+Open data
-Basic information
Entry | Database: PDB / ID: 7qtn | ||||||||||||||||||
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Title | Duplex RNA containing Xanthosine-Cytosine base pairs | ||||||||||||||||||
Components |
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Keywords | RNA / modified base | ||||||||||||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||||||||||||||
Authors | Ennifar, E. / Micura, R. | ||||||||||||||||||
Funding support | Austria, 5items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA. Authors: Mair, S. / Erharter, K. / Renard, E. / Brillet, K. / Brunner, M. / Lusser, A. / Kreutz, C. / Ennifar, E. / Micura, R. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qtn.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qtn.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 7qtn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qtn_validation.pdf.gz | 393.2 KB | Display | wwPDB validaton report |
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Full document | 7qtn_full_validation.pdf.gz | 393.6 KB | Display | |
Data in XML | 7qtn_validation.xml.gz | 5 KB | Display | |
Data in CIF | 7qtn_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/7qtn ftp://data.pdbj.org/pub/pdb/validation_reports/qt/7qtn | HTTPS FTP |
-Related structure data
Related structure data | 7qshC 7quaC 433dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 4481.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 4480.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Water | ChemComp-HOH / |
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: 2.33 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Magnesium sulfate, TRIS HCl, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 1894942 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 1 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.2→1.23 Å / Num. unique obs: 68877 / CC1/2: 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 433D Resolution: 1.2→38.87 Å / SU ML: 0.2268 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1576 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→38.87 Å
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Refine LS restraints |
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LS refinement shell |
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