+Open data
-Basic information
Entry | Database: PDB / ID: 6w9p | ||||||||||||||||||||||||||||
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Title | Tel26 Parallel Four-quartet G-quadruplex with K+ | ||||||||||||||||||||||||||||
Components | DNA (5'-D(P*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: 1.99 Å | Authors | McCarthy, S.E. / Yatsunyk, L.A. / Beseiso, D. / Miao, J. | Funding support | United States, 1items |
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w9p.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w9p.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 6w9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w9p_validation.pdf.gz | 369.3 KB | Display | wwPDB validaton report |
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Full document | 6w9p_full_validation.pdf.gz | 369.2 KB | Display | |
Data in XML | 6w9p_validation.xml.gz | 3 KB | Display | |
Data in CIF | 6w9p_validation.cif.gz | 3.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/6w9p ftp://data.pdbj.org/pub/pdb/validation_reports/w9/6w9p | HTTPS FTP |
-Related structure data
Related structure data | 6xt7C 7jkuC 7ll0C 1o0kS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 8289.277 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: DT26 has no base and only the phosphate is modeled. Source: (synth.) Tetrahymena thermophila (eukaryote) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 29.1 % Description: relatively think sheets, look clam-shell shaped. |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 32% PEG 2000, 0.3M sodium chloride, 0.05M sodium cacodylate pH 6.5 Temp details: Crystals grown at room temperature. |
-Data collection
Diffraction | Mean temperature: 196 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2020 |
Radiation | Monochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→64.9 Å / Num. obs: 4116 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 45.95 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.99→2.1 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 1.6 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O0K Resolution: 1.99→33.5 Å / SU ML: 0.234 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.504 Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.94 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→33.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.6721 Å / Origin y: 6.7064 Å / Origin z: 6.0994 Å
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Refinement TLS group | Selection details: ALL |