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Yorodumi- PDB-3w84: Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w84 | ||||||
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Title | Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-6-101 | ||||||
Components | Dihydroorotate dehydrogenase (fumarate)Dihydroorotate dehydrogenase (fumarate) | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Rossmann Fold / Oxidoreductase / Dihydroorotate/orotate and fumarate/succinate binding / Cytosol / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 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 Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-6-101 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 | 3w84.cif.gz | 147.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w84.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 3w84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/3w84 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/3w84 | HTTPS FTP |
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-Related structure data
Related structure data | 3w7mS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34067.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: PyrD / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q4D3W2, dihydroorotate dehydrogenase (fumarate) |
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-Non-polymers , 5 types, 497 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-NCO / | #6: 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: 2.33 Å3/Da / Density % sol: 47.27 % / Mosaicity: 1.246 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→30 Å / Num. obs: 48677 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.138 / Χ2: 2.581 / Net I/σ(I): 7.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3W7M Resolution: 1.93→29.34 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.896 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 72.24 Å2 / Biso mean: 17.7418 Å2 / Biso min: 5.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→29.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.926→1.976 Å / Total num. of bins used: 20
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