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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 structure of the N-terminal extracellular domain of the lymphocyte receptor CD5 (CD5 domain 1).

BMRB ID: 15189

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Graph for Solution structure of the N-terminal extracellular domain of the lymphocyte receptor CD5 (CD5 domain 1)

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_02662

RMSD against lowest energy structure for all residues

Structure Score
S_02662.pdb 9.5388
S_04910.pdb 10.9746
S_06612.pdb 13.3891
S_02017.pdb 11.8338
S_03811.pdb 11.8953
S_09150.pdb 12.2398
S_06557.pdb 11.6264
S_06146.pdb 11.4030
S_01861.pdb 12.4778
S_00521.pdb 12.1898
Averaged Ca-rmsd 11.757 +/- 1.017

RMSD against lowest energy structure for residues 65-73

Structure Score
S_02662.pdb 2.4144
S_04910.pdb 2.1449
S_06612.pdb 2.5726
S_02017.pdb 2.6301
S_03811.pdb 3.3149
S_09150.pdb 2.8893
S_06557.pdb 2.5264
S_06146.pdb 2.6880
S_01861.pdb 2.5547
S_00521.pdb 2.7182
Averaged Ca-rmsd 2.645 +/- 0.307

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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