Biological Magnetic Resonance Data Bank

A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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Results for submission NMR assignments for a helical diacylglycerol kinase (DAGK), 40 kDa membrane protein from E. coli.

BMRB ID: 15019

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Graph for NMR assignments for a helical diacylglycerol kinase (DAGK), 40 kDa membrane protein from E. coli

It appears this run did not converge (based on the residues marked non-flexible). While the best predicted structure is displayed, the lack of convergence means that this structure is unlikely to resemble the actual structure. Furthermore, it is not necessarily representative of the ensemble of structures formed.

Lowest energy structure: S_03652

RMSD against lowest energy structure for all residues

Structure Score
S_03652.pdb 4.9695
S_00413.pdb 7.6823
S_06927.pdb 5.8917
S_07473.pdb 8.1067
S_01009.pdb 7.6841
S_00270.pdb 5.4522
S_07213.pdb 8.6846
S_02679.pdb 7.2572
S_02290.pdb 8.0571
S_06569.pdb 9.6669
Averaged Ca-rmsd 7.345 +/- 1.485

RMSD against lowest energy structure for residues 52-88, 91-91, 94-94, 98-98

Structure Score
S_03652.pdb 2.0402
S_00413.pdb 2.3182
S_06927.pdb 2.9683
S_07473.pdb 2.2652
S_01009.pdb 2.0443
S_00270.pdb 2.5354
S_07213.pdb 2.6575
S_02679.pdb 3.2574
S_02290.pdb 3.0178
S_06569.pdb 2.5286
Averaged Ca-rmsd 2.563 +/- 0.416

This entry was calculated with Rosetta version 3.5 and version 3.2 of the CS-Rosetta Toolbox.

The flexible tails of this protein were automatically trimmed by the server. This means that the results you see might not have the same residue sequence as the data you submitted.

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Citation information:

"Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples" Oliver F. Lange; Paolo Rossi; Nikolaos G. Sgourakis; Yifan Song; Hsiau-Wei Lee; James M. Aramini; Asli Ertekin; Rong Xiao; Thomas B. Acton; Gaetano T. Montelione; David Baker; Proceedings of the National Academy of Sciences 109(27) 10873-10878 (2012) doi: 10.1073/pnas.1203013109

"De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds," Yang Shen; Philip N. Bryan; Yanan He; John Orban; David Baker; Ad Bax; Protein Science 19, 349-356 (2010) doi: 10.1002/pro.303

"De novo protein structure generation from incomplete chemical shift assignments," Yang Shen; Robert Vernon; David Baker; Ad Bax; J. Biomol. NMR 43, 63-78 (2009) doi: 10.1007/s10858-008-9288-5

"Consistent blind protein structure generation from NMR chemical shift data," Yang Shen; Oliver Lange; Frank Delaglio; Paolo Rossi; James M. Aramini; Gaohua Liu; Alexander Eletsky; Yibing Wu; Kiran K. Singarapu; Alexander Lemak; Alexandr Ignatchenko; Cheryl H. Arrowsmith; Thomas Szyperski; Gaetano T. Montelione; David Baker; Ad Bax; Proceedings of the National Academy of Sciences 105(12) 4685-4690 (2008) doi: 10.1073/pnas.0800256105

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