[English] 日本語
Yorodumi- PDB-3eaw: Replacement of Val3 in Human Thymidylate Synthase Affects Its Kin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eaw | ||||||
---|---|---|---|---|---|---|---|
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 / 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: 1.86 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3eaw.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3eaw.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 3eaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/3eaw ftp://data.pdbj.org/pub/pdb/validation_reports/ea/3eaw | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ebuC 3ed7C 3edwC 3ef9C 3ejlC 3gg5C 3gh0C 3gh2C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35979.211 Da / Num. of mol.: 1 / Mutation: V3Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pTS080 / Production host: Escherichia coli (E. coli) / Strain (production host): TX61- / References: UniProt: P04818, thymidylate synthase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.15 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20-25%ammonium sulfate, 20mM BME, 0.1M Tris PH8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM |
---|---|
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 33751 / % possible obs: 91.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.061 / Χ2: 1.563 / Net I/σ(I): 35.545 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.392 / Num. unique all: 2093 / Χ2: 1 / % possible all: 57.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.277 / WRfactor Rwork: 0.234 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.769 / SU B: 3.777 / SU ML: 0.111 / SU R Cruickshank DPI: 0.141 / SU Rfree: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.21 Å2 / Biso mean: 47.43 Å2 / Biso min: 20.05 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.86→1.908 Å / Total num. of bins used: 20
|