+Open data
-Basic information
Entry | Database: PDB / ID: 5tmb | ||||||
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Title | Crystal structure of Os79 from O. sativa in complex with UDP. | ||||||
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: 2.34 Å | ||||||
Authors | Wetterhorn, K.M. / 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 | 5tmb.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tmb.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/5tmb ftp://data.pdbj.org/pub/pdb/validation_reports/tm/5tmb | 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-Gold(DE3)pLysS AG' (bacteria) 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: 3.15 Å3/Da / Density % sol: 60.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM PIPES pH 6.0, 80 mM NaCl, 20% MPD, 15% taurine. |
-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: 2.34→50 Å / Num. obs: 27447 / % possible obs: 99.5 % / Redundancy: 10.3 % / Net I/σ(I): 24.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→36.325 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→36.325 Å
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Refine LS restraints |
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LS refinement shell |
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