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- PDB-6qxg: Crystal structure of His-tag human thymidylate synthase (HT-hTS) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6qxg | ||||||
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Title | Crystal structure of His-tag human thymidylate synthase (HT-hTS) in complex with FdUMP | ||||||
![]() | Thymidylate synthase![]() | ||||||
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Function / homology | ![]() uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / response to vitamin A / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pozzi, C. / Mangani, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Comparison ofEnterococcus faecalisand Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities. Authors: Pozzi, C. / Ferrari, S. / Luciani, R. / Tassone, G. / Costi, M.P. / Mangani, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 364.9 KB | Display | ![]() |
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PDB format | ![]() | 303.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qxhC ![]() 6qxsC ![]() 6qyaC ![]() 1hwyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 37168.453 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ChemComp-SO4 / | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 27-30 % wt/vol PEG4000, 30 mM ammonium sulfate and 0.1 M TRIS, pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.08→33.37 Å / Num. obs: 63324 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 37.05 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.048 / Rrim(I) all: 0.103 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.08→2.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2 / Num. unique obs: 9136 / CC1/2: 0.851 / Rpim(I) all: 0.287 / Rrim(I) all: 0.617 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1HWY Resolution: 2.08→32.36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.979 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.168
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.927 Å2
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Refine analyze | Luzzati coordinate error obs: 0.305 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→32.36 Å
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Refine LS restraints |
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