+Open data
-Basic information
Entry | Database: PDB / ID: 6jq5 | ||||||
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Title | The structure of Hatchet Ribozyme | ||||||
Components | RNA (82-MER) | ||||||
Keywords | RNA / Ribozyme / non-coding RNA / hatchet / cleavage / catalysis | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.059 Å | ||||||
Authors | Ren, A. / Zheng, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Hatchet ribozyme structure and implications for cleavage mechanism. Authors: Zheng, L. / Falschlunger, C. / Huang, K. / Mairhofer, E. / Yuan, S. / Wang, J. / Patel, D.J. / Micura, R. / Ren, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jq5.cif.gz | 187.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jq5.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jq5_validation.pdf.gz | 405.7 KB | Display | wwPDB validaton report |
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Full document | 6jq5_full_validation.pdf.gz | 408.5 KB | Display | |
Data in XML | 6jq5_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 6jq5_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/6jq5 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/6jq5 | HTTPS FTP |
-Related structure data
Related structure data | 6jq6SC S: Starting model for refinement C: citing same article (ref.) |
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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: RNA chain | Mass: 26380.668 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.10M HEPES, pH 6.8, 2.0M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 26, 2017 |
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→50 Å / Num. obs: 33380 / % possible obs: 99.6 % / Redundancy: 12.1 % / Rpim(I) all: 0.036 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 2→2.18 Å / Num. unique obs: 1867 / Rpim(I) all: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JQ6 Resolution: 2.059→33.523 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.059→33.523 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -32.5384 Å / Origin y: -15.4974 Å / Origin z: -15.8258 Å
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Refinement TLS group | Selection details: all |