2K0X
The actinorhodin holo acyl carrier protein from S. coelicolor
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
2 | 3D 1H-13C NOESY | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
3 | 3D 1H-15N NOESY | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
4 | 3D CBCA(CO)NH | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
5 | 3D HNCACB | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
6 | 3D HCCH-TOCSY | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
7 | 3D HNCO | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
8 | F1,F2 double filtered NOESY | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
9 | F1,F2 double filtered TOCSY | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 | ||
10 | F2-filtered NOESY | 1-2 mM [U-98% 13C; U-98% 15N] act holo-acp, 1-2 mM Phosphopantetheine side chain, 95 % H2O, 5 % D2O, 20 mM potassium phosphate, 5 mM TCEP, 1 mM sodium azide | 95% H2O/5% D2O | 5.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | All structure calculations were carried out using the Ambiguous Restraints for Iterative Assignment of NOEs (ARIA) protocol Version 1.2, which includes an algorithm that attempts to correct for the effects of spin diffusion, was use. Torsion Angle Likelihood Obtained from Shift and sequence similarity (TALOS) and was used to predict φ and ψ dihedral angle restraints. Initially, structure calculation runs contained 8 iterations of 20 structures each, with the best 7 structures in each iteration (sorted according to total energy) being used for analysis and assignment. The number of dynamics steps was increased over default values to 20000 and 16000 for the first and second cooling stages respectively. After each run, violated restraints were checked, and those arising from noise peaks or incorrect assignments were removed/reassigned. Final ensembles of 100 structures were calculated from calibrated restraint tables. The 20 best structures (sorted according to total energy) were selected for water refinement. Water refined structures were calculated using the slightly modified refinement script applied to the RECOORD database. PROCHECK and WHATCHECK and quality indicators were compared to the average values for the RECOORD database of protein NMR structures. | ARIA |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | ARIA | 1.2 | Linge, O'Donoghue and Nilges |
2 | processing | ARIA | 1.2 | Linge, O'Donoghue and Nilges |
3 | refinement | ARIA | 1.2 | Linge, O'Donoghue and Nilges |