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Yorodumi- PDB-7t6c: E. coli dihydroorotate dehydrogenase bound to the ubiquinone surr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t6c | ||||||
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Title | E. coli dihydroorotate dehydrogenase bound to the ubiquinone surrogate DCIP | ||||||
Components | Dihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / FMN binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.53 Å | ||||||
Authors | Horwitz, S.M. / Ambarian, J.A. / Davis, K.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Rsc Chem Biol / Year: 2022 Title: Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines. Authors: Horwitz, S.M. / Blue, T.C. / Ambarian, J.A. / Hoshino, S. / Seyedsayamdost, M.R. / Davis, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t6c.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t6c.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 7t6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/7t6c ftp://data.pdbj.org/pub/pdb/validation_reports/t6/7t6c | HTTPS FTP |
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-Related structure data
Related structure data | 7t5kSC 7t5yC 7t6hC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40285.258 Da / Num. of mol.: 2 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: pyrD, b0945, JW0928 / Plasmid: pET28a(+) / Details (production host): Kanamycin resistant / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A7E1, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 6 types, 118 molecules
#2: Chemical | ChemComp-PE4 / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.9 Å3/Da / Density % sol: 68.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: DL-malic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033184 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2021 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033184 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→48.3 Å / Num. obs: 38184 / % possible obs: 98.76 % / Redundancy: 7.5 % / Biso Wilson estimate: 53.94 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1695 / Rpim(I) all: 0.06516 / Rrim(I) all: 0.1819 / Net I/σ(I): 9.19 |
Reflection shell | Resolution: 2.53→2.62 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.317 / Num. unique obs: 3404 / CC1/2: 0.656 / CC star: 0.89 / Rpim(I) all: 0.5104 / % possible all: 89.23 |
-Processing
Software |
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Refinement | Method to determine structure: SIR Starting model: 7T5K Resolution: 2.53→48.3 Å / SU ML: 0.3194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1023 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 55.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→48.3 Å
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Refine LS restraints |
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LS refinement shell |
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