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Yorodumi- PDB-1evg: CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1evg | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI WITH UNMODIFIED CATALYTIC CYSTEINE | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / Thr167 E. coli Thymidylate Synthase with Unmodified Catalytic Cysteine | ||||||
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 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 | 1evg.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1evg.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 1evg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1evg ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1evg | 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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-Components
#1: Protein | Mass: 30725.924 Da / Num. of mol.: 1 / Mutation: S167T Source method: isolated from a genetically manipulated source Details: UNMODIFIED CATALYTIC CYSTEINE / 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: 3.12 Å3/Da / Density % sol: 60.52 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 48% saturated ammonium sulfate, 100 mM Tris HCl, 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: 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 Å / Num. all: 24936 / Num. obs: 24936 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 25.79 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.214 / Num. unique all: 2568 / % possible all: 99.6 |
Reflection shell | *PLUS % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Resolution: 2→6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3556497.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 96.21 Å2 / ksol: 0.996 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.018 / 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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