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Yorodumi- PDB-4xk0: Crystal structure of a tetramolecular RNA G-quadruplex in potassium -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xk0 | |||||||||||||||||||||||
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Title | Crystal structure of a tetramolecular RNA G-quadruplex in potassium | |||||||||||||||||||||||
Components | RNA (5'-(*Keywords | RNA / RNA G-quadruplex / tetramolecular G-quadruplex / intermolecular G-quadruplex | Function / homology | : / : / RNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.08 Å | Authors | Chen, M.C. / Murat, P. / Abecassis, K.A. / Ferre-D'Amare, A.R. / Balasubramanian, S. | Citation | Journal: Nucleic Acids Res. / Year: 2015 | Title: Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase. Authors: Chen, M.C. / Murat, P. / Abecassis, K. / Ferre-D'Amare, A.R. / Balasubramanian, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xk0.cif.gz | 24.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xk0.ent.gz | 15.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/4xk0 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/4xk0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 1948.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-K / #3: Chemical | #4: 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: 3.86 Å3/Da / Density % sol: 68.16 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 40 mM potassium cacodylic acid (pH 6.0), 35% 2-methyl-2,4-pentanediol, 5 mM spermine hydrochloride, 80 mM potassium chloride, 0.5 mM DHX36 fragment, 20 mM barium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.8266 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.07→50 Å / Num. obs: 25610 / % possible obs: 97.4 % / Redundancy: 12.1 % / Biso Wilson estimate: 4.683 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.034 / Rrim(I) all: 0.117 / Χ2: 1.367 / Net I/av σ(I): 19.705 / Net I/σ(I): 31.8 / Num. measured all: 310744 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.08→21.54 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.08→21.54 Å
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