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 2D18 | pdb_00002d18

Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the extended-duplex dimer


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O50mM NaCl7.0ambient283
21D-HSQC-selected spectrum0.4mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O50mM NaCl7.0ambient283
31D-HSQC-filtered spectrum0.4mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O50mM NaCl7.0ambient283
42D NOESY1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O50mM NaCl7.0ambient283
52D TOCSY1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O50mM NaCl7.0ambient298
62D NOESY1.8mM 25-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O50mM NaCl7.0ambient298
72D-w2-filtered NOESY0.4mM [G-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O50mM NaCl7.0ambient298
82D-w2-filtered NOESY0.2mM [A-13C/15N] labeled 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O50mM NaCl7.0ambient298
92D TOCSY1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O50mM NaCl7.0ambient298
102D NOESY1.0mM 39-mer RNA FRAGMENT; 10mM phosphate buffer, 50mM NaCl; 100% D2O100% D2O50mM NaCl7.0ambient298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX500
2BrukerDRX600
NMR Refinement
MethodDetailsSoftware
simulated annealingThe structures are based on a total of 598 restraints, 384 are NOE-derived distance constraints, 138 dihedral angle restraints, 76 distance restraints from hydrogen bonds.XwinNMR
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number100
Conformers Submitted Total Number11
Representative Model1 (minimized average structure)
Additional NMR Experimental Information
DetailsChemical synthesized 25-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized [G-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized [A-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized 39-mer RNA corresponding to the HIV-1 dimerization initiation site.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingXwinNMR2.6BRUKER
2data analysisFelix97.0Molecular Simulations
3structure solutionDiscover97.0Accelrys
4refinementDiscover97.0Accelrys