|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Restrained CS-Rosetta Solution NMR structure of the CARDB domain of PF1109 from Pyrococcus furiosus. Northeast Structural Genomics Consortium target PfR193A== | | ==Restrained CS-Rosetta Solution NMR structure of the CARDB domain of PF1109 from Pyrococcus furiosus. Northeast Structural Genomics Consortium target PfR193A== |
| - | <StructureSection load='2m8x' size='340' side='right' caption='[[2m8x]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2m8x' size='340' side='right'caption='[[2m8x]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2m8x]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M8X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M8X FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2m8x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M8X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M8X FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2kl6|2kl6]]</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2m8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m8x OCA], [http://pdbe.org/2m8x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2m8x RCSB], [http://www.ebi.ac.uk/pdbsum/2m8x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2m8x ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2m8x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m8x OCA], [https://pdbe.org/2m8x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m8x RCSB], [https://www.ebi.ac.uk/pdbsum/2m8x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m8x ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8U1U6_PYRFU Q8U1U6_PYRFU] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 20: |
Line 22: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aramini, J M]] | + | [[Category: Large Structures]] |
| - | [[Category: Mao, B]] | + | [[Category: Pyrococcus furiosus]] |
| - | [[Category: Montelione, G T]] | + | [[Category: Aramini JM]] |
| - | [[Category: Structural genomic]] | + | [[Category: Mao B]] |
| - | [[Category: Snyder, D A]] | + | [[Category: Montelione GT]] |
| - | [[Category: Tejero, R T]] | + | [[Category: Snyder DA]] |
| - | [[Category: Cardb domain]] | + | [[Category: Tejero RT]] |
| - | [[Category: Nesg]]
| + | |
| - | [[Category: Pfam 07705]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Psi-biology]]
| + | |
| - | [[Category: Unknown function]]
| + | |
| Structural highlights
Function
Q8U1U6_PYRFU
Publication Abstract from PubMed
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.
PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.,Tejero R, Snyder D, Mao B, Aramini JM, Montelione GT J Biomol NMR. 2013 Jul 30. PMID:23897031[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tejero R, Snyder D, Mao B, Aramini JM, Montelione GT. PDBStat: a universal restraint converter and restraint analysis software package for protein NMR. J Biomol NMR. 2013 Jul 30. PMID:23897031 doi:10.1007/s10858-013-9753-7
|
