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Yorodumi- PDB-1jut: E. coli Thymidylate Synthase Bound to dUMP and LY338529, A Pyrrol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jut | ||||||
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Title | E. coli Thymidylate Synthase Bound to dUMP and LY338529, A Pyrrolo(2,3-d)pyrimidine-based Antifolate | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / antifolate / dTMP synthesis / cancer / drug resistance | ||||||
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: 2.7 Å | ||||||
Authors | Sayre, P.H. / Finer-Moore, J.S. / Fritz, T.A. / Biermann, D. / Gates, S.B. / MacKellar, W.C. / Patel, V.F. / Stroud, R.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases. Authors: Sayre, P.H. / Finer-Moore, J.S. / Fritz, T.A. / Biermann, D. / Gates, S.B. / MacKellar, W.C. / Patel, V.F. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jut.cif.gz | 121.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jut.ent.gz | 95.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1jut ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1jut | HTTPS FTP |
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-Related structure data
Related structure data | 1jtqC 1jtuC 1ju6C 1jujC 2kceS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 30559.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: THYA / Plasmid: PTHYA-WT / Production host: Escherichia coli (E. coli) / Strain (production host): X2913 / References: UniProt: P0A884, thymidylate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.92 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: KPO4, MgCl2, DTT, EDTA, ammonium sulphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 28, 1998 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 16866 / Num. obs: 16866 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 97881 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.599 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2KCE Resolution: 2.7→29.59 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1797097.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.6405 Å2 / ksol: 0.365014 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→29.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 6.9 % / Rfactor obs: 0.22 / Rfactor Rfree: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.8 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.359 / % reflection Rfree: 6.6 % / Rfactor Rwork: 0.297 |