2NBI
Structure of the PSCD-region of the cell wall protein pleuralin-1
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D HNCA | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
2 | 3D CBCA(CO)NH | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
3 | 2D 1H-15N HSQC | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
4 | 1H-15N NOESY HSQC | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
5 | 1H-15N TOCSY HSQC | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
6 | 3D HNCO | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
7 | HACACO | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
8 | 3D HCCH-TOCSY | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
9 | 2D 1H-1H TOCSY | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
10 | 2D 1H-1H NOESY | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
11 | 3D HBHA(CO)NH | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
12 | 2D 1H-13C HSQC | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 | |||
13 | 2D 1H-15N HSQC | 0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP200 | 95% H2O/5% D2O | 6.5 | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
2 | Bruker | DRX | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, na | Structures were refined by using data imputation (. Cano, C., Brunner, Baskaran, K., K. Elsner, R., Munte, C. E. and Kalbitzer, H. R. (2009) Protein structure calculation with data imputation: the use of substitute restraints. J. Biomol. NMR 45, 397-411) and refinement in explicut water (Linge, J.P., Williams, M.A., Spronk, C.A.E.M., Bonvin, A.M.J.J. and Nilges, M. (2003). Refinement of protein structures in explicit solvent. Proteins 50, 496-506)., The structure of the PSCD4-domain has been simulated using the experimental restraints obtained from the NMR spectra. The other four domains have been modeled transfering the restraints of the PSCD4-domain for those residues that were kept identical in the sequences. Additional substitute restraints of each domain (Noe distances, hydrogen bonds and dihedral angles) have been obtained using the PERMOL routine | AUREMOL |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 2000 |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | The structure has been determined combining experimental restraints (J-coupling, Noe-distances, Hydrogen Bonds and dihedral angles) with additional substitute restraints obtained by homology modelling between the fourth and the other domains |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | peak picking | AUREMOL | 2.4.1 beta | Bruker Biospin |
2 | data analysis | AUREMOL | 2.4.1 beta | Bruker Biospin |
3 | processing | AUREMOL | 2.4.1 beta | Bruker Biospin |
4 | structure solution | CNS | 1.21 | Brunger, Adams, Clore, Gros, Nilges and Read |
5 | collection | Topspin | 3.1 | Bruker Biospin |
6 | processing | Topspin | 3.1 | Bruker Biospin |
7 | data analysis | Topspin | 3.1 | Bruker Biospin |
8 | refinement | CNS | ||
9 | refinement | AUREMOL |