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Yorodumi- PDB-7oa3: Crystal structure of Chili RNA aptamer in complex with DMHBO+ (Ir... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oa3 | ||||||
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Title | Crystal structure of Chili RNA aptamer in complex with DMHBO+ (Iridium hexammine co-crystallized form) | ||||||
Components | Chili RNA Aptamer | ||||||
Keywords | RNA / RNA aptamer / aptamer / Chili / fluorogenic RNA | ||||||
Function / homology | GUANOSINE-5'-TRIPHOSPHATE / : / : / DMHBO+ / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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 | 7oa3.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oa3.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 7oa3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oa3_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7oa3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7oa3_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 7oa3_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/7oa3 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oa3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-RNA chain , 1 types, 2 molecules AB
#1: RNA chain | Mass: 16932.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 15 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-IR / #6: Chemical | |
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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: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion Details: PEG400, MES , spermine tetrahydrochloride, iridium (III) hexamine 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: SLS / Beamline: X10SA / Wavelength: 1.1035 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 24, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1035 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45.92 Å / Num. obs: 8215 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 132.08 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.018 / Rrim(I) all: 0.067 / Rsym value: 0.06 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.8→2.95 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1177 / CC1/2: 0.534 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→45.92 Å / SU ML: 0.6033 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 41.8568 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: 155.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.92 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: 26.266804016 Å / Origin y: -1.0567545672 Å / Origin z: 9.69210838555 Å
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Refinement TLS group | Selection details: all |