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Yorodumi- PDB-3i65: Plasmodium falciparum dihydroorotate dehydrogenase bound with tri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i65 | ||||||
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Title | Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM1 | ||||||
Components | Dihydroorotate dehydrogenase homolog, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Plasmodium falciparum / dihydroorotate dehydrogenase / triazolopyrimidine / inhibitor / DSM1 / FAD / Flavoprotein / Membrane / Mitochondrion / Mitochondrion inner membrane / Pyrimidine biosynthesis / Transit peptide | ||||||
Function / homology | Function and homology information Pyrimidine biosynthesis / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Deng, X. / Phillips, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds. Authors: Deng, X. / Gujjar, R. / El Mazouni, F. / Kaminsky, W. / Malmquist, N.A. / Goldsmith, E.J. / Rathod, P.K. / Phillips, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i65.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i65.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 3i65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i65_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3i65_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3i65_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 3i65_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/3i65 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i65 | HTTPS FTP |
-Related structure data
Related structure data | 3i68C 3i6rC 1tv5S C: citing same article (ref.) 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: 46652.344 Da / Num. of mol.: 1 / Fragment: UNP residues 158-569 with 384-413 deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFF0160c, Plasmodium falciparum / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q08210, EC: 1.3.3.1 |
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-Non-polymers , 5 types, 128 molecules
#2: Chemical | ChemComp-JZ8 / |
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#3: Chemical | ChemComp-FMN / |
#4: Chemical | ChemComp-ORO / |
#5: Chemical | ChemComp-LDA / |
#6: 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: 3.16 Å3/Da / Density % sol: 61.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.16 M Ammonium sulfate, 0.1 M Sodium Acetate, pH 4.6, 18-20% PEG4000, 25% Glycerol, and 10 mM DTT, EVAPORATION, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2008 / Details: high-resolution double-crystal monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 45761 / Num. obs: 42194 / % possible obs: 91.5 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 12 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 45 |
Reflection shell | Resolution: 2→2.06 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.5 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TV5 Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.209 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R: 0.162 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 45.511 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.06 Å / Num. reflection Rwork: 1114 / Total num. of bins used: 20 |