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Yorodumi- PDB-2vce: Characterization and engineering of the bifunctional N- and O- gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vce | ||||||
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Title | Characterization and engineering of the bifunctional N- and O- glucosyltransferase involved in xenobiotic metabolism in plants | ||||||
Components | HYDROQUINONE GLUCOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / N-GLUCOSYLTRANSFERASE / S-GLUCOSYLTRANSFERASE / GLYCOSYLTRANSFERASE / PLANT GLYCOSYLATION / N-GLYCOSYLATION / O-GLYCOSYLATION / O- GLUCOSYLTRANSFERASE / UDP-GLUCOSE- DEPENDENT | ||||||
Function / homology | Function and homology information hydroquinone glucosyltransferase / hydroquinone glucosyltransferase activity / lignin biosynthetic process / UDP-glucosyltransferase activity / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / xenobiotic catabolic process / xenobiotic metabolic process / response to toxic substance Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Brazier-Hicks, M. / Offen, W.A. / Gershater, M.C. / Revett, T.J. / Lim, E.K. / Bowles, D.J. / Davies, G.J. / Edwards, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Characterization and Engineering of the Bifunctional N- and O-Glucosyltransferase Involved in Xenobiotic Metabolism in Plants. Authors: Brazier-Hicks, M. / Offen, W.A. / Gershater, M.C. / Revett, T.J. / Lim, E.K. / Bowles, D.J. / Davies, G.J. / Edwards, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vce.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vce.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/2vce ftp://data.pdbj.org/pub/pdb/validation_reports/vc/2vce | HTTPS FTP |
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-Related structure data
Related structure data | 2vchSC 2vg8C 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: 52992.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET-30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER References: UniProt: Q9M156, hydroquinone glucosyltransferase |
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#2: Chemical | ChemComp-U2F / |
#3: Chemical | ChemComp-TC7 / |
#4: Chemical | ChemComp-EDO / |
#5: 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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Details: 25 % (W/V) PEG 3350, 0.1 M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.67 Å / Num. obs: 37280 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VCH Resolution: 1.9→19.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.951 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5, 251-255, 317-320 AND 477-480 ARE DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.67 Å
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Refine LS restraints |
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