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Yorodumi- PDB-5fi8: Crystal structure of plasmodium falciparum dihydroorotate dehydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fi8 | ||||||
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Title | Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bounded with DSM422 (Tetrahydro-2-naphthyl and 2-indanyl triazolopyrimidine) | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / FMN / alpha/beta barrel / inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE / 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: 2.32 Å | ||||||
Authors | Deng, X. / Kokkonda, S. / Tomchick, D. / Phillips, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: Tetrahydro-2-naphthyl and 2-Indanyl Triazolopyrimidines Targeting Plasmodium falciparum Dihydroorotate Dehydrogenase Display Potent and Selective Antimalarial Activity. Authors: Kokkonda, S. / Deng, X. / White, K.L. / Coteron, J.M. / Marco, M. / de Las Heras, L. / White, J. / El Mazouni, F. / Tomchick, D.R. / Manjalanagara, K. / Rudra, K.R. / Chen, G. / Morizzi, J. ...Authors: Kokkonda, S. / Deng, X. / White, K.L. / Coteron, J.M. / Marco, M. / de Las Heras, L. / White, J. / El Mazouni, F. / Tomchick, D.R. / Manjalanagara, K. / Rudra, K.R. / Chen, G. / Morizzi, J. / Ryan, E. / Kaminsky, W. / Leroy, D. / Martinez-Martinez, M.S. / Jimenez-Diaz, M.B. / Bazaga, S.F. / Angulo-Barturen, I. / Waterson, D. / Burrows, J.N. / Matthews, D. / Charman, S.A. / Phillips, M.A. / Rathod, P.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fi8.cif.gz | 231.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fi8.ent.gz | 186.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fi8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5fi8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5fi8_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5fi8_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/5fi8 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/5fi8 | HTTPS FTP |
-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 / Fragment: UNP residues 158-569 Source method: isolated from a genetically manipulated source Details: Deletion of loop (384-413) Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PFF0160c / Plasmid: pET28b / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q08210, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 5 types, 69 molecules
#2: Chemical | ChemComp-5Y5 / |
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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: 3.28 Å3/Da / Density % sol: 66.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.16 M Ammonium sulfate, 0.1 M NaAcetate, pH 4.2, 9.5% PEG4000 (w/v), 24% Glycerol (v/v), and 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 315 / Detector: CCD / Date: Apr 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→31.5 Å / Num. obs: 25308 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 12.5 % / Rsym value: 0.048 / Net I/σ(I): 43.4 |
Reflection shell | Resolution: 2.32→2.36 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1 / % possible all: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I65 Resolution: 2.32→31.5 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.13 / 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: 2.32→31.5 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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