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Yorodumi- PDB-4ky8: Crystal structure of TS-DHFR from Cryptosporidium hominis in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ky8 | ||||||
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Title | Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, methotrexate, FdUMP and 4-((2-amino-6-methyl-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)thio)-2-chlorophenyl)-L-glutamic acid | ||||||
Components | Bifunctional thymidylate synthase-dihydrofolate reductase | ||||||
Keywords | TRANSFERASE / OXIDOREDUCTASE/INHIBITOR / bifunctional enzyme / oxidoreductase / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Cryptosporidium hominis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.084 Å | ||||||
Authors | Kumar, V.P. / Anderson, K.S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Substituted pyrrolo[2,3-d]pyrimidines as Cryptosporidium hominis thymidylate synthase inhibitors. Authors: Kumar, V.P. / Frey, K.M. / Wang, Y. / Jain, H.K. / Gangjee, A. / Anderson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ky8.cif.gz | 524.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ky8.ent.gz | 435 KB | Display | PDB format |
PDBx/mmJSON format | 4ky8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ky8_validation.pdf.gz | 5.4 MB | Display | wwPDB validaton report |
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Full document | 4ky8_full_validation.pdf.gz | 5.5 MB | Display | |
Data in XML | 4ky8_validation.xml.gz | 95.3 KB | Display | |
Data in CIF | 4ky8_validation.cif.gz | 117.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/4ky8 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/4ky8 | HTTPS FTP |
-Related structure data
Related structure data | 1qzfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 60262.520 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Gene: Chro.40506, TS-DHFR / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): PA414 References: UniProt: Q5CGA3, thymidylate synthase, dihydrofolate reductase #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-UFP / #4: Chemical | ChemComp-MTX / #5: Chemical | ChemComp-1UF / |
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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: 4.48 Å3/Da / Density % sol: 72.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14% (w/v) PEG 6000, 60 mM ammonium sulfate, 200 mM lithium sulfate and 100 mM Tris pH 8.0. ChTS-DHFR enzyme (~ 7 mg/ml) with 1 mM NADPH, 1 mM MTX, 1 mM FdUMP and 0.5 mM inhibitor., VAPOR ...Details: 14% (w/v) PEG 6000, 60 mM ammonium sulfate, 200 mM lithium sulfate and 100 mM Tris pH 8.0. ChTS-DHFR enzyme (~ 7 mg/ml) with 1 mM NADPH, 1 mM MTX, 1 mM FdUMP and 0.5 mM inhibitor., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2013 / Details: monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally focusing at 3.3:1 demagnification Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.08→48.12 Å / Num. obs: 70173 / % possible obs: 71.6 % / Observed criterion σ(F): 1.5 / Redundancy: 3 % / Biso Wilson estimate: 70.12 Å2 / Rmerge(I) obs: 0.207 / Rsym value: 0.207 / Net I/σ(I): 4.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QZF Resolution: 3.084→48.12 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 29.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.3969 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.084→48.12 Å
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Refine LS restraints |
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LS refinement shell |
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