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Yorodumi- PDB-3bgx: E. coli Thymidylate Synthase C146S mutant complexed with dTMP and MTF -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bgx | ||||||
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Title | E. coli Thymidylate Synthase C146S mutant complexed with dTMP and MTF | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / methyltransferase / Nucleotide biosynthesis / Repressor / RNA-binding / Translation regulation | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.93 Å | ||||||
Authors | Roberts, S.A. / Montfort, W.R. | ||||||
Citation | Journal: To be Published Title: Structural Studies of Early Events in Catalysis by Thymidylate Synthase Authors: Arendall III, W.B. / Roberts, S.A. / Hyatt, D.C. / Weichsel, A. / Dahlgren, A.L. / 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 | 3bgx.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bgx.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bgx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/3bgx ftp://data.pdbj.org/pub/pdb/validation_reports/bg/3bgx | 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: 30543.600 Da / Num. of mol.: 1 / Mutation: C146S 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-MEF / | #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: 56.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.5 M ammonium sulfate, 20 mM KH2PO4, 4MM DTT, 4MM dTMP, 4MM methylene tetrahydrofolate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: Dec 11, 1996 |
Radiation | Monochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 26908 / Num. obs: 26908 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.068 / Net I/σ(I): 7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.93→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.753 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 18.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→1.977 Å / Total num. of bins used: 20
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