+Open data
-Basic information
Entry | Database: PDB / ID: 4kdr | ||||||
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Title | Crystal Structure of UBIG/SAH complex | ||||||
Components | 3-demethylubiquinone-9 3-methyltransferase | ||||||
Keywords | TRANSFERASE / Rossmann Fold | ||||||
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 / 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone 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 / 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinone 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: 2.003 Å | ||||||
Authors | Zhu, Y. / Teng, M. / Li, X. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the UBIG/SAH complex Authors: Zhu, Y. / Teng, M. / Li, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kdr.cif.gz | 54.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kdr.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/4kdr ftp://data.pdbj.org/pub/pdb/validation_reports/kd/4kdr | 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: 24832.242 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: Chemical | ChemComp-SAH / |
#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: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M citric acid PH 5.0 and 20% v/v 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9793 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.003→38.03 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.003→38.03 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 22.84 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.321 Å2
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Refinement step | Cycle: LAST / Resolution: 2.003→38.03 Å
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Refine LS restraints |
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LS refinement shell |
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