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Yorodumi- PDB-6jjf: Crystal structure of a two-quartet DNA mixed-parallel/antiparalle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jjf | ||||||||||||||||||||||||||||
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Title | Crystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / two-quartet / mixed-parallel/antiparallel | Function / homology | : / COBALT HEXAMMINE(III) / DNA / DNA (> 10) | Function and homology information Biological species | Pseudorabies virus Ea | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å | Authors | Zhang, Y.S. / EI Omari, K. / Duman, R. / Wagner, A. / Parkinson, G.N. / Wei, D.G. | Funding support | China, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2020 | Title: Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths. Authors: Zhang, Y. / El Omari, K. / Duman, R. / Liu, S. / Haider, S. / Wagner, A. / Parkinson, G.N. / Wei, D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jjf.cif.gz | 47 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jjf.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/6jjf ftp://data.pdbj.org/pub/pdb/validation_reports/jj/6jjf | HTTPS FTP |
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-Related 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: 4362.816 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudorabies virus Ea #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.19 Å3/Da / Density % sol: 43.93 % / Description: square |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Potassium cacodylate, Sodium cacodylate, Potassium chloride, Sodium chloride, Lithium chloride, Hexammine cobalt (III) chloride, MPD |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 6JJF / Redundancy: 6.4 %
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Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.47→23.8 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.86 / Stereochemistry target values: ML
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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 max: 91.76 Å2 / Biso mean: 33.7619 Å2 / Biso min: 19.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.47→23.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -3.603 Å / Origin y: -7.6468 Å / Origin z: -7.6421 Å
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Refinement TLS group |
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