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Yorodumi- PDB-5del: Crystal structure of Plasmodium falciparum dihydroorotate dehydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5del | |||||||||
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Title | Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM59 | |||||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone) | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / alpha/beta barrel / mitochondrial membrane / FMN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||
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 (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Phillips, M. / Deng, X. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: The X-ray structure of Plasmodium falciparum dihydroorotate dehydrogenase bound to a potent and selective N-phenylbenzamide inhibitor reveals novel binding-site interactions. Authors: Deng, X. / Matthews, D. / 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 | 5del.cif.gz | 236 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5del.ent.gz | 191.9 KB | Display | PDB format |
PDBx/mmJSON format | 5del.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/5del ftp://data.pdbj.org/pub/pdb/validation_reports/de/5del | HTTPS FTP |
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-Related structure data
Related structure data | 3i65S 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, 1 molecules A
#1: Protein | Mass: 45385.914 Da / Num. of mol.: 1 / Mutation: UNP residues 158-569, delta(384-413) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate 3D7 / Gene: PFF0160c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q08210, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 6 types, 129 molecules
#2: Chemical | ChemComp-FMN / | ||||
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#3: Chemical | ChemComp-ORO / | ||||
#4: Chemical | ChemComp-D59 / | ||||
#5: Chemical | #6: Chemical | ChemComp-LDA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.35 Details: 0.16 M Ammonium sulfate, 0.1 M NaAcetate, pH 5.35, 13.5% PEG4000, 24% Glycerol, 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.02 Å / Num. obs: 24803 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 28.45 Å2 / Rsym value: 0.048 / Net I/σ(I): 30.28 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3I65 Resolution: 2.2→38.955 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.955 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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