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Yorodumi- PDB-5ze6: CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ze6 | ||||||
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Title | CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM ESCHERICHIA COLI WITH BPH-981 | ||||||
Components | Octaprenyl diphosphate synthase | ||||||
Keywords | TRANSFERASE/INHIBITOR / PRENYLTRANSFERASE / SITE-DIRECTED MUTAGENESIS / PRODUCT CHAIN LENGTH / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information all-trans-octaprenyl-diphosphate synthase / octaprenyl pyrophosphate synthase activity / polyprenol biosynthetic process / ubiquinone biosynthetic process / prenyltransferase activity / isoprenoid biosynthetic process / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Han, X. / Liu, W.D. / Zheng, Y.Y. / Ko, T.P. / Chen, C.C. / Guo, R.T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2019 Title: Discovery of Lipophilic Bisphosphonates That Target Bacterial Cell Wall and Quinone Biosynthesis. Authors: Malwal, S.R. / Chen, L. / Hicks, H. / Qu, F. / Liu, W. / Shillo, A. / Law, W.X. / Zhang, J. / Chandnani, N. / Han, X. / Zheng, Y. / Chen, C.C. / Guo, R.T. / AbdelKhalek, A. / Seleem, M.N. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ze6.cif.gz | 249.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ze6.ent.gz | 201.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ze6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/5ze6 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/5ze6 | HTTPS FTP |
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-Related structure data
Related structure data | 5zheC 5zlfC 3wjkS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35249.879 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: ispB, cel, yhbD, b3187, JW3154 / Plasmid: pET46Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0AD57, all-trans-octaprenyl-diphosphate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % / Mosaicity: 0.51 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.3M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M TRIS-HCL, 24%(W/V) POLYETHYLENE GLYCOL 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→25 Å / Num. obs: 49730 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.097 / Χ2: 1.451 / Net I/σ(I): 9.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WJK Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.964 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.307 / 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: 41.108 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→25 Å
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Refine LS restraints |
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