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Yorodumi- PDB-3ebu: Replacement of Val3 in Human Thymidylate Synthase Affects Its Kin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ebu | ||||||
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Title | Replacement of Val3 in Human Thymidylate Synthase Affects Its Kinetic Properties and Intracellular Stability | ||||||
Components | Thymidylate synthase | ||||||
Keywords | 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 / 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: 2.05 Å | ||||||
Authors | Huang, X. / Gibson, L.M. / Bell, B.J. / Lovelace, L.L. / Pena, M.M. / Berger, F.G. / Berger, S.H. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Replacement of Val3 in human thymidylate synthase affects its kinetic properties and intracellular stability . Authors: Huang, X. / Gibson, L.M. / Bell, B.J. / Lovelace, L.L. / Pena, M.M. / Berger, F.G. / Berger, S.H. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ebu.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ebu.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 3ebu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/3ebu ftp://data.pdbj.org/pub/pdb/validation_reports/eb/3ebu | HTTPS FTP |
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-Related structure data
Related structure data | 3eawC 3ed7C 3edwC 3ef9C 3ejlC 3gg5C 3gh0C 3gh2C 1hw3S 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: 35993.262 Da / Num. of mol.: 1 / Mutation: V3T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OK/SW-cl.29, TS, TYMS / Plasmid: PTSO80 / Production host: Escherichia coli (E. coli) / Strain (production host): TX61- / References: UniProt: P04818, thymidylate synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: 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: 3.01 Å3/Da / Density % sol: 59.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris PH8.5, 35-40%ammonium sulfate, 20mM BME, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 26097 / % possible obs: 95.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Χ2: 3.573 / Net I/σ(I): 49.95 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.224 / Num. unique all: 2084 / Χ2: 2.575 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1HW3 Resolution: 2.05→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.793 / σ(F): 0
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Solvent computation | Bsol: 76.014 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.2 Å2 / Biso mean: 59.635 Å2 / Biso min: 30.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å | ||||||||||||||||||||||||||||||||||||
Xplor file |
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