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- PDB-6uy4: Crystal structure of dihydroorotate dehydrogenase from Schistosom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uy4 | |||||||||
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Title | Crystal structure of dihydroorotate dehydrogenase from Schistosoma mansoni | |||||||||
![]() | Dihydroorotate dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE/INHIBITOR / SmDHODH / class 2 dihydroorotate dehydrogenase / Schistosoma mansoni / FLAVOPROTEIN / OXIDOREDUCTASE-INHIBITOR complex | |||||||||
Function / homology | ![]() dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mori, R.M. / Zapata, L.C.C. / Nonato, M.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the function and inhibition of dihydroorotate dehydrogenase from Schistosoma mansoni. Authors: de Mori, R.M. / Aleixo, M.A.A. / Zapata, L.C.C. / Calil, F.A. / Emery, F.S. / Nonato, M.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.7 KB | Display | ![]() |
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PDB format | ![]() | 62.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 403.7 KB | Display | ![]() |
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Full document | ![]() | 403.9 KB | Display | |
Data in XML | ![]() | 1.7 KB | Display | |
Data in CIF | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uoy S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 41342.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: G4VFD7, dihydroorotate dehydrogenase (fumarate) | ||||||
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#2: Chemical | ChemComp-QLA / | ||||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-FMN / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.4 % / Description: Yellow cube |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 MES pH 6.5; 1.4 M CITRIC ACID |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2019 |
Radiation | Monochromator: Cryogenically colled channel cut crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.796→47 Å / Num. obs: 14354 / % possible obs: 99.83 % / Redundancy: 39.8 % / CC1/2: 0.997 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Num. unique obs: 2047 / CC1/2: 0.404 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6UOY ![]() 6uoy Resolution: 2.796→46.995 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.05 / Stereochemistry target values: ML
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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 max: 172.68 Å2 / Biso mean: 79.8748 Å2 / Biso min: 51.19 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.796→46.995 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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