6n4z: Difference between revisions
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<StructureSection load='6n4z' size='340' side='right'caption='[[6n4z]], [[Resolution|resolution]] 1.40Å' scene=''> | <StructureSection load='6n4z' size='340' side='right'caption='[[6n4z]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6n4z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4Z FirstGlance]. <br> | <table><tr><td colspan='2'>[[6n4z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'bacillus_thermoproteolyticus' 'bacillus thermoproteolyticus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4Z FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">npr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1427 'Bacillus thermoproteolyticus'])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thermolysin Thermolysin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.27 3.4.24.27] </span></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=6n4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4z OCA], [http://pdbe.org/6n4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n4z RCSB], [http://www.ebi.ac.uk/pdbsum/6n4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4z ProSAT]</span></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=6n4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4z OCA], [http://pdbe.org/6n4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n4z RCSB], [http://www.ebi.ac.uk/pdbsum/6n4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4z ProSAT]</span></td></tr> | ||
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== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease. | [[http://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease. | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Cryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro-gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited. | |||
A comparison of gas stream cooling and plunge cooling of macromolecular crystals.,Harrison K, Wu Z, Juers DH J Appl Crystallogr. 2019 Aug 23;52(Pt 5):1222-1232. doi:, 10.1107/S1600576719010318. eCollection 2019 Oct 1. PMID:31636524<ref>PMID:31636524</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6n4z" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus thermoproteolyticus]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Thermolysin]] | [[Category: Thermolysin]] | ||
Revision as of 11:26, 6 November 2019
Tetragonal thermolysin (with 50% xylose) plunge cooled in liquid nitrogen to 77 KTetragonal thermolysin (with 50% xylose) plunge cooled in liquid nitrogen to 77 K
Structural highlights
Function[THER_BACTH] Extracellular zinc metalloprotease. Publication Abstract from PubMedCryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro-gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited. A comparison of gas stream cooling and plunge cooling of macromolecular crystals.,Harrison K, Wu Z, Juers DH J Appl Crystallogr. 2019 Aug 23;52(Pt 5):1222-1232. doi:, 10.1107/S1600576719010318. eCollection 2019 Oct 1. PMID:31636524[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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