+Open data
-Basic information
Entry | Database: PDB / ID: 2ftn | ||||||
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Title | E. coli thymidylate synthase Y94F mutant | ||||||
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 / SYNCHROTRON / Started with coordinates from isomorphous structure IAJM / Resolution: 1.6 Å | ||||||
Authors | Montfort, W.R. / Roberts, S.A. | ||||||
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 | 2ftn.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ftn.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ftn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/2ftn ftp://data.pdbj.org/pub/pdb/validation_reports/ft/2ftn | 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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Details | The biological assembly is a dimer. There is one monomer in the asymetric unit. To generate the second monomer of the dimer, apply the symmetry operation -x,1/2-y,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 | ChemComp-SO4 / #3: 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: 3.08 Å3/Da / Density % sol: 60.03 % |
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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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→11.2 Å / Num. all: 48479 / Num. obs: 48479 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 10 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.1 / Num. unique all: 4865 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Started with coordinates from isomorphous structure IAJM Resolution: 1.6→11.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.397 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS AND TLS REFINEMENT PERFORMED
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.713 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→11.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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