+Open data
-Basic information
Entry | Database: PDB / ID: 5tdk | ||||||||||||||||||||
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Title | RNA decamer duplex with eight 2'-5'-linkages | ||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / 2'-5'-LINKAGE / PLANT PROTEIN | Function / homology | STRONTIUM ION / RNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | Authors | Luo, Z. / Sheng, J. | Citation | Journal: Nucleic Acids Res. / Year: 2017 | Title: Structural insights into RNA duplexes with multiple 2 -5 -linkages. Authors: Shen, F. / Luo, Z. / Liu, H. / Wang, R. / Zhang, S. / Gan, J. / Sheng, J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tdk.cif.gz | 37 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tdk.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/5tdk ftp://data.pdbj.org/pub/pdb/validation_reports/td/5tdk | HTTPS FTP |
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-Related structure data
Related structure data | 5tdjC 4msbS 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 3206.980 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CHEMICALLY SYNTHESIZED BY SOLID PHASE SYNTHESIS AND PURIFIED BY HPLC Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-SR / #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: 1.94 Å3/Da / Density % sol: 36.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 40 mM sodium cacodylate buffer (pH 7.0), 10% (v/v) MPD (2-methyl-2,4-pentanediol), 12 mM spermine tetrahydrochloride, 40 mM LiCl, 80 mM SrCl2 and 20 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→18.7 Å / Num. obs: 8980 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.43→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MSB Resolution: 1.43→18.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.929 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.014 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→18.7 Å
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Refine LS restraints |
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