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Yorodumi- PDB-7fgy: Toxoplasma gondii dihydrofolate reductase thymidylate synthase (T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fgy | ||||||
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Title | Toxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with P40, NADPH and dUMP | ||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
Keywords | OXIDOREDUCTASE / Toxoplasma gondii / dihydrofolate reductase / thymidylate synthase / antifolate | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Vanichtanankul, J. / Yoomuang, A. / Taweechai, S. / Saeyang, T. / Yuvaniyama, J. / Tarnchompoo, B. / Yuthavong, Y. / Kamchonwongpaisan, S. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: Structural Insight into Effective Inhibitors' Binding to Toxoplasma gondii Dihydrofolate Reductase Thymidylate Synthase. Authors: Vanichtanankul, J. / Yoomuang, A. / Taweechai, S. / Saeyang, T. / Pengon, J. / Yuvaniyama, J. / Tarnchompoo, B. / Yuthavong, Y. / Kamchonwongpaisan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fgy.cif.gz | 572.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fgy.ent.gz | 376.8 KB | Display | PDB format |
PDBx/mmJSON format | 7fgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fgy_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 7fgy_full_validation.pdf.gz | 3.8 MB | Display | |
Data in XML | 7fgy_validation.xml.gz | 86.8 KB | Display | |
Data in CIF | 7fgy_validation.cif.gz | 116.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fgy ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fgy | HTTPS FTP |
-Related structure data
Related structure data | 7fgwC 7fgxC 7xi7C 4eilS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 68842.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q07422, dihydrofolate reductase, thymidylate synthase #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-4TS / #4: Chemical | ChemComp-UMP / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.68 Å3/Da / Density % sol: 54.18 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium nitrate, 14% (w/v) PEG4000 and 0.1 M Bis-Tris propane pH 7.5, 2.5% Benzamidine HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→50 Å / Num. obs: 77348 / % possible obs: 96.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 40.08 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.274 / Num. unique obs: 7612 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EIL Resolution: 2.67→41.04 Å / SU ML: 0.341 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.6253 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.67→41.04 Å
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Refine LS restraints |
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LS refinement shell |
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