+Open data
-Basic information
Entry | Database: PDB / ID: 4kdc | ||||||
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Title | Crystal Structure of UBIG | ||||||
Components | 3-demethylubiquinone-9 3-methyltransferase | ||||||
Keywords | TRANSFERASE / Rossmann Fold / O-methylation / ubiquinone biosynthesis | ||||||
Function / homology | Function and homology information 2-polyprenyl-6-hydroxyphenol methylase / 3-demethylubiquinol 3-O-methyltransferase / 2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity / 3,4-dihydroxy-5-polyprenylbenzoic acid O-methyltransferase activity / 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase activity / 3-demethylubiquinol-n 3-O-methyltransferase activity / 2-polyprenyl-6-hydroxyphenol methylase activity / ubiquinone biosynthesis complex / phosphatidylglycerol binding / hyperosmotic salinity response ...2-polyprenyl-6-hydroxyphenol methylase / 3-demethylubiquinol 3-O-methyltransferase / 2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity / 3,4-dihydroxy-5-polyprenylbenzoic acid O-methyltransferase activity / 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone methyltransferase activity / 3-demethylubiquinol-n 3-O-methyltransferase activity / 2-polyprenyl-6-hydroxyphenol methylase activity / ubiquinone biosynthesis complex / phosphatidylglycerol binding / hyperosmotic salinity response / ubiquinone biosynthetic process / cytoplasmic side of plasma membrane / methylation / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Zhu, Y. / Teng, M. / Li, X. | ||||||
Citation | Journal: Biochem. J. / Year: 2015 Title: Structural and biochemical studies reveal UbiG/Coq3 as a class of novel membrane-binding proteins. Authors: Zhu, Y. / Wu, B. / Zhang, X. / Fan, X. / Niu, L. / Li, X. / Wang, J. / Teng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kdc.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kdc.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/4kdc ftp://data.pdbj.org/pub/pdb/validation_reports/kd/4kdc | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 27420.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ubiG, pufX, yfaB, b2232, JW2226 / Production host: Escherichia coli (E. coli) References: UniProt: P17993, 3-demethylubiquinol 3-O-methyltransferase, 2-polyprenyl-6-hydroxyphenol methylase |
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#2: 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: 2.48 Å3/Da / Density % sol: 50.42 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH7.5 and 20% polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9994 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 12, 2010 |
Radiation | Monochromator: NiFILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9994 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→29.51 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→29.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.164 / 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: 28.188 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→29.51 Å
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