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Yorodumi- PDB-2c1x: Structure and activity of a flavonoid 3-O glucosyltransferase rev... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c1x | ||||||
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Title | Structure and activity of a flavonoid 3-O glucosyltransferase reveals the basis for plant natural product modification | ||||||
Components | UDP-GLUCOSE FLAVONOID 3-O GLYCOSYLTRANSFERASE | ||||||
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: 1.9 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 | 2c1x.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c1x.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 2c1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/2c1x ftp://data.pdbj.org/pub/pdb/validation_reports/c1/2c1x | 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-B3P / |
#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% V/V PLURONIC ACID |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9793 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40.19 Å / Num. obs: 37371 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→40.19 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.877 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.139 / 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: 23.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40.19 Å
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Refine LS restraints |
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