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- PDB-6aje: Crystal structure of DHODH in complex with ferulenol from Eimeria... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6aje | ||||||
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Title | Crystal structure of DHODH in complex with ferulenol from Eimeria tenella | ||||||
![]() | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
![]() | MEMBRANE PROTEIN / Coccidium / mitochondria / electron transport chain / dihydroorotate dehydrogenase | ||||||
Function / homology | ![]() dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shiba, T. / Inaoka, D.K. / Sato, D. / Hartuti, E.D. / Amalia, E. / Nagahama, M. / Yoshioka, Y. / Matsubayashi, M. / Balogun, E.O. / Tsuji, N. ...Shiba, T. / Inaoka, D.K. / Sato, D. / Hartuti, E.D. / Amalia, E. / Nagahama, M. / Yoshioka, Y. / Matsubayashi, M. / Balogun, E.O. / Tsuji, N. / Kita, K. / Harada, S. | ||||||
![]() | ![]() Title: Structural and Biochemical Features of Eimeria tenella Dihydroorotate Dehydrogenase, a Potential Drug Target. Authors: Sato, D. / Hartuti, E.D. / Inaoka, D.K. / Sakura, T. / Amalia, E. / Nagahama, M. / Yoshioka, Y. / Tsuji, N. / Nozaki, T. / Kita, K. / Harada, S. / Matsubayashi, M. / Shiba, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 582.4 KB | Display | ![]() |
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PDB format | ![]() | 482.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 57.4 KB | Display | |
Data in CIF | ![]() | 75.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6aj5SC ![]() 6idjC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48792.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: U6KL66, dihydroorotate dehydrogenase (quinone) #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-ORO / #4: Chemical | ChemComp-9AU / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES, 1.8 M Triammonium citrate, 1 mM ferulenol PH range: 7.0-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.65→50 Å / Num. obs: 24158 / % possible obs: 96.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.65→3.71 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1187 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6AJ5 Resolution: 3.65→20 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.767 / SU B: 96.038 / SU ML: 0.684 / Cross valid method: THROUGHOUT / ESU R Free: 0.874 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.906 Å2
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Refinement step | Cycle: 1 / Resolution: 3.65→20 Å
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Refine LS restraints |
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