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- PDB-2tsr: THYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX -
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Open data
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Basic information
Entry | Database: PDB / ID: 2tsr | ||||||
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Title | THYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX | ||||||
![]() | THYMIDYLATE SYNTHASE | ||||||
![]() | METHYLTRANSFERASE / THYMIDYLATE SYNTHASE / DUMP / TOMUDEX / ANTIFOLATE | ||||||
Function / homology | ![]() Interconversion of nucleotide di- and triphosphates / pyrimidine nucleobase metabolic process / uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / tetrahydrofolate metabolic process / response to folic acid / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding ...Interconversion of nucleotide di- and triphosphates / pyrimidine nucleobase metabolic process / uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / tetrahydrofolate metabolic process / 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 / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to organic cyclic compound / response to toxic substance / circadian rhythm / regulation of translation / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / mRNA binding / protein homodimerization activity / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sotelo-Mundo, R.R. / Ciesla, J. / Dzik, J.M. / Rode, W. / Maley, F. / Maley, G. / Hardy, L.W. / Montfort, W.R. | ||||||
![]() | ![]() Title: Crystal structures of rat thymidylate synthase inhibited by Tomudex, a potent anticancer drug. Authors: Sotelo-Mundo, R.R. / Ciesla, J. / Dzik, J.M. / Rode, W. / Maley, F. / Maley, G.F. / Hardy, L.W. / Montfort, W.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.4 KB | Display | ![]() |
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PDB format | ![]() | 192.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 41.9 KB | Display | |
Data in CIF | ![]() | 54.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35060.023 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-UMP / #3: Chemical | ChemComp-D16 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop contained 1:1 mixture of protein and reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jan 1, 1998 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→8 Å / Num. obs: 35484 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.24 / % possible all: 71 |
Reflection shell | *PLUS % possible obs: 71 % / Rmerge(I) obs: 0.214 |
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Processing
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Refinement | Method to determine structure: ![]() Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED.
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Displacement parameters | Biso mean: 36.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.64 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.241 |