2NBI

Structure of the PSCD-region of the cell wall protein pleuralin-1


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D HNCA0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
23D CBCA(CO)NH0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
32D 1H-15N HSQC0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
41H-15N NOESY HSQC0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
51H-15N TOCSY HSQC0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
63D HNCO0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
7HACACO0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
83D HCCH-TOCSY0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
92D 1H-1H TOCSY0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
102D 1H-1H NOESY0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
113D HBHA(CO)NH0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
122D 1H-13C HSQC0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
132D 1H-15N HSQC0.8 mM [U-97% 13C, U-98% 15N] Pleuralin, formerly HEP20095% H2O/5% D2O6.5298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX600
2BrukerDRX800
NMR Refinement
MethodDetailsSoftware
simulated annealing, naStructures 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 routineAUREMOL
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number2000
Conformers Submitted Total Number1
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsThe 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
#ClassificationVersionSoftware NameAuthor
1peak pickingAUREMOL2.4.1 betaBruker Biospin
2data analysisAUREMOL2.4.1 betaBruker Biospin
3processingAUREMOL2.4.1 betaBruker Biospin
4structure solutionCNS1.21Brunger, Adams, Clore, Gros, Nilges and Read
5collectionTopspin3.1Bruker Biospin
6processingTopspin3.1Bruker Biospin
7data analysisTopspin3.1Bruker Biospin
8refinementCNS
9refinementAUREMOL