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Open data
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Basic information
Entry | Database: PDB / ID: 7qp2 | ||||||||||||||||||
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Title | 1-deazaguanosine modified-RNA Sarcin Ricin Loop | ||||||||||||||||||
![]() | RNA (27-MER) | ||||||||||||||||||
![]() | RNA / modified-RNA | ||||||||||||||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||||||||||||||
Biological species | synthetic construct (others) | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Ennifar, E. / Micura, R. / Bereiter, R. / Renard, E. / Kreutz, C. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: 1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis. Authors: Bereiter, R. / Renard, E. / Breuker, K. / Kreutz, C. / Ennifar, E. / Micura, R. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.9 KB | Display | ![]() |
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PDB format | ![]() | 45.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.1 KB | Display | ![]() |
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Full document | ![]() | 413.2 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dvzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: RNA chain | Mass: 8743.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→50 Å / Num. obs: 48142 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 9.54 Å2 / CC1/2: 1 / Net I/σ(I): 35.27 |
Reflection shell | Resolution: 0.9→0.92 Å / Num. unique obs: 3548 / CC1/2: 0.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DVZ Resolution: 0.9→29.48 Å / SU ML: 0.0984 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.7714 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.9→29.48 Å
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Refine LS restraints |
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LS refinement shell |
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