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- PDB-3irn: Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase CO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3irn | ||||||
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Title | Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase COMPLEXED WITH NADPH AND Cycloguanil | ||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
![]() | OXIDOREDUCTASE / TRANSFERASE / Trypanosoma cruzi / DHFR-TS antifolate complex / Methyltransferase / Multifunctional enzyme / NADP / Nucleotide biosynthesis / One-carbon metabolism | ||||||
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 | ![]() ![]() | ||||||
![]() | Chitnumsub, P. / Yuvaniyama, J. / Yuthavong, Y. | ||||||
![]() | ![]() Title: Structural basis of antifolate inhibition of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase Authors: Chitnumsub, P. / Yuvaniyama, J. / Vilaivan, T. / Vanichtanankul, J. / 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 | ![]() | 416.9 KB | Display | ![]() |
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PDB format | ![]() | 340 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 83.6 KB | Display | |
Data in CIF | ![]() | 110.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3invC ![]() 3irmSC ![]() 3iroC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 58928.121 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q27793, dihydrofolate reductase, thymidylate synthase #2: Chemical | ChemComp-1CY / #3: Chemical | ChemComp-NDP / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow | Temperature: 297 K / Method: microbatch / pH: 5.6 Details: PEG4000, NH4OAc, pH 5.6, microbatch, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Kappa CCD / Detector: CCD / Date: Mar 16, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→44.48 Å / Num. all: 59449 / Num. obs: 59498 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 45 Å2 / Limit h max: 26 / Limit h min: -30 / Limit k max: 63 / Limit k min: -30 / Limit l max: 32 / Limit l min: 0 / Observed criterion F max: 2047492.86 / Observed criterion F min: 21.6 / Rsym value: 0.073 / Χ2: 1.201 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Num. unique all: 5192 / Rsym value: 0.296 / Χ2: 1.474 / % possible all: 82.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: The partial structure of 3IRM Resolution: 2.6→44.48 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 28.3081 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.37 Å2 / Biso mean: 33.46 Å2 / Biso min: 2.37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→44.48 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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