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Yorodumi- PDB-6bk0: Crystal structure of Os79 Q202A from O. sativa in complex with UDP. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bk0 | ||||||
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Title | Crystal structure of Os79 Q202A from O. sativa in complex with UDP. | ||||||
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 subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 | 6bk0.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bk0.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bk0_validation.pdf.gz | 815.4 KB | Display | wwPDB validaton report |
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Full document | 6bk0_full_validation.pdf.gz | 830.2 KB | Display | |
Data in XML | 6bk0_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 6bk0_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/6bk0 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/6bk0 | HTTPS FTP |
-Related structure data
Related structure data | 6bk1C 6bk2C 6bk3C 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: 51087.156 Da / Num. of mol.: 1 / Mutation: Q202A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: UGT79, OS79, Os04g0206600, LOC_Os04g12970, OsJ_13826, OSJNBa0052O21.15 Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: Q7XT97, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-UDP / |
#3: 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: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM 3-(N- Morpholino)propanesulfonic acid pH 7.5, 15% methyl ether polyethylene glycol 5000 (MEPEG 5K), 160 mM potassium glutamate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→50 Å / Num. obs: 79234 / % possible obs: 99.2 % / Redundancy: 13.1 % / Net I/σ(I): 41.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5tme Resolution: 1.47→43.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.863 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.061 / 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: 19.157 Å2
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Refinement step | Cycle: 1 / Resolution: 1.47→43.46 Å
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Refine LS restraints |
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