+Open data
-Basic information
Entry | Database: PDB / ID: 1ev5 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF ALA167 MUTANT OF ESCHERICHIA COLI | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / Ala167 E. coli Thymidylate Synthase | ||||||
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 / Resolution: 1.7 Å | ||||||
Authors | Phan, J. / Mahdavian, E. / Nivens, M.C. / Minor, W. / Berger, S. / Spencer, H.T. / Dunlap, R.B. / Lebioda, L. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Catalytic cysteine of thymidylate synthase is activated upon substrate binding. Authors: Phan, J. / Mahdavian, E. / Nivens, M.C. / Minor, W. / Berger, S. / Spencer, H.T. / Dunlap, R.B. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ev5.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ev5.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ev5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1ev5 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1ev5 | 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 monomer. |
-Components
#1: Protein | Mass: 30772.014 Da / Num. of mol.: 1 / Mutation: S167A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBLUESCRIPT SK / Production host: Escherichia coli (E. coli) / References: UniProt: P0A884, thymidylate synthase | ||
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#2: Chemical | #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: 3.15 Å3/Da / Density % sol: 60.92 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 38% saturated ammonium sulfate, 100 mM Tris HCl, 40 mM sodium phosphate, 20 mM 2-mercaptoethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 18K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 138 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID |
Detector | Type: OTHER / Detector: CCD / Date: Nov 25, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→6 Å / Num. all: 41533 / Num. obs: 41527 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 11.07 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 46.57 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.45 / Num. unique all: 4184 / % possible all: 0.62 |
Reflection | *PLUS Highest resolution: 1.7 Å / % possible obs: 99.9 % / Num. measured all: 459585 |
-Processing
Software |
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Refinement | Resolution: 1.7→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3046599.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 1
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 104.9 Å2 / ksol: 0.851 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.8 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 3 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.235 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.215 |