+Open data
-Basic information
Entry | Database: PDB / ID: 1ev8 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / Cys167 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 / Resolution: 2.6 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 | 1ev8.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ev8.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ev8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1ev8 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1ev8 | 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
#1: Protein | Mass: 30880.197 Da / Num. of mol.: 1 / Mutation: S167C 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: 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: 3.41 Å3/Da / Density % sol: 63.96 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 68% saturated ammonium sulfate, 100 mM sodium phosphate, pH 8.5, 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: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 25, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→6 Å / Num. all: 11991 / Num. obs: 11099 / % possible obs: 92.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 12.27 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 17.05 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.55 / Num. unique all: 410 / % possible all: 31.7 |
Reflection | *PLUS Num. measured all: 136184 |
Reflection shell | *PLUS % possible obs: 31.7 % |
-Processing
Software |
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Refinement | Resolution: 2.6→6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2336470.49 / 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: 137.4 Å2 / ksol: 1.113 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.75 Å / Rfactor Rfree error: 0.034 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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