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Yorodumi- PDB-7oaw: Crystal structure of the Chili RNA aptamer in complex with DMHBI+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oaw | ||||||
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Title | Crystal structure of the Chili RNA aptamer in complex with DMHBI+ | ||||||
Components | Chili RNA Aptamer | ||||||
Keywords | RNA / RNA aptamer / aptamer / Chili / fluorogenic RNA | ||||||
Function / homology | GUANOSINE-5'-TRIPHOSPHATE / : / SPERMINE / DMHBI+ / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Mieczkowski, M. / Pena, V. / Hoebartner, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine. Authors: Mieczkowski, M. / Steinmetzger, C. / Bessi, I. / Lenz, A.K. / Schmiedel, A. / Holzapfel, M. / Lambert, C. / Pena, V. / Hobartner, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oaw.cif.gz | 295.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oaw.ent.gz | 201 KB | Display | PDB format |
PDBx/mmJSON format | 7oaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/7oaw ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oaw | HTTPS FTP |
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-Related structure data
Related structure data | 7oa3SC 7oavC 7oaxC 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
-RNA chain , 1 types, 4 molecules ABCD
#1: RNA chain | Mass: 16932.012 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 6 types, 24 molecules
#2: Chemical | ChemComp-GTP / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-V6T / #5: Chemical | #6: Chemical | ChemComp-SPM / | #7: Chemical | ChemComp-CL / | |
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-Details
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: 2.54 Å3/Da / Density % sol: 51.48 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 400, MES, Spermine tetrahydrochloride / PH range: 5.4 - 5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→49.48 Å / Num. obs: 15716 / % possible obs: 99.7 % / Redundancy: 13 % / Biso Wilson estimate: 101.52 Å2 / Rmerge(I) obs: 0.195 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.89→3.06 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2474 / CC1/2: 0.317 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7OA3 Resolution: 2.95→46.44 Å / SU ML: 0.5638 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.5422 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: 103.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→46.44 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: 0.0390407038628 Å / Origin y: 1.35467901234 Å / Origin z: 3.29944026693 Å
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Refinement TLS group | Selection details: all |