+Open data
-Basic information
Entry | Database: PDB / ID: 6idj | ||||||
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Title | Crystal structure of human DHODH in complex with ferulenol | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | MEMBRANE PROTEIN / Coccidium / mitochondria / electron transport chain / dihydroorotate dehydrogenase | ||||||
Function / homology | Function and homology information pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 6idj.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6idj.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 6idj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6idj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6idj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6idj_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 6idj_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/6idj ftp://data.pdbj.org/pub/pdb/validation_reports/id/6idj | HTTPS FTP |
-Related structure data
Related structure data | 6aj5C 6ajeC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42636.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli (E. coli) References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 6 types, 141 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-FMN / | #5: Chemical | ChemComp-ORO / | #6: Chemical | ChemComp-9AU / | #7: 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: 3.39 Å3/Da / Density % sol: 63.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 100 MM SODIUM ACETATE, 1.8-1.9 M AMMONIUM SULPHATE, 40 MM C11DAO, 20.8 MM DDAO, 2 MM DIHYDROOROTATE, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2011 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 46303 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.729 / Num. unique obs: 2316 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W7R Resolution: 1.9→19.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.118 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.091 / 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: 29.991 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→19.89 Å
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Refine LS restraints |
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