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Yorodumi- PDB-7zer: Crystal structure of UGT85B1 from Sorghum bicolor in complex with UDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zer | ||||||
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Title | Crystal structure of UGT85B1 from Sorghum bicolor in complex with UDP | ||||||
Components | Cyanohydrin beta-glucosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase / cyanogenic / dhurrin biosynthesis / GT-B fold | ||||||
Function / homology | cyanohydrin beta-glucosyltransferase / dhurrin biosynthetic process / cyanohydrin beta-glucosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / endoplasmic reticulum membrane / URIDINE-5'-DIPHOSPHATE / Cyanohydrin beta-glucosyltransferase Function and homology information | ||||||
Biological species | Sorghum bicolor (sorghum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Putkaradze, N. / Fredslund, F. / Welner, D.H. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Plant J. / Year: 2022 Title: Structure-guided engineering of key amino acids in UGT85B1 controlling substrate and stereo-specificity in aromatic cyanogenic glucoside biosynthesis. Authors: Del Giudice, R. / Putkaradze, N. / Dos Santos, B.M. / Hansen, C.C. / Crocoll, C. / Motawia, M.S. / Fredslund, F. / Laursen, T. / Welner, D.H. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Authors: Liebschner, D. / Afonine, P.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zer.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zer.ent.gz | 150.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zer_validation.pdf.gz | 858.6 KB | Display | wwPDB validaton report |
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Full document | 7zer_full_validation.pdf.gz | 861.1 KB | Display | |
Data in XML | 7zer_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 7zer_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/7zer ftp://data.pdbj.org/pub/pdb/validation_reports/ze/7zer | HTTPS FTP |
-Related structure data
Related structure data | 7zf0C C: citing same article (ref.) |
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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: 53798.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: UGT85B1, HMNGT / Production host: Escherichia coli (E. coli) References: UniProt: Q9SBL1, cyanohydrin beta-glucosyltransferase | ||||
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#2: Chemical | ChemComp-UDP / | ||||
#3: Chemical | ChemComp-EDO / #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: 2.99 Å3/Da / Density % sol: 58.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM MES/imidazole, 12.5% (w/v) PEG8000, 12.5% (v/v) ethylene glycol, 120 mM MORPHEUS monosaccharides mix |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2020 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→45.07 Å / Num. obs: 121023 / % possible obs: 99.19 % / Redundancy: 5 % / Biso Wilson estimate: 22.02 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.84 |
Reflection shell | Resolution: 1.42→1.471 Å / Num. unique obs: 44070 / CC1/2: 0.426 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UGT85H2 Resolution: 1.42→45.07 Å / SU ML: 0.1936 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3694 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: 26.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→45.07 Å
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Refine LS restraints |
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LS refinement shell |
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