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- PDB-3q50: Structural analysis of a class I PreQ1 riboswitch aptamer in the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q50 | ||||||
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Title | Structural analysis of a class I PreQ1 riboswitch aptamer in the metabolite-bound state | ||||||
![]() | PREQ1 RIBOSWITCH | ||||||
![]() | RNA / PREQ1 / PREQ0 / RIBOSOMAL BINDING SITE / APTAMER / METABOLITE / Pseudoknot / H-type / RIBOSWITCH | ||||||
Function / homology | 7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jenkins, J.L. / Krucinska, J. / Wedekind, J.E. | ||||||
![]() | ![]() Title: Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation. Authors: Jenkins, J.L. / Krucinska, J. / McCarty, R.M. / Bandarian, V. / Wedekind, J.E. #1: ![]() Title: The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. Authors: Spitale, R.C. / Torelli, A.T. / Krucinska, J. / Bandarian, V. / Wedekind, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29 KB | Display | ![]() |
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PDB format | ![]() | 19.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3q51C ![]() 3gcaS S: Starting model for refinement C: citing same article ( |
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Similar 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: 10599.417 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The RNA strand was chemically synthesized based on the sequence of class I, Type 1 PreQ1 riboswitch aptamer from T. Tengcongensis | ||
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#2: Chemical | ChemComp-PRF / | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.98 Å3/Da / Density % sol: 75.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 1.8 M Li2SO4, 0.05 M MES pH 5.6, and 0.01 M MgCl2(H20)6, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2009 / Details: Rh coated Si vertical focus mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Horizontal focusing 5.05 asymmetric cut Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9769 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.725→25 Å / Num. obs: 6041 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3GCA Resolution: 2.75→22.01 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.35 / σ(F): 0.13 / Phase error: 23.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.544 Å2 / ksol: 0.247 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati sigma a obs: 0.36 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→22.01 Å
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Refine LS restraints |
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LS refinement shell |
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