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Yorodumi- PDB-1jtu: E. coli Thymidylate Synthase in a Complex with dUMP and LY338913,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jtu | ||||||
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Title | E. coli Thymidylate Synthase in a Complex with dUMP and LY338913, A Polyglutamylated Pyrrolo(2,3-d)pyrimidine-based Antifolate | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / antifolate / dTMP synthesis / cancer / drug resistance / polyglutamylation | ||||||
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: 2.2 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. #1: Journal: Biochemistry / Year: 1992 Title: Structural Basis for Recognition of Polyglutamyl Folates by Thymidylate Synthase Authors: Kamb, A. / Finer-Moore, J. / Calvert, A.H. / Stroud, R.M. #2: Journal: Biochemistry / Year: 1995 Title: Crystal Structure of Human Thymidylate Synthase: A Structural Mechanism for Guiding Substrates into the Active Site Authors: Schiffer, C.A. / Clifton, I.J. / Davisson, V.J. / Santi, D.V. / 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 | 1jtu.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jtu.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jtu ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jtu | HTTPS FTP |
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-Related structure data
Related structure data | 1jtqC 1ju6C 1jujC 1jutC 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: 2.61 Å3/Da / Density % sol: 52.94 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: potassium phosphate, MgCl2, ammonium sulfate, DTT, EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 17, 1997 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 30601 / Num. obs: 30601 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.2 / % possible all: 84 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2KCE Resolution: 2.2→32.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 240066.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.9922 Å2 / ksol: 0.299744 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→32.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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