[English] 日本語
Yorodumi- PDB-7ll0: Crystal structure of a four-tetrad, parallel, and K+ stabilized T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ll0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a four-tetrad, parallel, and K+ stabilized Tetrahymena thermophila telomeric G-quadruplex | |||||||||
Components | 26-mer DNA | |||||||||
Keywords | DNA / G-quadruplex / Parallel / Four-quartets / propeller loops | |||||||||
Function / homology | : / DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Yatsunyk, L.A. / Chen, E.V. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes. Authors: Beseiso, D. / Chen, E.V. / McCarthy, S.E. / Martin, K.N. / Gallagher, E.P. / Miao, J. / Yatsunyk, L.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ll0.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ll0.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ll0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/7ll0 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/7ll0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6w9pC 6xt7C 7jkuSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: DNA chain | Mass: 8289.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote) | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-K / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32 % / Description: Irregular clamshell shaped crystals. |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: sodium cacodylate, KCl, PEG, NaCl, ethylene glycol |
-Data collection
Diffraction | Mean temperature: 196 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→53.25 Å / Num. obs: 4313 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 63.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.025 / Rrim(I) all: 0.074 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.99→2.05 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 299 / CC1/2: 0.418 / Rpim(I) all: 0.753 / % possible all: 95.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JKU Resolution: 2→30.09 Å / SU ML: 0.352 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.2386 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.11 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.09 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -2.97017377611 Å / Origin y: -13.9998889043 Å / Origin z: 6.20978816577 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |