[English] 日本語
Yorodumi- PDB-6r2e: Crystal structure of the human thymidylate synthase (hTS) interfa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r2e | ||||||
---|---|---|---|---|---|---|---|
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 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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Pozzi, C. / Mangani, M. | ||||||
Funding support | Italy, 1items
| ||||||
Citation | Journal: Biomolecules / Year: 2019 Title: 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6r2e.cif.gz | 997.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
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
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 |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04818, thymidylate synthase #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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04818, thymidylate synthase |
---|
-Non-polymers , 5 types, 2465 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-FFO / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.56 % |
---|---|
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 |
---|---|
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→94.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|