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Yorodumi- PDB-6a2m: Crystal structure of wild type Plasmodium falciparum DHFR-TS comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a2m | ||||||
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Title | Crystal structure of wild type Plasmodium falciparum DHFR-TS complexed with BT2, NADPH, and dUMP | ||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / Dual-binding Inhibitor | ||||||
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 / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Model details | Crystal structure of wild type Plasmodium falciparum DHFR-TS complexed with BT2, NADPH, and dUMP | ||||||
Authors | Chitnumsub, P. / Jaruwat, A. / Tarnchampoo, B. / Yuthavong, Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Med Chem Lett / Year: 2018 Title: Hybrid Inhibitors of Malarial Dihydrofolate Reductase with Dual Binding Modes That Can Forestall Resistance. Authors: Tarnchompoo, B. / Chitnumsub, P. / Jaruwat, A. / Shaw, P.J. / Vanichtanankul, J. / Poen, S. / Rattanajak, R. / Wongsombat, C. / Tonsomboon, A. / Decharuangsilp, S. / Anukunwithaya, T. / ...Authors: Tarnchompoo, B. / Chitnumsub, P. / Jaruwat, A. / Shaw, P.J. / Vanichtanankul, J. / Poen, S. / Rattanajak, R. / Wongsombat, C. / Tonsomboon, A. / Decharuangsilp, S. / Anukunwithaya, T. / Arwon, U. / Kamchonwongpaisan, S. / Yuthavong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a2m.cif.gz | 256.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a2m.ent.gz | 201.3 KB | Display | PDB format |
PDBx/mmJSON format | 6a2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a2m_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 6a2m_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 6a2m_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 6a2m_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/6a2m ftp://data.pdbj.org/pub/pdb/validation_reports/a2/6a2m | HTTPS FTP |
-Related structure data
Related structure data | 6a2kC 6a2lC 6a2nC 6a2oC 6a2pC 6a7cC 6a7eC 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
-Protein , 1 types, 2 molecules AB
#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) Gene: DHFR-TS, dhfr-ts / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7UD81 |
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-Non-polymers , 5 types, 689 molecules
#2: Chemical | #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: 2.65 Å3/Da / Density % sol: 53.64 % / Mosaicity: 0.433 ° |
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Crystal grow | Temperature: 297 K / Method: microbatch / pH: 4.5 / Details: PEG 4000, NH4OAc |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→30 Å / Num. obs: 77583 / % possible obs: 98.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.034 / Χ2: 0.983 / Net I/σ(I): 20.8 / Num. measured all: 338494 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J3I Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.385 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 120 Å2 / Biso mean: 40.471 Å2 / Biso min: 9.71 Å2
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Refinement step | Cycle: final / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.259 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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