[English] 日本語
Yorodumi- PDB-6qya: Crystal structure of Enteroccocus faecalis thymidylate synthase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qya | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with dUMP | ||||||||||||
Components | (Thymidylate synthase) x 2 | ||||||||||||
Keywords | TRANSFERASE / Enteroccocus faecalis thymidylate synthase / EfTS / folate pathway / substrate / dUMP | ||||||||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||||||||
Authors | Pozzi, C. / Mangani, M. | ||||||||||||
Citation | Journal: Molecules / Year: 2019 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qya.cif.gz | 530.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qya.ent.gz | 437 KB | Display | PDB format |
PDBx/mmJSON format | 6qya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/6qya ftp://data.pdbj.org/pub/pdb/validation_reports/qy/6qya | HTTPS FTP |
---|
-Related structure data
Related structure data | 6qxgC 6qxhC 6qxsC 3uwlS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 36401.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: thyA, EF_1576 / Production host: Escherichia coli (E. coli) / References: UniProt: Q834R3, thymidylate synthase #2: Protein | Mass: 36462.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: thyA, EF_1576 / Production host: Escherichia coli (E. coli) / References: UniProt: Q834R3, thymidylate synthase |
---|
-Non-polymers , 6 types, 1478 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2-2.5 M ammonium sulfate and 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→73.01 Å / Num. obs: 125005 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 10.4 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.072 / Rrim(I) all: 0.131 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.76→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 18480 / CC1/2: 0.891 / Rpim(I) all: 0.233 / Rrim(I) all: 0.425 / % possible all: 96.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UWL Resolution: 1.76→68.07 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.975 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.674 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→68.07 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|