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Yorodumi- PDB-6r2e: Crystal structure of the human thymidylate synthase (hTS) interfa... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 6r2e | ||||||
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| Title | Crystal structure of the human thymidylate synthase (hTS) interface variant Q62R | ||||||
Components | (Thymidylate synthase) x 2 | ||||||
Keywords | TRANSFERASE / human thymidylate synthase / folate pathway / Q62R / interface variant | ||||||
| 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 / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Pozzi, C. / Mangani, M. | ||||||
| Funding support | Italy, 1items
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Citation | Journal: Biomolecules / Year: 2019Title: Evidence of Destabilization of the Human Thymidylate Synthase (hTS) Dimeric Structure Induced by the Interface Mutation Q62R. Authors: Pozzi, C. / Lopresti, L. / Santucci, M. / 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 | 6r2e.cif.gz | 997.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6r2e.ent.gz | 835.3 KB | Display | PDB format |
| PDBx/mmJSON format | 6r2e.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6r2e_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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| Full document | 6r2e_full_validation.pdf.gz | 2.6 MB | Display | |
| Data in XML | 6r2e_validation.xml.gz | 118.5 KB | Display | |
| Data in CIF | 6r2e_validation.cif.gz | 165.8 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/6r2e ftp://data.pdbj.org/pub/pdb/validation_reports/r2/6r2e | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 1hvyS S: Starting model for refinement |
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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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| 4 | ![]()
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| Unit cell |
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Components
-Protein , 2 types, 8 molecules ACDBFHEG
| #1: Protein | Mass: 37349.754 Da / Num. of mol.: 6 / Mutation: Q62R 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: Protein | Mass: 37319.730 Da / Num. of mol.: 2 / Mutation: Q62R 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: ![]() |
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-Non-polymers , 5 types, 2465 molecules 








| #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-FFO / #5: Chemical | ChemComp-CL / #6: Chemical | #7: 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: 4.18 Å3/Da / Density % sol: 70.56 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 2.0-2.2 M ammonium sulfate, 0.1 M bicine pH 9.0 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.96861 Å |
| Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2017 |
| Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.96861 Å / Relative weight: 1 |
| Reflection | Resolution: 2.55→94.99 Å / Num. obs: 145044 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 26.83 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.072 / Rrim(I) all: 0.178 / Net I/σ(I): 6.9 |
| Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 20911 / CC1/2: 0.83 / Rpim(I) all: 0.334 / Rrim(I) all: 0.782 / % possible all: 99.6 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 1HVY Resolution: 2.55→94.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 16.576 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.264
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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: 44.012 Å2
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| Refine analyze | Luzzati coordinate error obs: 0.334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.55→94.99 Å
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| Refine LS restraints |
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Homo sapiens (human)
X-RAY DIFFRACTION
Italy, 1items
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