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- PDB-6hbt: 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: 6hbt | |||||||||||||||||||||||||||||||
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Title | The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with arcaine | |||||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / guanidine II riboswitch / stem-loop / tetra loop / dimer | Function / homology | 1-(4-carbamimidamidobutyl)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 | ![]() | 37.3 KB | Display | ![]() |
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PDB format | ![]() | 26.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418 KB | Display | ![]() |
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Full document | ![]() | 417.8 KB | Display | |
Data in XML | ![]() | 3.5 KB | Display | |
Data in CIF | ![]() | 4.3 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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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.) ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-FXQ / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.81 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→27.73 Å / Num. obs: 17902 / % possible obs: 98.88 % / Observed criterion σ(I): 1.3 / Redundancy: 4.79 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.028 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 5 % / Rmerge(I) obs: 1.316 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 463 / CC1/2: 0.571 / Rpim(I) all: 0.647 / % possible all: 97.06 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→27.73 Å
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Refine LS restraints |
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LS refinement shell |
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