+Open data
-Basic information
Entry | Database: PDB / ID: 6aj5 | ||||||
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Title | Crystal structure of ligand-free type DHODH from Eimeria tenella | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | MEMBRANE PROTEIN / Coccidium / mitochondria / electron transport chain / dihydroorotate dehydrogenase | ||||||
Function / homology | Function and homology information dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / nucleotide binding Similarity search - Function | ||||||
Biological species | Eimeria tenella (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Genes (Basel) / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aj5.cif.gz | 578.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aj5.ent.gz | 479.7 KB | Display | PDB format |
PDBx/mmJSON format | 6aj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aj5_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6aj5_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6aj5_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 6aj5_validation.cif.gz | 71.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/6aj5 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/6aj5 | HTTPS FTP |
-Related structure data
Related structure data | 6ajeC 6idjC 3w7rS 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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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.) Eimeria tenella (eukaryote) / Gene: ETH_00004975 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) References: UniProt: U6KL66, dihydroorotate dehydrogenase (quinone) #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-ORO / |
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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: 3.29 Å3/Da / Density % sol: 62.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 3.0 M ammonium sulfate / PH range: 7.0-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 32346 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 1587 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W7R Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.731 / SU B: 99.954 / SU ML: 0.692 / Cross valid method: THROUGHOUT / ESU R Free: 0.811 / 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: 47.361 Å2
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Refinement step | Cycle: 1 / Resolution: 3.5→20 Å
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Refine LS restraints |
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