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Yorodumi- PDB-5neo: The structure of the G. violaceus guanidine II riboswitch P1 stem-loop -
+Open data
-Basic information
Entry | Database: PDB / ID: 5neo | |||||||||||||||||||||||||||||||
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Title | The structure of the G. violaceus guanidine II riboswitch P1 stem-loop | |||||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / guanidine II riboswitch / stem-loop / tetra loop / dimer | Function / homology | AMMONIUM ION / RNA / RNA (> 10) | Function and homology information Biological species | Gloeobacter violaceus (bacteria) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å | Authors | Huang, L. / Wang, J. / Lilley, D.M.J. | Funding support | United Kingdom, 1items |
Citation | Journal: Cell Chem Biol / Year: 2017 | Title: The Structure of the Guanidine-II Riboswitch. Authors: Huang, L. / Wang, J. / Lilley, D.M.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5neo.cif.gz | 35.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5neo.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 5neo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/5neo ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5neo | HTTPS FTP |
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-Related structure data
Related structure data | 5ndhC 5ndiC 5nefC 5nepC 5neqC 5nexC 5nomC 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 5880.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gloeobacter violaceus (bacteria) | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-NH4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.01 M Magnesium Acetate, 0.05 M MES pH 5.6, 2.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92011 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92011 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→38.6 Å / Num. obs: 16551 / % possible obs: 99.9 % / Observed criterion σ(I): 1.6 / Redundancy: 19.04 % / CC1/2: 0.95 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.016 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.69→1.72 Å / Redundancy: 18.5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 422 / CC1/2: 0.956 / Rpim(I) all: 0.432 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.69→27.651 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→27.651 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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