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- PDB-3qgt: Crystal structure of Wild-type PfDHFR-TS COMPLEXED WITH NADPH, dU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qgt | ||||||
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Title | Crystal structure of Wild-type PfDHFR-TS COMPLEXED WITH NADPH, dUMP AND PYRIMETHAMINE | ||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chitnumsub, P. / Yuthavong, Y. | ||||||
![]() | ![]() Title: Trypanosomal dihydrofolate reductase reveals natural antifolate resistance Authors: Vanichtanankul, J. / Taweechai, S. / Yuvaniyama, J. / Vilaivan, T. / Chitnumsub, P. / Kamchonwongpaisan, S. / Yuthavong, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.2 KB | Display | ![]() |
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PDB format | ![]() | 195.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qfxC ![]() 3qg2C ![]() 3rg9C ![]() 1j3iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 71828.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: TM4 / Gene: DHFR-TS / Plasmid: pET17b / Production host: ![]() ![]() ![]() References: UniProt: A7UD81, ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Sequence details | THE ENTIRE PROTEIN (INCLUDING 2 DOMAINS: REDUCTASE DOMAIN: RESIDUES 1-231; SYNTHASE DOMAIN: ...THE ENTIRE PROTEIN (INCLUDING 2 DOMAINS: REDUCTASE DOMAIN: RESIDUES 1-231; SYNTHASE DOMAIN: RESIDUES 283-608) WAS EXPRESSED IN ONE POLYPEPTID | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.25 % / Mosaicity: 0.604 ° |
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Crystal grow![]() | Temperature: 297 K / Method: microbatch / pH: 4.5 Details: PEG 4000, NH4OAc, pH 4.5, microbatch, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Aug 29, 2004 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 16.03 / Number: 294701 / Rmerge(I) obs: 0.082 / Χ2: 1.55 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 63667 / % possible obs: 99.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 63667 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 33.9 / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.55 / Net I/σ(I): 16.027 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1J3I Resolution: 2.3→44.62 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8204 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 48.7924 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.8 Å2 / Biso mean: 43.0398 Å2 / Biso min: 13.08 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→44.62 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50
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Xplor file |
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