2M8X

Restrained CS-Rosetta Solution NMR structure of the CARDB domain of PF1109 from Pyrococcus furiosus. Northeast Structural Genomics Consortium target PfR193A

Summary for 2M8X

• Entry DOI: 10.2210/pdb2m8x/pdb
• Related: 2KL6
• Descriptor: Uncharacterized protein (1 entity in total)
• Functional Keywords: cardb domain, pfam 07705, unknown function, structural genomics, northeast structural genomics consortium, nesg, psi-biology, protein structure initiative
• Biological source: Pyrococcus furiosus
• Total number of polymer chains: 1
• Total formula weight: 12868.41

Authors

Mao, B.,Tejero, R.T.,Aramini, J.M.,Snyder, D.A.,Montelione, G.T.,Northeast Structural Genomics Consortium (NESG) (deposition date: 2013-05-29, release date: 2013-08-21, Last modification date: 2024-05-15)

Primary citation

Tejero, R.,Snyder, D.,Mao, B.,Aramini, J.M.,Montelione, G.T.
PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.
J.Biomol.Nmr, 56:337-351, 2013

PubMed Abstract: The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.

PubMed: 23897031
DOI: 10.1007/s10858-013-9753-7

Experimental method

SOLUTION NMR