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Yorodumi- PDB-6qir: Crystal structure of CAG repeats with synthetic CMBL3a compound (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qir | ||||||||||||||||||||||||||||
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Title | Crystal structure of CAG repeats with synthetic CMBL3a compound (model I) | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / CAG repeats / CMBL / RNA complex with ligand | Function / homology | CMBL3a / RNA | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.531 Å | Authors | Kiliszek, A. / Blaszczyk, L. / Rypniewski, W. / Nakatani, K. | Funding support | Poland, 1items |
Citation | Journal: Nucleic Acids Res. / Year: 2019 | Title: Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats. Authors: Mukherjee, S. / Blaszczyk, L. / Rypniewski, W. / Falschlunger, C. / Micura, R. / Murata, A. / Dohno, C. / Nakatani, K. / Kiliszek, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qir.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qir.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qir_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6qir_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6qir_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 6qir_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/6qir ftp://data.pdbj.org/pub/pdb/validation_reports/qi/6qir | HTTPS FTP |
-Related structure data
Related structure data | 6qiqSC 6qisC 6qitC 6qivC 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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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 2564.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-J48 / #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: 3.7 Å3/Da / Density % sol: 66.75 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10mM MgCl2 and 1M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9171 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9171 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→42.158 Å / Num. obs: 43700 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.86 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.53→1.62 Å / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6954 / CC1/2: 0.872 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QIQ Resolution: 1.531→42.158 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.61
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Solvent computation | Shrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.531→42.158 Å
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Refine LS restraints |
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LS refinement shell |
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