+Open data
-Basic information
Entry | Database: PDB / ID: 1uuo | ||||||
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Title | Rat dihydroorotate dehydrogenase (DHOD)in complex with brequinar | ||||||
Components | DIHYDROOROTATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DIHYDROOROTATE DEHYDROGENASE / BREQUINAR / ATOVAQUONE / NUCLEOTIDE METABOLISM | ||||||
Function / homology | Function and homology information Pyrimidine biosynthesis / response to L-arginine / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / UDP biosynthetic process / ubiquinone binding / response to caffeine ...Pyrimidine biosynthesis / response to L-arginine / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / UDP biosynthetic process / ubiquinone binding / response to caffeine / regulation of mitochondrial fission / response to starvation / quinone binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / response to organic cyclic compound / FMN binding / mitochondrial inner membrane / response to xenobiotic stimulus / positive regulation of apoptotic process / neuronal cell body Similarity search - Function | ||||||
Biological species | RATTUS RATTUS (black rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Hansen, M. / Le Nours, J. / Johansson, E. / Antal, T. / Ullrich, A. / Loffler, M. / Larsen, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Inhibitor Binding in a Class 2 Dihydroorotate Dehydrogenase Causes Variations in the Membrane-Associated N-Terminal Domain Authors: Hansen, M. / Le Nours, J. / Johansson, E. / Antal, T. / Ullrich, A. / Loffler, M. / Larsen, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uuo.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uuo.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 1uuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uuo ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uuo | HTTPS FTP |
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-Related 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: 40340.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS RATTUS (black rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q63707, EC: 1.3.99.11 |
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-Non-polymers , 6 types, 46 molecules
#2: Chemical | ChemComp-BRF / |
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#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-ORO / |
#5: Chemical | ChemComp-NI / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | 29 FIRST RESIDUES IN N-TERMINAL DELETED AND HIS-TAQ ADDED |
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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: 2.1 Å3/Da / Density % sol: 41 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: VAPOUR DIFFUSION HANGING DROP WITH MOTHER LIQUOR: 65% MPD, 0.1M TRIS/HCL, PH=8.5 PROTEIN SOLUTION:15 MG/ML PROTEIN, 2 MM OROTATE, 15 MG/ML PROTEIN, 2 MM OROTATE, 0.1 % BETA-OCTYLGLUCOSIDE, 0. ...Details: VAPOUR DIFFUSION HANGING DROP WITH MOTHER LIQUOR: 65% MPD, 0.1M TRIS/HCL, PH=8.5 PROTEIN SOLUTION:15 MG/ML PROTEIN, 2 MM OROTATE, 15 MG/ML PROTEIN, 2 MM OROTATE, 0.1 % BETA-OCTYLGLUCOSIDE, 0.1 MM ATOVAQUONE, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.076 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.076 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→20 Å / Num. obs: 12989 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 2.44→2.5 Å / Rmerge(I) obs: 0.414 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 204139.23 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.0386 Å2 / ksol: 0.357183 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.44→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.5 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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