+Open data
-Basic information
Entry | Database: PDB / ID: 5k7c | ||||||
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Title | The native structure of native pistol ribozyme | ||||||
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 / SAD / Resolution: 2.73 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 | 5k7c.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k7c.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 5k7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k7c_validation.pdf.gz | 387 KB | Display | wwPDB validaton report |
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Full document | 5k7c_full_validation.pdf.gz | 390.8 KB | Display | |
Data in XML | 5k7c_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 5k7c_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/5k7c ftp://data.pdbj.org/pub/pdb/validation_reports/k7/5k7c | HTTPS FTP |
-Related 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: 2.18 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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.73→48.7 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.73→48.7 Å
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