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NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
1mM unlabeled PK1, 50mM NaCl, 0.5 mM EDTA
95%H2O-5%D2O and 100% D2O
50mM NaCl
6.3
ambient
278
2
HCN, 1H 13C HSQC, 1H 13C constant time HSQC, 1H 13C long-range HSQC, HCCH-TOCSY, HCCH E.COSY, HCC-TOCSY-CCH-E.COSY, 3D NOESY-HSQC
0.7mM 13C,15N PK1, 50mM NaCl, 0.5 mM EDTA
95%H2O-5%D2O and 100% D2O
50mM NaCl
6.3
ambient
293
3
HMBC, 1H 15N TROSY, 2JNN HNN-COSY, 2JNH HNN-COSY, 3D NOESY-HMBC
0.7mM 13C,15N PK1, 50mM NaCl, 0.5 mM EDTA
95%H2O-5%D2O and 100% D2O
50mM NaCl
6.3
ambient
278
4
2D NOESY, TOCSY
1mM unlabeled PK1, 50mM NaCl, 0.5 mM EDTA
95%H2O-5%D2O and 100% D2O
50mM NaCl
6.3
ambient
293
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
CNS dynamical annealing protocol for nucleic acids
A- dynamical annealing protocol:
1. TAMD 30 ps at 20000K
2. first cooling stage TAMD 40ps
3. second slow cooling annealing stage, restrained molecular dynamics 35ps.
4. 10 cycles of energy minimization of 300 steps each.
B- Energy minimization:
1-TAMD 10ps at 300K,
2- cooling over 9 ps and 10 Powell cycles of 800 steps each.
UXNMR
NMR Ensemble Information
Conformer Selection Criteria
structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy