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Yorodumi- PDB-6y08: Mouse thymidylate synthase cocrystallized with dUMP and soaked in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y08 | ||||||
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Title | Mouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / Fragment Screening / Fragment / Inhibitor / Thymidylate Synthase | ||||||
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 / thymidylate synthase / response to vitamin A / 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 / thymidylate synthase / response to vitamin A / 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 / response to glucocorticoid / liver regeneration / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / circadian rhythm / response to toxic substance / regulation of translation / methylation / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / mRNA binding / protein homodimerization activity / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å | ||||||
Authors | Maj, P. / Jarmula, A. / Wilk, P. / Weiss, M.S. / Rode, W. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Mouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole Authors: Maj, P. / Jarmula, A. / Wilk, P. / 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 | 6y08.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y08.ent.gz | 97.7 KB | Display | PDB format |
PDBx/mmJSON format | 6y08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y08_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6y08_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6y08_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 6y08_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/6y08 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/6y08 | HTTPS FTP |
-Related structure data
Related structure data | 3ihiS 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: 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: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.43 Å3/Da / Density % sol: 64.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.15M Na/K Tartrate, 22% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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 4, 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: 2.297→49.17 Å / Num. obs: 41996 / % possible obs: 99.4 % / Redundancy: 3.38 % / Biso Wilson estimate: 44.22 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.087 / Net I/σ(I): 12.73 |
Reflection shell | Resolution: 2.297→2.44 Å / Mean I/σ(I) obs: 1.95 / Num. unique obs: 6704 / CC1/2: 0.799 / Rrim(I) all: 0.662 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IHI Resolution: 2.297→49.169 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.67 Å2 / Biso mean: 48.055 Å2 / Biso min: 20.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.297→49.169 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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