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Yorodumi- PDB-6jji: Crystal structure of a two-quartet RNA parallel G-quadruplex comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jji | ||||||||||||||||||||||||||||
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Title | Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4 (1:1) | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / G-quadruplex / two-quartet / complex | Function / homology | : / Chem-POH / RNA / RNA (> 10) | Function and homology information Biological species | Pseudorabies virus Ea | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | Authors | Zhang, Y.S. / 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 | 6jji.cif.gz | 32.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jji.ent.gz | 20.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/6jji ftp://data.pdbj.org/pub/pdb/validation_reports/jj/6jji | HTTPS FTP |
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-Related structure data
Related structure data | 6jjfC 6jjhSC 6tqiC 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 4572.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudorabies virus Ea | ||||
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#2: Chemical | #3: Chemical | ChemComp-POH / ( | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.14 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Potassium cacodylate, Sodium cacodylate, Potassium chloride, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→16.042 Å / Num. obs: 825 / % possible obs: 96.57 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.403 / Num. unique obs: 79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JJH Resolution: 3.1→16.042 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2.17 / Phase error: 16.95 / Stereochemistry target values: LS_WUNIT_K1
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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: 166.81 Å2 / Biso mean: 71.0763 Å2 / Biso min: 34.62 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→16.042 Å
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LS refinement shell | Resolution: 3.1→3.21 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 8.0762 Å / Origin y: 2.9584 Å / Origin z: 4.4843 Å
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Refinement TLS group |
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