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Yorodumi- PDB-1j3i: Wild-type Plasmodium falciparum dihydrofolate reductase-thymidyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j3i | ||||||
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Title | Wild-type 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: 2.33 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 | 1j3i.cif.gz | 260.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j3i.ent.gz | 206.5 KB | Display | PDB format |
PDBx/mmJSON format | 1j3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j3i ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j3i | 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: 33133.180 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-280 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, 794 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: 2.71 Å3/Da / Density % sol: 54.25 % | ||||||||||||||||||||||||||||||
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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: 2.33→33 Å / Num. obs: 64441 / % possible obs: 97.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.057 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.33→2.43 Å / Rsym value: 0.313 / % possible all: 89 |
Reflection | *PLUS Lowest resolution: 33 Å / Num. measured all: 653647 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 89 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→29.4 Å / Rfactor Rfree error: 0.004 / 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: 42.9581 Å2 / ksol: 0.322084 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.33→29.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.41 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 29.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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