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 Solution NMR Structure of Ribosome Modulation Factor VP1593 from Vibrio parahaemolyticus. Northeast Structural Genomics Target VpR55.

BMRB ID: 15339

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Graph for Solution NMR Structure of Ribosome Modulation Factor VP1593 from Vibrio parahaemolyticus. Northeast Structural Genomics Target VpR55

This run appears to have converged (based on the residues marked non-flexible). That means that the results may be a meaningful prediction of the real structure. Please validate the structure against your experimental data.

Lowest energy structure: S_05916

RMSD against lowest energy structure for all residues

Structure Score
S_05916.pdb 1.7377
S_00785.pdb 1.7584
S_00962.pdb 3.2542
S_01258.pdb 2.3022
S_00132.pdb 2.2186
S_05653.pdb 2.4758
S_06573.pdb 2.2714
S_00849.pdb 1.9580
S_04105.pdb 2.1367
S_04211.pdb 3.2097
Averaged Ca-rmsd 2.332 +/- 0.529

RMSD against lowest energy structure for residues 2-62

Structure Score
S_05916.pdb 1.2718
S_00785.pdb 1.3566
S_00962.pdb 2.1642
S_01258.pdb 1.6848
S_00132.pdb 1.9061
S_05653.pdb 2.0064
S_06573.pdb 1.6311
S_00849.pdb 1.5235
S_04105.pdb 1.5721
S_04211.pdb 2.6739
Averaged Ca-rmsd 1.779 +/- 0.421

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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