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| | ==Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy== | | ==Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy== |
| - | <StructureSection load='2jsv' size='340' side='right'caption='[[2jsv]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='2jsv' size='340' side='right'caption='[[2jsv]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2jsv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Strsg Strsg]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JSV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2jsv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_sp._'group_G' Streptococcus sp. 'group G']. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JSV FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2gi9|2gi9]]</div></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solid-state NMR</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">spg ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1320 STRSG])</td></tr>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jsv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jsv OCA], [https://pdbe.org/2jsv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jsv RCSB], [https://www.ebi.ac.uk/pdbsum/2jsv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jsv 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=2jsv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jsv OCA], [https://pdbe.org/2jsv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jsv RCSB], [https://www.ebi.ac.uk/pdbsum/2jsv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jsv ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SPG2_STRSG SPG2_STRSG] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Strsg]] | + | [[Category: Streptococcus sp. 'group G']] |
| - | [[Category: Franks, W]] | + | [[Category: Franks W]] |
| - | [[Category: Frericks, H L]] | + | [[Category: Frericks HL]] |
| - | [[Category: Graesser, D T]] | + | [[Category: Graesser DT]] |
| - | [[Category: Mayrhofer, R]] | + | [[Category: Mayrhofer R]] |
| - | [[Category: Nieuwkoop, A J]] | + | [[Category: Nieuwkoop AJ]] |
| - | [[Category: Rienstra, C M]] | + | [[Category: Rienstra CM]] |
| - | [[Category: Shah, G J]] | + | [[Category: Shah GJ]] |
| - | [[Category: Wylie, B J]] | + | [[Category: Wylie BJ]] |
| - | [[Category: Cell wall]]
| + | |
| - | [[Category: Gb1]]
| + | |
| - | [[Category: Igg-binding protein]]
| + | |
| - | [[Category: Immune system]]
| + | |
| - | [[Category: Peptidoglycan-anchor]]
| + | |
| - | [[Category: Ssnmr]]
| + | |
| - | [[Category: Tensor refinement]]
| + | |
| Structural highlights
Function
SPG2_STRSG
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.
Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR.,Franks WT, Wylie BJ, Schmidt HL, Nieuwkoop AJ, Mayrhofer RM, Shah GJ, Graesser DT, Rienstra CM Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4621-6. Epub 2008 Mar 14. PMID:18344321[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Franks WT, Wylie BJ, Schmidt HL, Nieuwkoop AJ, Mayrhofer RM, Shah GJ, Graesser DT, Rienstra CM. Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4621-6. Epub 2008 Mar 14. PMID:18344321
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