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Yorodumi- PDB-5lqt: RNA duplex has central consecutive GA pairs flanked by G-C basepairs -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lqt | |||||||||||||||||||||||
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Title | RNA duplex has central consecutive GA pairs flanked by G-C basepairs | |||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / N6-methyladenine / RNA folding / Watson-Crick basepairs | Function / homology | RNA | Function and homology information Biological species | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | Authors | Huang, L. / Lilley, D.M.J. | Citation | Journal: EMBO Rep. / Year: 2017 | Title: Control of box C/D snoRNP assembly by N(6)-methylation of adenine. Authors: Huang, L. / Ashraf, S. / Wang, J. / Lilley, D.M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lqt.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lqt.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lqt_validation.pdf.gz | 406.6 KB | Display | wwPDB validaton report |
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Full document | 5lqt_full_validation.pdf.gz | 413.3 KB | Display | |
Data in XML | 5lqt_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 5lqt_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/5lqt ftp://data.pdbj.org/pub/pdb/validation_reports/lq/5lqt | 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: RNA chain | Mass: 3323.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Chemical | ChemComp-CA / | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: 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: 2.29 Å3/Da / Density % sol: 46.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.02 M Calcium Chloride dihydrate, 0.1 M Sodium Acetate trihydrate pH 4.6, 30% v/v 2-Methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9193 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9193 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.35 Å / Num. obs: 10522 / % possible obs: 100 % / Observed criterion σ(I): 1.3 / Redundancy: 11.9 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 12.4 % / Rmerge(I) obs: 2.08 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→32.583 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→32.583 Å
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Refine LS restraints |
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LS refinement shell |
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