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Yorodumi- PDB-1f4e: CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f4e | ||||||
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Title | CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH TOSYL-D-PROLINE | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / Crystal Structure of E. Coli Thymidylate Synthase Complexed with Tosyl-D-Proline | ||||||
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: 1.9 Å | ||||||
Authors | Erlanson, D.A. / Braisted, A.C. / Raphael, D.R. / Randal, M. / Stroud, R.M. / Gordon, E. / Wells, J.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Site-directed ligand discovery. Authors: Erlanson, D.A. / Braisted, A.C. / Raphael, D.R. / Randal, M. / Stroud, R.M. / Gordon, E.M. / Wells, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f4e.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f4e.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 1f4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f4e_validation.pdf.gz | 504.3 KB | Display | wwPDB validaton report |
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Full document | 1f4e_full_validation.pdf.gz | 509.6 KB | Display | |
Data in XML | 1f4e_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1f4e_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/1f4e ftp://data.pdbj.org/pub/pdb/validation_reports/f4/1f4e | HTTPS FTP |
-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 dimer constructed from chain A and a symmetry partner generated by the two-fold |
-Components
#1: Protein | Mass: 30559.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): C2913 / References: UniProt: P0A884, thymidylate synthase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #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: 3.1 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.0 M ammonium sulphate, 20 mM potassium phosphate, 0.2 M EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: Perry, K.M., (1990) Proteins: Struct.,Funct., Genet., 8, 315. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 1999 |
Radiation | 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→10 Å / Num. all: 31422 / Num. obs: 31422 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2822 / % possible all: 99.5 |
Reflection | *PLUS % possible obs: 100 % / Num. measured all: 202300 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.282 |
-Processing
Software |
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Refinement | Resolution: 1.9→10 Å / SU B: 3.66 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.136 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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