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Yorodumi- PDB-6bk3: Crystal structure of Os79 from O. sativa in complex with UDP and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bk3 | ||||||
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Title | Crystal structure of Os79 from O. sativa in complex with UDP and deoxynivalenol-3-glucoside (glucose moitey not resolved) | ||||||
Components | UDP-glycosyltransferase 79 | ||||||
Keywords | TRANSFERASE / UDP-glucosyltransferase / trichothecene | ||||||
Function / homology | Function and homology information detoxification / quercetin 7-O-glucosyltransferase activity / quercetin 3-O-glucosyltransferase activity / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Wetterhorn, K. / Gabardi, K. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Determinants and Expansion of Specificity in a Trichothecene UDP-Glucosyltransferase from Oryza sativa. Authors: Wetterhorn, K.M. / Gabardi, K. / Michlmayr, H. / Malachova, A. / Busman, M. / McCormick, S.P. / Berthiller, F. / Adam, G. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bk3.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bk3.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 6bk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bk3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6bk3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6bk3_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 6bk3_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/6bk3 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/6bk3 | HTTPS FTP |
-Related structure data
Related structure data | 6bk0C 6bk1C 6bk2C 5tmeS 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: 51144.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: UGT79, OS79, Os04g0206600, LOC_Os04g12970, OsJ_13826, OSJNBa0052O21.15 Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7XT97, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-B2S / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM sodium acetate pH 5.0, 40% pentaerythritol propoxylate 426, 320 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→50 Å / Num. obs: 33082 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.086 / Net I/av σ(I): 29.1 / Net I/σ(I): 29.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5tme Resolution: 2.17→46.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.548 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 37.07 Å2
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Refinement step | Cycle: 1 / Resolution: 2.17→46.14 Å
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Refine LS restraints |
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