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Yorodumi- PDB-2fto: Y94F mutant of thymidylate synthase bound to thymidine-5'-phospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fto | ||||||
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Title | Y94F mutant of thymidylate synthase bound to thymidine-5'-phosphate and 10-propargyl-5,8-dideazafolid acid | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / methyltransferase | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Started with coordinates from isomorphous structure 1TSN / Resolution: 2 Å | ||||||
Authors | Roberts, S.A. / Montfort, W.R. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006 Title: Structure of the Y94F mutant of Escherichia coli thymidylate synthase. Authors: Roberts, S.A. / Hyatt, D.C. / Honts, J.E. / Changchien, L. / Maley, G.F. / Maley, F. / Montfort, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fto.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fto.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 2fto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/2fto ftp://data.pdbj.org/pub/pdb/validation_reports/ft/2fto | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer. There is a monomer in the asymmetric unit. The second monomer can be generated using the symmetry operation x-y,-y,2/3-z |
-Components
#1: Protein | Mass: 30543.666 Da / Num. of mol.: 1 / Mutation: Y94F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: thyA / Plasmid: BLUSCRIPT SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): Xac25 Thy / References: UniProt: P0A884, thymidylate synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TMP / | #4: Chemical | ChemComp-CB3 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.5 M ammonium sulfate, 20 mM KH2PO4, 4 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 17, 1996 / Details: graphite monochromator |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 24431 / Num. obs: 24431 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.069 |
-Processing
Software |
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Refinement | Method to determine structure: Started with coordinates from isomorphous structure 1TSN Resolution: 2→8.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.94 / SU ML: 0.083 / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 24.703 Å2
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Refinement step | Cycle: LAST / Resolution: 2→8.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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