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Yorodumi- PDB-4cqa: Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cqa | ||||||
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Title | Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with IDI-6273 | ||||||
Components | DIHYDROOROTATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / DHODH | ||||||
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 / nucleotide binding / plasma membrane Similarity search - Function | ||||||
Biological species | PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.82 Å | ||||||
Authors | Rowland, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: In Vitro Resistance Selections for Plasmodium Falciparum Dihydroorotate Dehydrogenase Inhibitors Give Mutants with Multiple Point Mutations in the Drug-Binding Site and Altered Growth. Authors: Ross, L.S. / Javier Gamo, F. / Lafuente-Monasterio, M.J.E. / Singh, O.M.P. / Rowland, P. / Wiegand, R.C. / Wirth, D.F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cqa.cif.gz | 318 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cqa.ent.gz | 258.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cqa_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4cqa_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4cqa_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 4cqa_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/4cqa ftp://data.pdbj.org/pub/pdb/validation_reports/cq/4cqa | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45385.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESIDUES 384-413 DELETED Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q54A96, UniProt: Q08210*PLUS, EC: 1.3.3.1 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.92 Å3/Da / Density % sol: 57.83 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: CO-CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20 DEGREES C FROM A SOLUTION OF PROTEIN AT 10 MG/ML IN BUFFER (10 MM HEPES PH 7.8, 100 MM SODIUM CHLORIDE, 5% GLYCEROL, 10 MM DTT, 1 MM LDAO) ...Details: CO-CRYSTALS WERE GROWN BY VAPOUR DIFFUSION AT 20 DEGREES C FROM A SOLUTION OF PROTEIN AT 10 MG/ML IN BUFFER (10 MM HEPES PH 7.8, 100 MM SODIUM CHLORIDE, 5% GLYCEROL, 10 MM DTT, 1 MM LDAO) CONTAINING 2 MM L-DIHYDROOROTATE, 2 MM GENZ-669178, 10 MM LDAO, MIXED WITH AN EQUAL VOLUME OF PRECIPITANT (20% PEG 3350, 0.1M MES PH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→166.41 Å / Num. obs: 24603 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 72.58 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 0 |
Reflection shell | Resolution: 2.82→2.82 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.82→60.1 Å / Cor.coef. Fo:Fc: 0.9301 / Cor.coef. Fo:Fc free: 0.8899 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.366 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 67.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.354 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→60.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→2.97 Å / Total num. of bins used: 10
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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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