+Open data
-Basic information
Entry | Database: PDB / ID: 4ena | ||||||
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Title | Crystal structure of fluoride riboswitch, soaked in Cs+ | ||||||
Components | Fluoride riboswitch | ||||||
Keywords | RNA / pseudoknot | ||||||
Function / homology | : / FLUORIDE ION / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Thermotoga petrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Ren, A.M. / Rajashankar, K.R. / Patel, D.J. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Authors: Ren, A. / Rajashankar, K.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 | 4ena.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ena.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ena.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/4ena ftp://data.pdbj.org/pub/pdb/validation_reports/en/4ena | HTTPS FTP |
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-Related structure data
Related structure data | 3vrsC 4en5C 4enbSC 4encC 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
#1: RNA chain | Mass: 16936.996 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA polymerase. Source: (synth.) Thermotoga petrophila (bacteria) | ||||||
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#2: Chemical | ChemComp-CS / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-F / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.1 M sodium cacodylate, pH 7.0, 20 mM spermine, 100 mM cesium chloride, 50 mM magnesium chloride, 20% MPD, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.85→20 Å / Num. obs: 4798 / Redundancy: 4.4 % / Rmerge(I) obs: 0.106 / Rsym value: 0.102 / Net I/σ(I): 13.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ENB Resolution: 2.85→19.973 Å / SU ML: 0.52 / σ(F): 1.35 / Phase error: 27.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.015 Å2 / ksol: 0.287 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.85→19.973 Å
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Refine LS restraints |
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LS refinement shell |
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