+Open data
-Basic information
Entry | Database: PDB / ID: 7q3s | ||||||||||||
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Title | Crystal structure of UGT706F8 from Zea mays | ||||||||||||
Components | Glycosyltransferase | ||||||||||||
Keywords | TRANSFERASE / UGT / silibinin / glycosyltransferase | ||||||||||||
Function / homology | UDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase Function and homology information | ||||||||||||
Biological species | Zea mays (maize) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||||||||
Authors | Fredslund, F. / Bidart, G.N. / Welner, D.H. | ||||||||||||
Funding support | Denmark, 3items
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Citation | Journal: Acs Sustain Chem Eng / Year: 2022 Title: Family 1 Glycosyltransferase UGT706F8 from Zea mays Selectively Catalyzes the Synthesis of Silibinin 7- O -beta-d-Glucoside. Authors: Bidart, G.N. / Putkaradze, N. / Fredslund, F. / Kjeldsen, C. / Ruiz, A.G. / Duus, J.O. / Teze, D. / Welner, D.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q3s.cif.gz | 335.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q3s.ent.gz | 225.9 KB | Display | PDB format |
PDBx/mmJSON format | 7q3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/7q3s ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q3s | HTTPS FTP |
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-Related structure data
Related structure data | 5nlmS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53222.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: 100193773, ZEAMMB73_Zm00001d047504 / Production host: Escherichia coli (E. coli) References: UniProt: B4FG90, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-UDP / |
#3: 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: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: PEG 6000 (20%), Tris 100mM, NaCl 200mM, pH 8.1 12 mg/ml 2:1 drops |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryojet / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 13, 2019 / Details: KB-mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→43.2 Å / Num. obs: 62014 / % possible obs: 94.89 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0623 / Rpim(I) all: 0.02555 / Net I/σ(I): 17.56 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 1.4 % / Rmerge(I) obs: 1.001 / Num. unique obs: 4725 / CC1/2: 0.631 / CC star: 0.88 / Rpim(I) all: 0.4238 / % possible all: 72.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NLM Resolution: 1.59→43.2 Å / SU ML: 0.2072 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6419 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: 31.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→43.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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