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Yorodumi- PDB-7zf0: Crystal structure of UGT85B1 from Sorghum bicolor in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zf0 | ||||||
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Title | Crystal structure of UGT85B1 from Sorghum bicolor in complex with UDP and p-hydroxymandelonitrile | ||||||
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 / (2S)-HYDROXY(4-HYDROXYPHENYL)ETHANENITRILE / URIDINE-5'-DIPHOSPHATE / Cyanohydrin beta-glucosyltransferase Function and homology information | ||||||
Biological species | Sorghum bicolor (sorghum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zf0.cif.gz | 233.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zf0.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 7zf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zf0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7zf0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7zf0_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 7zf0_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/7zf0 ftp://data.pdbj.org/pub/pdb/validation_reports/zf/7zf0 | HTTPS FTP |
-Related structure data
Related structure data | 7zerSC S: Starting model for refinement 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: Chemical | ChemComp-DHR / ( | #5: 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: 3.02 Å3/Da / Density % sol: 59.25 % |
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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: 1.5→45.69 Å / Num. obs: 104591 / % possible obs: 99.86 % / Redundancy: 5.6 % / Biso Wilson estimate: 29.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.55 |
Reflection shell | Resolution: 1.5→1.554 Å / Num. unique obs: 10304 / CC1/2: 0.329 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZER Resolution: 1.5→45.69 Å / SU ML: 0.2392 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2041 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: 38.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.69 Å
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Refine LS restraints |
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LS refinement shell |
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