SOLUTION NMR / Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data.
structures with acceptable covalent geometry, structures with favorable non-bond energy
Representative
-
Components
#1: RNA chain
HEPATITISCVIRUSIRESDOMAINIIID
Mass: 8800.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Transcribed using T7 RNA polymerase
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D NOESY
1
2
2
2D NOESY
2
3
2
2D NOESY
2
4
3
2D NOESY
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1.2mMRNA, 8mMsodiumphosphatebufferpH6.6
90% H2O/10% D2O
2
1.2mMRNA, 8mMsodiumphosphatebufferpH6.6
100% D2O
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
8mMNaphosphate
6.6
ambient
278K
2
8mMNaphosphate
6.6
ambient
298K
3
8mMNaphosphate
6.6
ambient
303K
Crystal grow
*PLUS
Method: other / Details: NMR
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker DRX
Bruker
DRX
500
1
Bruker DMX
Bruker
DMX
600
2
-
Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
2.5
Bruker
collection
NMRPipe
1.7
Delaglio
processing
Sparky
3.66
Goddard & Kneller
dataanalysis
CHARMM
25.2
Brooksetal.
refinement
Insight II
97
MSI
refinement
Refinement
Method: Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S- ...Method: Using a motif-based approach, a model was constructed from X-ray, NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data. Software ordinal: 1 Details: Motifs (i) to (vi) were obtained from the following sources: (i) idealized A-form coordinates (InsightII, MSI); (ii)&(iii) PDB 430D.pdb; (iv) PDB 1ETG.pdb; (vi) PDB 1QA6.pdb; Motif (v) was constructed manually.
NMR ensemble
Conformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy Conformers calculated total number: 1 / Conformers submitted total number: 1
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