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Yorodumi- PDB-3w3o: Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w3o | ||||||
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Title | Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-4-053 | ||||||
Components | 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 / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Matsuoka, S. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Rocha, J.R. / Balogun, E.O. ...Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Matsuoka, S. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Rocha, J.R. / 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-4-053 Authors: Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Matsuoka, S. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Rocha, J.R. / Balogun, E.O. / Nara, T. / Aoki, T. / Inoue, M. / Honma, T. / Tanaka, A. ...Authors: Inaoka, D.K. / Iida, M. / Tabuchi, T. / Lee, N. / Matsuoka, S. / Shiba, T. / Sakamoto, K. / Suzuki, S. / Rocha, J.R. / 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 | 3w3o.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w3o.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 3w3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w3o_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3w3o_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3w3o_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 3w3o_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/3w3o ftp://data.pdbj.org/pub/pdb/validation_reports/w3/3w3o | HTTPS FTP |
-Related structure data
Related structure data | 3w2uS 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, 435 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: 2.31 Å3/Da / Density % sol: 46.72 % |
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Crystal grow | Temperature: 298 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 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Mar 4, 2009 |
Radiation | Monochromator: SI(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 45625 / Num. obs: 45252 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.97→2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 5.04 / Num. unique all: 2248 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W2U Resolution: 1.96→27.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.937 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.136 / 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: 20.527 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→27.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.956→2.007 Å / Total num. of bins used: 20
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