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Yorodumi- PDB-3w7r: Structure of Human dihydroorotate dehydrogenase in complex with m... -
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-Basic information
Entry | Database: PDB / ID: 3w7r | ||||||
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Title | Structure of Human dihydroorotate dehydrogenase in complex with mii-4-097 | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Rossmann Fold / Oxidoreductase / Dihydroorotate/orotate and ubiquinone/ubiquinol / Mitochondrial inner membrane / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
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: 1.68 Å | ||||||
Authors | Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Hashimoto, S. / Matsuoka, S. / Kuranaga, T. / Shiba, T. / Sakamoto, K. / Suzuki, S. ...Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Hashimoto, S. / Matsuoka, S. / Kuranaga, T. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Balogun, E.O. / Nara, T. / Aoki, T. / Inoue, M. / Honma, T. / Tanaka, A. / Harada, S. / Kita, K. | ||||||
Citation | Journal: To be Published Title: Structure of Human dihydroorotate dehydrogenase in complex with mii-4-097 Authors: Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Hashimoto, S. / Matsuoka, S. / Kuranaga, T. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Balogun, E.O. / Nara, T. / Aoki, T. / Inoue, M. / ...Authors: Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Hashimoto, S. / Matsuoka, S. / Kuranaga, T. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Balogun, E.O. / Nara, T. / Aoki, T. / Inoue, M. / Honma, T. / Tanaka, A. / Harada, S. / Kita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w7r.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w7r.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 3w7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/3w7r ftp://data.pdbj.org/pub/pdb/validation_reports/w7/3w7r | HTTPS FTP |
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-Related structure data
Related structure data | 3zwsS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42636.414 Da / Num. of mol.: 1 / Fragment: UNP residues 29-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PyrD / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PyrD- References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 9 types, 360 molecules
#2: Chemical | ChemComp-CL / | ||||||||||||||
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#3: Chemical | ChemComp-DDQ / #4: Chemical | ChemComp-W7A / | #5: Chemical | ChemComp-FMN / | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-ORO / | #8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-ACT / #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 100mM SODIUM ACETATE, 1.8-1.9M AMMONIUM SULPHATE, 40mM C11DAO, 20.8mM DDAO, 2mM DIHYDROOROTATE, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 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: Jan 29, 2012 |
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: 1.68→50 Å / Num. all: 66931 / Num. obs: 66902 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 11 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 6.31 / Num. unique all: 3300 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZWS Resolution: 1.68→36.34 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.101 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.782 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→36.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.679→1.723 Å / Total num. of bins used: 20
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