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- PDB-6hc5: The structure of the G. violaceus guanidine II riboswitch P2 stem... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hc5 | ||||||||||||||||||||||||||||
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Title | The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with audouine | ||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / guanidine II riboswitch / stem-loop / tetra loop / dimer | Function / homology | 1-(5-carbamimidamidopentyl)guanidine / RNA / RNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() Huang, L. / Lilley, D.M.J. | Funding support | | ![]()
![]() ![]() Title: Structure-guided design of a high-affinity ligand for a riboswitch. Authors: Huang, L. / Wang, J. / Wilson, T.J. / Lilley, D.M.J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.7 KB | Display | ![]() |
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PDB format | ![]() | 23.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424 KB | Display | ![]() |
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Full document | ![]() | 424.7 KB | Display | |
Data in XML | ![]() | 3.7 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-FXT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.01 M Magnesium Acetate, 0.05 M MES pH 5.0, 2.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 1.413→27.913 Å / Num. obs: 28892 / % possible obs: 98 % / Observed criterion σ(I): 0.8 / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.021 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.413→1.437 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.92 / Num. unique obs: 775 / CC1/2: 0.428 / Rpim(I) all: 0.813 / % possible all: 100 |
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Processing
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Refinement | Resolution: 1.413→27.913 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.413→27.913 Å
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Refine LS restraints |
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LS refinement shell |
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