6svx: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
<StructureSection load='6svx' size='340' side='right'caption='[[6svx]], [[Resolution|resolution]] 1.16Å' scene=''> | <StructureSection load='6svx' size='340' side='right'caption='[[6svx]], [[Resolution|resolution]] 1.16Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6svx]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6svx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SVX FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.16Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6svx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6svx OCA], [https://pdbe.org/6svx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6svx RCSB], [https://www.ebi.ac.uk/pdbsum/6svx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6svx ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 17: | Line 19: | ||
</div> | </div> | ||
<div class="pdbe-citations 6svx" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6svx" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Trypsin 3D structures|Trypsin 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
| Line 23: | Line 28: | ||
[[Category: Bos taurus]] | [[Category: Bos taurus]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Ahlberg Gagner V]] | ||
[[Category: Bourenkov | [[Category: Bourenkov G]] | ||
[[Category: Friedman | [[Category: Friedman R]] | ||
[[Category: Garcia-Bonete MJ]] | |||
[[Category: Garcia-Bonete | [[Category: Katona G]] | ||
[[Category: Katona | [[Category: Lundholm I]] | ||
[[Category: Lundholm | [[Category: Rodilla H]] | ||
[[Category: Rodilla | [[Category: Schneider T]] | ||
[[Category: Schneider | [[Category: Stake J]] | ||
[[Category: Stake | [[Category: Zhaunerchyk V]] | ||
[[Category: Zhaunerchyk | |||
Latest revision as of 13:29, 23 October 2024
Reference structure of bovine trypsin (odd frames of crystal x33)Reference structure of bovine trypsin (odd frames of crystal x33)
Structural highlights
FunctionPublication Abstract from PubMedLow-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments. Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties.,Gagner VA, Lundholm I, Garcia-Bonete MJ, Rodilla H, Friedman R, Zhaunerchyk V, Bourenkov G, Schneider T, Stake J, Katona G Sci Rep. 2019 Dec 17;9(1):19281. doi: 10.1038/s41598-019-55777-5. PMID:31848402[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||