num. obs: 33929 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Rrim(I) all: 0.087 / Χ2: 1.809 / Net I/σ(I): 11.6 / Num. measured all: 261957 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2pq6 Resolution: 2.02→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.335 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.27 Å2 / Biso mean: 40.054 Å2 / Biso min: 19.78 Å2
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Refinement step | Cycle: final / Resolution: 2.02→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.072 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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