+Open data
-Basic information
Entry | Database: PDB / ID: 5k7e | ||||||
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Title | The structure of pistol ribozyme, soaked with Mn2+ | ||||||
Components |
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Keywords | RNA/DNA / ribozyme / RNA structure / pistol / RNA-DNA complex | ||||||
Function / homology | : / DNA/RNA hybrid / DNA/RNA hybrid (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å | ||||||
Authors | Ren, A. / Patel, D. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k7e.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k7e.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 5k7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/5k7e ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k7e | HTTPS FTP |
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-Related structure data
Related structure data | 5k7cC 5k7dSC C: citing same article (ref.) S: Starting model for refinement |
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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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: containing 0.1 M Na-cacodylate, pH 6.5, 0.05 M Mg(OAc)2 and 32% MPD and supplemented with 150 mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 3.27→89.5 Å / Num. obs: 3743 / % possible obs: 95.7 % / Redundancy: 3.1 % / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.27→3.53 Å / % possible obs: 98.5 % / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.1 / Rpim(I) all: 0.589 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K7D Resolution: 3.27→48.5 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.27→48.5 Å
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