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Yorodumi- PDB-4dpd: WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dpd | ||||||
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Title | WILD TYPE PLASMODIUM FALCIPARUM DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE (PfDHFR-TS), DHF COMPLEX, NADP+, dUMP | ||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
Keywords | OXIDOREDUCTASE / TRANSFERASE / DHFR / Rossmann fold / Reductase / NADPH binding | ||||||
Function / homology | Function and homology information thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / nucleotide binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Yuthavong, Y. / Vilaivan, T. / Kamchonwongpaisan, S. / Charman, S.A. / McLennan, D.N. / White, K.L. / Vivas, L. / Bongard, E. / Chitnumsub, P. / Tarnchompoo, B. ...Yuthavong, Y. / Vilaivan, T. / Kamchonwongpaisan, S. / Charman, S.A. / McLennan, D.N. / White, K.L. / Vivas, L. / Bongard, E. / Chitnumsub, P. / Tarnchompoo, B. / Thongphanchang, C. / Taweechai, S. / Vanichtanakul, J. / Arwon, U. / Fantauzzi, P. / Yuvaniyama, J. / Charman, W.N. / Matthews, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target Authors: Yuthavong, Y. / Tarnchompoo, B. / Vilaivan, T. / Chitnumsub, P. / Kamchonwongpaisan, S. / Charman, S.A. / McLennan, D.N. / White, K.L. / Vivas, L. / Bongard, E. / Thongphanchang, C. / ...Authors: Yuthavong, Y. / Tarnchompoo, B. / Vilaivan, T. / Chitnumsub, P. / Kamchonwongpaisan, S. / Charman, S.A. / McLennan, D.N. / White, K.L. / Vivas, L. / Bongard, E. / Thongphanchang, C. / Taweechai, S. / Vanichtanankul, J. / Rattanajak, R. / Arwon, U. / Fantauzzi, P. / Yuvaniyama, J. / Charman, W.N. / Matthews, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dpd.cif.gz | 242.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dpd.ent.gz | 192.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/4dpd ftp://data.pdbj.org/pub/pdb/validation_reports/dp/4dpd | HTTPS FTP |
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-Related structure data
Related structure data | 4ddrC 4dp3C 4dphC 1j3iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: TM4 / Gene: DHFR-TS / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7UD81, dihydrofolate reductase #2: Chemical | ChemComp-DHF / | #3: Chemical | ChemComp-NAP / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE ENTIRE PROTEIN (REDUCTASE DOMAIN: RESIDUES 1-231; SYNTHASE DOMAIN: RESIDUES 283-608) WAS ...THE ENTIRE PROTEIN (REDUCTASE DOMAIN: RESIDUES 1-231; SYNTHASE DOMAIN: RESIDUES 283-608) WAS EXPRESSED IN ONE POLYPEPTID | |
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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: 2.61 Å3/Da / Density % sol: 52.95 % |
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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: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Oct 29, 2004 / Details: mirrors |
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: 2.5→49.82 Å / Num. obs: 53309 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8344 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1J3I Resolution: 2.5→49.82 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.878 / SU B: 8.741 / SU ML: 0.198 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.47 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.262 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→49.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Xplor file |
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