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Yorodumi- PDB-4ky4: Crystal structure of non-classical TS inhibitor 2 in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ky4 | ||||||
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Title | Crystal structure of non-classical TS inhibitor 2 in complex with Toxoplasma gondii TS-DHFR | ||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | ||||||
Keywords | OXIDOREDUCTASE / TRANSFERASE / synthase / 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 / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Sharma, H. / Anderson, K.S. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2013 Title: Discovery of potent and selective inhibitors of Toxoplasma gondii thymidylate synthase for opportunistic infections. Authors: Zaware, N. / Sharma, H. / Yang, J. / Devambatla, R.K. / Queener, S.F. / Anderson, K.S. / Gangjee, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ky4.cif.gz | 804.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ky4.ent.gz | 664.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ky4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ky4_validation.pdf.gz | 8.7 MB | Display | wwPDB validaton report |
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Full document | 4ky4_full_validation.pdf.gz | 8.6 MB | Display | |
Data in XML | 4ky4_validation.xml.gz | 149.4 KB | Display | |
Data in CIF | 4ky4_validation.cif.gz | 190.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/4ky4 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/4ky4 | HTTPS FTP |
-Related structure data
Related structure data | 4kyaC 4eilS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 68842.656 Da / Num. of mol.: 8 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 | ChemComp-UMP / #3: Chemical | ChemComp-04J / #4: Chemical | ChemComp-NDP / #5: Chemical | ChemComp-1UE / |
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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: 2.49 Å3/Da / Density % sol: 50.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 18% PEG 3350, 0.1 M Potassium Formate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | |||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2012 | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.79→48.28 Å / Num. all: 128608 / Num. obs: 121332 / % possible obs: 94.34 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EIL Resolution: 2.79→48.28 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.42 / SU B: 16.948 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.395 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 202.23 Å2 / Biso mean: 79.025 Å2 / Biso min: 42.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→48.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.793→2.866 Å / Total num. of bins used: 20
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