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Yorodumi- PDB-2c9z: Structure and activity of a flavonoid 3-0 glucosyltransferase rev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c9z | ||||||
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Title | Structure and activity of a flavonoid 3-0 glucosyltransferase reveals the basis for plant natural product modification | ||||||
Components | UDP GLUCOSE\:FLAVONOID 3-O-GLUCOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / FLAVONOID / WINE / CATALYSIS / GLYCOSYLATION | ||||||
Function / homology | Function and homology information anthocyanidin 3-O-glucosyltransferase / flavonol 3-O-glucosyltransferase / quercetin O-glucoside biosynthetic process / cyanidin 3-O-glucoside biosynthetic process / anthocyanidin 3-O-glucosyltransferase activity / flavonol 3-O-glucosyltransferase activity / daphnetin 3-O-glucosyltransferase activity / myricetin 3-O-glucosyltransferase activity / anthocyanin-containing compound biosynthetic process Similarity search - Function | ||||||
Biological species | VITIS VINIFERA (wine grape) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Offen, W. / Martinez-Fleites, C. / Kiat-Lim, E. / Yang, M. / Davis, B.G. / Tarling, C.A. / Ford, C.M. / Bowles, D.J. / Davies, G.J. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Structure of a Flavonoid Glucosyltransferase Reveals the Basis for Plant Natural Product Modification. Authors: Offen, W. / Martinez-Fleites, C. / Yang, M. / Kiat-Lim, E. / Davis, B.G. / Tarling, C.A. / Ford, C.M. / Bowles, D.J. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c9z.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c9z.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 2c9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9z ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9z | 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: 50188.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VITIS VINIFERA (wine grape) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 References: UniProt: O22304, UniProt: P51094*PLUS, flavonol 3-O-glucosyltransferase |
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#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-QUE / |
#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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | pH: 7 Details: 20% PEG 10000, 0.1M BIS-TRIS PROPANE PH 7.0, 0.5% PRUCORONIC F-68 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 29411 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.733 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.183 / 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: 27.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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