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Yorodumi- PDB-2rd8: Human Thymidylate Synthase Stabilized in Active Conformation by R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rd8 | ||||||
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Title | Human Thymidylate Synthase Stabilized in Active Conformation by R163K Mutation: Asymmetry and Reactivity of Cys195 | ||||||
Components | (Thymidylate synthase) x 2 | ||||||
Keywords | TRANSFERASE / METHYL TRANSFERASE / Methyltransferase / Nucleotide biosynthesis | ||||||
Function / homology | Function and homology information uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A / thymidylate synthase / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / 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 / DNA biosynthetic process / G1/S-Specific Transcription / 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 / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Gibson, L.M. / Lovelace, L.L. / Lebioda, L. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: The R163K Mutant of Human Thymidylate Synthase Is Stabilized in an Active Conformation: Structural Asymmetry and Reactivity of Cysteine 195. Authors: Gibson, L.M. / Lovelace, L.L. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rd8.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rd8.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 2rd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/2rd8 ftp://data.pdbj.org/pub/pdb/validation_reports/rd/2rd8 | HTTPS FTP |
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-Related structure data
Related structure data | 2rdaC 1hvyS 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: 35734.926 Da / Num. of mol.: 1 / Mutation: R163K Source method: isolated from a genetically manipulated source Details: CYS at position 195 / Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase | ||
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#2: Protein | Mass: 35811.039 Da / Num. of mol.: 1 / Mutation: R163K Source method: isolated from a genetically manipulated source Details: CME at position 195 / Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS / Production host: Escherichia coli (E. coli) / References: UniProt: P04818, thymidylate synthase | ||
#3: Chemical | ChemComp-BME / | ||
#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: 3.82 Å3/Da / Density % sol: 67.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 10-20% PEG 4000, 3mM potassium phosphate, 20mM 2-mercaptoethanol, 0.1M TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97243 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97243 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→33.8 Å / Num. obs: 30034 / % possible obs: 69.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.138 / Χ2: 1.708 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 7.8 / Num. unique all: 651 / Χ2: 0.693 / % possible all: 15.3 |
-Processing
Software |
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Refinement | Starting model: 1HVY Resolution: 2.5→33.8 Å / FOM work R set: 0.774 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 25.192 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.036 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→33.8 Å
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Refine LS restraints |
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Xplor file |
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