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- PDB-6q57: X-ray crystal structure of the tetrahydrofolate riboswitch aptame... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6q57 | ||||||
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Title | X-ray crystal structure of the tetrahydrofolate riboswitch aptamer bound to 5-deazatetrahydropterin | ||||||
![]() | tetrahydrofolate riboswitch aptamer | ||||||
![]() | RNA / Aptamer / riboswitch | ||||||
Function / homology | 5-deazatetrahydropterin / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dunstan, M.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tetrahydrofolate Riboswitches Provide Distinct Genetic Outputs to Synthetic and Natural Signals. Authors: Vincent, H.A. / Leigh, J. / Robinson, C.J. / Dunstan, M.S. / Ferrer Rios, M.G. / Micklefield, 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 | ![]() | 60.2 KB | Display | ![]() |
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PDB format | ![]() | 42.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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
#1: RNA chain | Mass: 28849.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, sitting drop Details: 6% 2,4-methyl-pentanediol, 10 mM spermine, 40 mM Na-cacodylate, pH 7.0, 80 mM NaCl and 1 mM DTT |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→51.741 Å / Num. obs: 8282 / % possible obs: 98 % / Redundancy: 6.1 % / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.72→2.82 Å |
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Processing
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Refinement | Resolution: 2.72→51.741 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.84 Å2 / Biso mean: 60.1665 Å2 / Biso min: 25.48 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.72→51.741 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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