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Yorodumi- 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 | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / human thymidylate synthase / folate pathway / inhibitor / FdUMP | ||||||
| Function / homology | Function and homology informationthymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription ...thymidylate synthase / Interconversion of nucleotide di- and triphosphates / sequence-specific mRNA binding / folic acid binding / thymidylate synthase activity / tetrahydrofolate interconversion / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / mRNA regulatory element binding translation repressor activity / methylation / negative regulation of translation / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Pozzi, C. / Mangani, M. | ||||||
| Funding support | 1items
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Citation | Journal: Molecules / Year: 2019Title: 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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6qxg.cif.gz | 364.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6qxg.ent.gz | 303.6 KB | Display | PDB format |
| PDBx/mmJSON format | 6qxg.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/6qxg ftp://data.pdbj.org/pub/pdb/validation_reports/qx/6qxg | 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.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pQE80L / Production host: ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
| 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: 0.97625 Å / Relative weight: 1 |
| 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: MOLECULAR REPLACEMENTStarting 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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