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Yorodumi- PDB-6aoi: Crystal structure of Toxoplasma gondii TS-DHFR complexed with NAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aoi | ||||||
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Title | Crystal structure of Toxoplasma gondii TS-DHFR complexed with NADPH, dUMP, PDDF, and 5-(4-phenylpiperazin-1-yl)-6-propylpyrimidine-2,4-diamine (TRC-2528) | ||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
Keywords | OXIDOREDUCTASE / Toxoplasma gondii / Pyrimethamine / DHFR | ||||||
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 | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å | ||||||
Authors | Thomas, S.B. / Li, Y. / Chen, Z. / Lu, H. | ||||||
Citation | Journal: To Be Published Title: Identification of selective, brain penetrant Toxoplasma gondii dihydrofolate reductase inhibitors for the treatment of toxoplasmosis Authors: Thomas, S.B. / Hopper, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aoi.cif.gz | 225.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aoi.ent.gz | 178.2 KB | Display | PDB format |
PDBx/mmJSON format | 6aoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/6aoi ftp://data.pdbj.org/pub/pdb/validation_reports/ao/6aoi | HTTPS FTP |
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-Related structure data
Related structure data | 6aogC 6aohC 4eilS C: citing same article (ref.) S: Starting model for refinement |
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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: 64214.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: Q07422, dihydrofolate reductase, thymidylate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | |
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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: 2.47 Å3/Da / Density % sol: 50.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 0.2 M ammonium citrate, pH 4.6, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979282 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979282 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→50 Å / Num. obs: 26892 / % possible obs: 91.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.97→3.08 Å / Rmerge(I) obs: 0.596 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4EIL Resolution: 2.97→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / ESU R Free: 0.49
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.287 Å2
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Refinement step | Cycle: 1 / Resolution: 2.97→50 Å
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Refine LS restraints |
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