This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3v3x

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:16, 14 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3v3x' size='340' side='right'caption='[[3v3x]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3v3x' size='340' side='right'caption='[[3v3x]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3v3x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Strsg Strsg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V3X FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3v3x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_sp._'group_G' Streptococcus sp. 'group G']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V3X FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</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>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MTN:S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL]+METHANESULFONOTHIOATE'>MTN</scene></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=3v3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v3x OCA], [https://pdbe.org/3v3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v3x RCSB], [https://www.ebi.ac.uk/pdbsum/3v3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v3x 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=3v3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v3x OCA], [https://pdbe.org/3v3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v3x RCSB], [https://www.ebi.ac.uk/pdbsum/3v3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v3x ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/SPG2_STRSG SPG2_STRSG]
-
X-ray crystallography has been a useful tool in the development of site-directed spin labeling by resolving rotamers of the nitroxide spin-label side chain in a variety of alpha-helical environments. In this work, the crystal structure of a doubly spin-labeled N8C/K28C mutant of the B1 immunoglobulin-binding domain of protein G (GB1) was solved. The double mutant formed a domain-swapped dimer under crystallization conditions. Two rotameric states of the spin-label were resolved at the solvent-exposed alpha-helical site, at residue 28; these are in good agreement with rotamers previously reported for helical structures. The second site, at residue 8 on an interior beta-strand, shows the presence of three distinct solvent-exposed side-chain rotamers. One of these rotamers is rarely observed within crystal structures of R1 sites and suggests that the H(alpha) and S(delta) hydrogen bond that is common to alpha-helical sites is absent at this interior beta-strand residue. Variable temperature continuous wave (CW) experiments of the beta-strand site showed two distinct components that were correlated to the rotameric states observed in crystallography. Interestingly, the CW data at room temperature could be fit without the use of an order parameter, which is consistent with the lack of the H(alpha) and S(delta) interaction. Additionally, double electron electron resonance (DEER) spectroscopy was performed on the GB1 double mutant in its monomeric form and yielded a most probable interspin distance of 25 +/- 1 A. In order to evaluate the accuracy of the measured DEER distance, the rotamers observed in the crystal structure of the domain-swapped GB1 dimer were modeled into a high-resolution structure of the wild type monomeric GB1. The distances generated in the resulting GB1 structural models match the most probable DEER distance within approximately 2 A. The results are interesting as they indicate by direct experimental measurement that the rotameric states of R1 found in this crystal provide a very close match to the most probable distance measured by DEER.
+
-
 
+
-
High-Resolution Structure of a Protein Spin-Label in a Solvent-Exposed beta-Sheet and Comparison with DEER Spectroscopy.,Cunningham TF, McGoff MS, Sengupta I, Jaroniec CP, Horne WS, Saxena S Biochemistry. 2012 Aug 1. PMID:22809334<ref>PMID:22809334</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3v3x" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
*[[Protein G|Protein G]]
*[[Protein G|Protein G]]
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Strsg]]
+
[[Category: Streptococcus sp. 'group G']]
-
[[Category: Cunningham, T F]]
+
[[Category: Cunningham TF]]
-
[[Category: Horne, W S]]
+
[[Category: Horne WS]]
-
[[Category: Jaroniec, C P]]
+
[[Category: Jaroniec CP]]
-
[[Category: McGoff, M S]]
+
[[Category: McGoff MS]]
-
[[Category: Saxena, S K]]
+
[[Category: Saxena SK]]
-
[[Category: Sengupta, I]]
+
[[Category: Sengupta I]]
-
[[Category: Domain-swapped dimer]]
+
-
[[Category: Immune system]]
+
-
[[Category: Nitroxide spin label]]
+

Current revision

Nitroxide Spin Labels in Protein GB1: N8/K28 Double Mutant

PDB ID 3v3x

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3v3x"
Personal tools