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Yorodumi- PDB-6gko: Mouse thymidylate synthase cocrystallized with dUMP and soaked in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gko | ||||||
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Title | Mouse thymidylate synthase cocrystallized with dUMP and soaked in phenolphthalein | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / fragment screening / fragment / inhibitor | ||||||
Function / homology | Function and homology information Interconversion of nucleotide di- and triphosphates / uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...Interconversion of nucleotide di- and triphosphates / uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / heterocyclic compound binding / developmental growth / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to progesterone / response to cytokine / liver regeneration / response to toxic substance / circadian rhythm / regulation of translation / methylation / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / mRNA binding / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å | ||||||
Authors | Maj, P. / Wilk, P. / Jarmula, A. / Weiss, M.S. / Rode, W. | ||||||
Citation | Journal: To Be Published Title: Thymidylate synthase fragment screening Authors: Maj, P. / Wilk, P. / Jarmula, A. / Weiss, M.S. / Rode, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gko.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gko.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 6gko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/6gko ftp://data.pdbj.org/pub/pdb/validation_reports/gk/6gko | HTTPS FTP |
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-Related structure data
Related structure data | 6gyjC 3ihiS S: Starting model for refinement C: citing same article (ref.) |
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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: 35001.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tyms / Production host: Escherichia coli (E. coli) / References: UniProt: P07607, thymidylate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 3.42 Å3/Da / Density % sol: 64.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.15M Na/K Tartrate, 22% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.839→45.494 Å / Num. obs: 80859 / % possible obs: 98.8 % / Redundancy: 3.39 % / CC1/2: 0.998 / Rrim(I) all: 0.066 / Net I/σ(I): 12.56 |
Reflection shell | Resolution: 1.839→1.95 Å / Num. unique obs: 12387 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ihi Resolution: 1.839→45.494 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.839→45.494 Å
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Refine LS restraints |
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LS refinement shell |
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