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Yorodumi- PDB-5neq: The structure of the G. violaceus guanidine II riboswitch P1 stem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5neq | ||||||||||||||||||||||||||||
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Title | The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with aminoguanidine | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / guanidine II riboswitch / stem-loop / tetra loop / dimer / aminoguanidine | Function / homology | AMINOGUANIDINE / RNA / RNA (> 10) | Function and homology information Biological species | Gloeobacter violaceus (bacteria) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 | 5neq.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5neq.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 5neq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5neq_validation.pdf.gz | 409.7 KB | Display | wwPDB validaton report |
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Full document | 5neq_full_validation.pdf.gz | 409.8 KB | Display | |
Data in XML | 5neq_validation.xml.gz | 3.7 KB | Display | |
Data in CIF | 5neq_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/5neq ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5neq | HTTPS FTP |
-Related structure data
Related structure data | 5ndhC 5ndiC 5nefC 5neoSC 5nepC 5nexC 5nomC 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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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-AGU / | ||||
#3: Chemical | #4: Chemical | ChemComp-NA / #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: 3.28 Å3/Da / Density % sol: 62.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop 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: I24 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→38.66 Å / Num. obs: 16376 / % possible obs: 99.8 % / Observed criterion σ(I): 1.3 / Redundancy: 14.13 % / Biso Wilson estimate: 35.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0716 / Rpim(I) all: 0.02 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.69→1.72 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.5 / Num. unique obs: 436 / CC1/2: 0.866 / Rpim(I) all: 0.713 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NEO Resolution: 1.69→38.658 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→38.658 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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