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Yorodumi- PDB-1j3k: Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j3k | ||||||
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Title | Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with WR99210, NADPH, and dUMP | ||||||
Components | (Bifunctional dihydrofolate reductase-thymidylate ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / TRANSFERASE / bifunctional | ||||||
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 Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yuvaniyama, J. / Chitnumsub, P. / Kamchonwongpaisan, S. / Vanichtanankul, J. / Sirawaraporn, W. / Taylor, P. / Walkinshaw, M. / Yuthavong, Y. | ||||||
Citation | Journal: NAT.STRUCT.BIOL. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j3k.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j3k.ent.gz | 215 KB | Display | PDB format |
PDBx/mmJSON format | 1j3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j3k ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j3k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Bifunctional dihydrofolate reductase-thymidylate ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 33213.309 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-280 / Mutation: N51I, C59R, S108N, I164L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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.) Plasmodium falciparum (malaria parasite P. falciparum) Plasmid: pLysS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P13922, dihydrofolate reductase, thymidylate synthase |
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-Non-polymers , 4 types, 1253 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 53.26 % | ||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→33 Å / Num. obs: 90060 / % possible obs: 97.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.055 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.09→2.14 Å / Rsym value: 0.28 / % possible all: 90.4 |
Reflection | *PLUS Lowest resolution: 33 Å / Num. measured all: 661139 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 90.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.98 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.891 Å2 / ksol: 0.363339 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.16 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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