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Yorodumi- PDB-5tmd: Crystal structure of Os79 from O. sativa in complex with U2F and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tmd | ||||||
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Title | Crystal structure of Os79 from O. sativa in complex with U2F and trichothecene. | ||||||
Components | Glycosyltransferase, Os79 | ||||||
Keywords | TRANSFERASE / mycotoxin / UDP-glucosyltransferase / trichothecene / detoxification | ||||||
Function / homology | Function and homology information quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / detoxification / 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: 2.19 Å | ||||||
Authors | Wetterhorn, K. / Newmister, S.A. / Caniza, R.K. / Busman, M. / McCormick, S.P. / Berthiller, F. / Adam, G. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Crystal Structure of Os79 (Os04g0206600) from Oryza sativa: A UDP-glucosyltransferase Involved in the Detoxification of Deoxynivalenol. Authors: Wetterhorn, K.M. / Newmister, S.A. / Caniza, R.K. / 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 | 5tmd.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tmd.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 5tmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/5tmd ftp://data.pdbj.org/pub/pdb/validation_reports/tm/5tmd | HTTPS FTP |
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-Related 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 subsp. japonica (Japanese rice) Gene: Os04g0206600, Os04g0206600, OSJNBa0052O21.15, OSNPB_040206600 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q7XT97, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-U2F / |
#3: Chemical | ChemComp-7E0 / |
#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: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES pH 6.5, 200 mM glycine, 23% MEPEG 2000. |
-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: ADSC QUANTUM 315r / 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: 2.19→43.5 Å / Num. obs: 25837 / % possible obs: 99.6 % / Redundancy: 7.8 % / Net I/σ(I): 19.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→43.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.438 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.186 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.808 Å2
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Refinement step | Cycle: 1 / Resolution: 2.19→43.5 Å
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Refine LS restraints |
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