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Open data
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Basic information
Entry | Database: PDB / ID: 3fu2 | ||||||
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Title | Cocrystal structure of a class-I preQ1 riboswitch | ||||||
![]() | PreQ1 riboswitch | ||||||
![]() | RNA / aptamer / riboswitch / queuosine / PreQ1 | ||||||
Function / homology | 7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Klein, D.J. / Edwards, T.E. / Ferre-D'Amare, A.R. | ||||||
![]() | ![]() Title: Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase Authors: Klein, D.J. / Edwards, T.E. / Ferre-D'Amare, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.9 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.8 KB | Display | ![]() |
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Full document | ![]() | 444 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.3 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: RNA chain | Mass: 10835.524 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: Chemically synthesized RNA corresponding to the natural sequence from Bacillus subtilis #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.86 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% PEG 550 MME, 50 mM CaCl2, 100 mM Hepes-KOH pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30 Å / Num. all: 7147 / Num. obs: 7147 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.126 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 68.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.85→30 Å
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Refine LS restraints |
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