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- PDB-1j3j: Double mutant (C59R+S108N) Plasmodium falciparum dihydrofolate re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j3j | ||||||
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Title | Double mutant (C59R+S108N) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with pyrimethamine, NADPH, and dUMP | ||||||
![]() | (Bifunctional dihydrofolate reductase-thymidylate ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / TRANSFERASE / bifunctional | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Yuvaniyama, J. / Chitnumsub, P. / Kamchonwongpaisan, S. / Vanichtanankul, J. / Sirawaraporn, W. / Taylor, P. / Walkinshaw, M. / Yuthavong, Y. | ||||||
![]() | ![]() Title: Insights into antifolate resistance from malarial DHFR-TS structures. Authors: Yuvaniyama, J. / Chitnumsub, P. / Kamchonwongpaisan, S. / Vanichtanankul, J. / Sirawaraporn, W. / Taylor, P. / Walkinshaw, M.D. / 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 | ![]() | 255.9 KB | Display | ![]() |
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PDB format | ![]() | 203 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 56.3 KB | Display | |
Data in CIF | ![]() | 78.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Bifunctional dihydrofolate reductase-thymidylate ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 33214.254 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-280 / Mutation: C59R, S108N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pLysS / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P13922, dihydrofolate reductase, thymidylate synthase #2: Protein | Mass: 38712.949 Da / Num. of mol.: 2 / Fragment: RESIDUES 281-608 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pLysS / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: P13922, dihydrofolate reductase, thymidylate synthase |
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-Non-polymers , 4 types, 739 molecules ![](data/chem/img/CP6.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/UMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/UMP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 51.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 4.6 Details: PEG 4000, ammonium acetate, sodium acetate, pH 4.6, microbatch under oil, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0414 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→23.83 Å / Num. obs: 62528 / % possible obs: 90.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.063 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Rsym value: 0.24 / % possible all: 77.2 |
Reflection | *PLUS Num. measured all: 214956 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 77.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.0655 Å2 / ksol: 0.35576 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→23.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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