1Z1Z
NMR structure of the gpu tail protein from lambda bacteriophage
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_13C-separated_NOESY | 0.9 mM gpU, U-15N,13C, 10 mM Tris-d11, pH 7.8, 50 mM potassium chloride, 0.02% sodium azide | 10% D2O, 90% H2O | 50 mM KCl | 7.8 | 1 atm | 293 | |
2 | 3D_15N-separated_NOESY | 0.9 mM gpU, U-15N,13C, 10 mM Tris-d11, pH 7.8, 50 mM potassium chloride, 0.02% sodium azide | 10% D2O, 90% H2O | 50 mM KCl | 7.8 | 1 atm | 293 | |
3 | 3D_13C-separated-aromatic_NOESY | 0.9 mM gpU, U-15N,13C, 10 mM Tris-d11, pH 7.8, 50 mM potassium chloride, 0.02% sodium azide | 10% D2O, 90% H2O | 50 mM KCl | 7.8 | 1 atm | 293 | |
4 | 2D-IPAP-15N_HSQC | 0.9 mM gpU, U-15N,13C, 10 mM Tris-d11, pH 7.8, 50 mM potassium chloride, 0.02% sodium azide | 10% D2O, 90% H2O | 50 mM KCl | 7.8 | 1 atm | 293 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Varian | INOVA | 800 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | 1180 NOE distance restraints (876 intramolecular, 505 short-range, 128 medium range, 371 long-range), 42 pairs of hydrogen bond distance restraints, 106 pairs of phi/psi dihedral angle restraints and 41 amide residual dipolar coupling restraints were incorporated into the structure calculation. NOE calibration was performed with CANDID module of CYANA. Initially, 200 structures were calcuated with XPLOR-NIH. From this ensemble, 50 low-energy structure were refined in water using the XPLOR-NIH protocol by C. Spronk. The top 20 structures by energy had a backbone RMSD of 0.96 +/- 0.16 A on the secondary structure elements. In addition to residues 1-3 and 128-131 at the termini, a large loop spanning residues 45-60 is disordered. | NMRPipe |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | |
Conformers Calculated Total Number | |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
---|---|
Details | This structure was determined using standard 3D heteronuclear techniques |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | Delaglio | |
2 | data analysis | NMRView | 5.2 | Johnson |
3 | structure solution | CYANA | 2.1.3 | Guntert |
4 | refinement | XPLOR-NIH | 2.9.9 |