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Yorodumi- PDB-4isw: Crystal Structure of Phosphorylated C.elegans Thymidylate Synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4isw | ||||||
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Title | Crystal Structure of Phosphorylated C.elegans Thymidylate Synthase in Complex with dUMP | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / PHOSPHOPROTEIN / PROTEIN HOMODIMER / DEOXYNUCLEOTIDE BIOSYNTHESIS / Phosphorylation | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.14 Å | ||||||
Authors | Wilk, P. / Dowiercial, A. / Banaszak, K. / Jarmula, A. / Rypniewski, W. / Rode, W. | ||||||
Citation | Journal: Bioorg.Chem. / Year: 2013 Title: Crystal structure of phosphoramide-phosphorylated thymidylate synthase reveals pSer127, reflecting probably pHis to pSer phosphotransfer. Authors: Wilk, P. / Jarmua, A. / Ruman, T. / Banaszak, K. / Rypniewski, W. / Ciesla, J. / Dowiercia, A. / Rode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4isw.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4isw.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 4isw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/4isw ftp://data.pdbj.org/pub/pdb/validation_reports/is/4isw | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 35935.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pPIGDM4+stop / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y052, thymidylate synthase #2: Chemical | #3: 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: 5.51 Å3/Da / Density % sol: 77.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 0.2M (NH4)2SO4, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Date: Dec 2, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.14→50 Å / Num. obs: 27888 / % possible obs: 99.1 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.15 / Χ2: 1.022 / Net I/σ(I): 6.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→38.52 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.2256 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8101 / SU B: 15.432 / SU ML: 0.27 / SU R Cruickshank DPI: 0.6033 / SU Rfree: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.603 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 140.6 Å2 / Biso mean: 58.5263 Å2 / Biso min: 13.31 Å2
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Refinement step | Cycle: LAST / Resolution: 3.14→38.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.14→3.223 Å / Total num. of bins used: 20
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