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Open data
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Basic information
Entry | Database: PDB / ID: 5k7c | ||||||
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Title | The native structure of native pistol ribozyme | ||||||
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![]() | RNA/DNA / ribozyme / RNA structure / pistol / RNA-DNA complex | ||||||
Function / homology | DNA/RNA hybrid / DNA/RNA hybrid (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ren, A. / Patel, D. | ||||||
![]() | ![]() Title: Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage. Authors: Ren, A. / Vusurovic, N. / Gebetsberger, J. / Gao, P. / Juen, M. / Kreutz, C. / Micura, R. / Patel, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.5 KB | Display | ![]() |
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PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387 KB | Display | ![]() |
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Full document | ![]() | 390.8 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: DNA/RNA hybrid | Mass: 15096.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: DNA/RNA hybrid | Mass: 3514.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Na-cacodylate, pH 6.5, Mg(OAc)2 0.2 M and 32% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→89.3 Å / Num. obs: 4612 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rpim(I) all: 0.037 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.73→2.86 Å / % possible obs: 100 % / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.9 / Rpim(I) all: 0.727 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.73→48.7 Å
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