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 structure of the E.coli protein NirD, Northeast Structural Genomics target ET100.

BMRB ID: 15139

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Graph for NMR structure of the E.coli protein NirD, Northeast Structural Genomics target ET100

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_03815

RMSD against lowest energy structure for all residues

Structure Score
S_03815.pdb 2.8518
S_07461.pdb 3.7447
S_04250.pdb 5.7379
S_08145.pdb 4.0209
S_02791.pdb 4.1734
S_05051.pdb 12.1787
S_09297.pdb 3.8663
S_03782.pdb 6.9473
S_04010.pdb 3.2589
S_05949.pdb 11.9139
Averaged Ca-rmsd 5.869 +/- 3.468

RMSD against lowest energy structure for residues 30-31, 46-47, 56-98

Structure Score
S_03815.pdb 2.0248
S_07461.pdb 2.1422
S_04250.pdb 2.7350
S_08145.pdb 2.2407
S_02791.pdb 2.3253
S_05051.pdb 4.3008
S_09297.pdb 2.5484
S_03782.pdb 3.1512
S_04010.pdb 1.7882
S_05949.pdb 4.7866
Averaged Ca-rmsd 2.804 +/- 0.999

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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