Bioisis

"Unfolded Lysine Riboswitch in Mg2+ Free Buffer"

Experimental SAS Curve

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Low_res_thumbnail

Experimental Mass

52,433 Da

Experimental Details for BID:  2LYSRR
Experiment ID: 19    In addition, this experiment links to experiment(s):  18  20
Collected at: ALS BL 12.3.1
Contributors: Garst, A.D. ,  Heroux, A. ,  Rambo, R.P. ,  Batey, R.T.
Part of a larger set of experiments examining the various conformational states of the lysine riboswitch in solution. Though the RNA is considered unfolded in the absence of Mg2+, the P(r) distribution shows a major peak at ~50 Angstroms suggesting the RNA still maintains a significant amount of side-by-side helical packing. The Kratky plot suggests the RNA is behaving more like a random coil, thus the RNA is flexible in the absence of Mg2+ with significant side-by-side helical packing. Note the shoulder at 23 Angstroms is consistent with the width of an A-form helix.

Electron Pair Distribution

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       Dmax → 172 Å


Guinier Plot

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     Guinier Rg → 41.8 Å

Real Space Rg → 47.3 Å

The Guinier plot is used to estimate the radius of gyration, Rg, which is taken from the slope of a line observed at low scattering angles (typically in the range where q* Rg < 1.3). This should be in reasonable agreement with the real space Rg.


Kratky Plot

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No structural model was attempted with this data set. Mg2+ appears to be important for folding the Lysine riboswitch into a compact/stable structure. The Kratky plot suggests the riboswitch is behaving like a random coil in solution with a maximum dimension of 172 Angstroms which is greatly reduced to 108 Angstroms when Mg2+ is present.

The Kratky plot can be used to visually assess the degree of "unfoldedness" of a protein or RNA sample. The plot of a well-behaved folded protein approaches the baseline at high q values creating a parabolic shape.


No Model

No structural model was used to interpret the SAXS data, please read the following:

Part of a larger set of experiments examining the various conformational states of the lysine riboswitch in solution. Though the RNA is considered unfolded in the absence of Mg2+, the P(r) distribution shows a major peak at ~50 Angstroms suggesting the RNA still maintains a significant amount of side-by-side helical packing. The Kratky plot suggests the RNA is behaving more like a random coil, thus the RNA is flexible in the absence of Mg2+ with significant side-by-side helical packing. Note the shoulder at 23 Angstroms is consistent with the width of an A-form helix.


Additional Experimental Details
Title

Unfolded Lysine Riboswitch in Mg2+ Free Buffer

Description

Part of a larger set of experiments examining the various conformational states of the lysine riboswitch in solution. Though the RNA is considered unfolded in the absence of Mg2+, the P(r) distribution shows a major peak at ~50 Angstroms suggesting the RNA still maintains a significant amount of side-by-side helical packing. The Kratky plot suggests the RNA is behaving more like a random coil, thus the RNA is flexible in the absence of Mg2+ with significant side-by-side helical packing. Note the shoulder at 23 Angstroms is consistent with the width of an A-form helix.

Publication

Crystal structure of the lysine riboswitch regulatory mRNA element. Journal of Biological Chemistry, Journal of Biological Chemistry, Vol. 283, Issue 33, 22347-22351, August 15, 2008

Contributors

Garst, A.D. ,  Heroux, A. ,  Rambo, R.P. ,  Batey, R.T.

Genomics and Proteomics

The experiment is composed of a single gene/ORF

Abbreviated name: LYSRBSWTCH

Annotation: Thermotoga maritima asd lysine riboswitch ligand binding domain (161 nt). Found in B. subtilis and E. coli and is implicated in conferring S-(2-aminoethyl)-L-cysteine (AEC) resistance.

GGACGGAGGC GCGCCCGAGA UGAGUAGGCU GUCCCACAGG GGAGGAAUCG GGGACGGCUG AAAGGCGAGG GCGCCGAAGC GAGCAGAGUU CCUCCCGCUC UGCUUGGCUG GGGGUGAGGG GAAUACCCUU ACCACUGUCG CGAAAGCGGA GAGCCGUCCA
categoryResidue composition (%)
Nucleotides G (40.0) C (26.2) A (20.6) U (13.1) T (0.0)
Mass: 52,364 Da | Total residues: 160