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- PDB-7fgx: Toxoplasma gondii dihydrofolate reductase thymidylate synthase (T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7fgx | ||||||
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Title | Toxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with P39, NADPH and dUMP | ||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
![]() | OXIDOREDUCTASE / Toxoplasma gondii / dihydrofolate reductase / thymidylate synthase / antifolate | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vanichtanankul, J. / Yoomuang, A. / Taweechai, S. / Saeyang, T. / Yuvaniyama, J. / Tarnchompoo, B. / Yuthavong, Y. / Kamchonwongpaisan, S. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 595.9 KB | Display | ![]() |
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PDB format | ![]() | 389.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
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Full document | ![]() | 3.8 MB | Display | |
Data in XML | ![]() | 92.8 KB | Display | |
Data in CIF | ![]() | 130.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fgwC ![]() 7fgyC ![]() 7xi7C ![]() 4eilS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 68842.656 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q07422, dihydrofolate reductase, thymidylate synthase #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-4RI / #4: Chemical | ChemComp-UMP / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.77 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30.065 Å / Num. obs: 170447 / % possible obs: 95.6 % / Redundancy: 2.1 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.407 / Num. unique obs: 16489 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EIL Resolution: 2.05→30.05 Å / SU ML: 0.2404 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.4972 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: 43.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→30.05 Å
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Refine LS restraints |
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LS refinement shell |
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