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6d5t

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Current revision (14:32, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6d5t' size='340' side='right'caption='[[6d5t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='6d5t' size='340' side='right'caption='[[6d5t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6d5t]] 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=6D5T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6D5T FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6d5t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D5T FirstGlance]. <br>
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</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=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.0000372&#8491;</td></tr>
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<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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<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=6d5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d5t OCA], [http://pdbe.org/6d5t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6d5t RCSB], [http://www.ebi.ac.uk/pdbsum/6d5t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6d5t ProSAT]</span></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=6d5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d5t OCA], [https://pdbe.org/6d5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d5t RCSB], [https://www.ebi.ac.uk/pdbsum/6d5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d5t ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/THER_BACTH THER_BACTH]] Extracellular zinc metalloprotease.
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[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Cryocooling of macromolecular crystals is commonly employed to limit radiation damage during X-ray diffraction data collection. However, cooling itself affects macromolecular conformation and often damages crystals via poorly understood processes. Here, the effects of cryosolution thermal contraction on macromolecular conformation and crystal order in crystals ranging from 32 to 67% solvent content are systematically investigated. It is found that the solution thermal contraction affects macromolecule configurations and volumes, unit-cell volumes, crystal packing and crystal order. The effects occur through not only thermal contraction, but also pressure caused by the mismatched contraction of cryosolvent and pores. Higher solvent-content crystals are more affected. In some cases the solvent contraction can be adjusted to reduce mosaicity and increase the strength of diffraction. Ice formation in some crystals is found to cause damage via a reduction in unit-cell volume, which is interpreted through solvent transport out of unit cells during cooling. The results point to more deductive approaches to cryoprotection optimization by adjusting the cryosolution composition to reduce thermal contraction-induced stresses in the crystal with cooling.
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The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.,Juers DH, Farley CA, Saxby CP, Cotter RA, Cahn JKB, Holton-Burke RC, Harrison K, Wu Z Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):922-938. doi:, 10.1107/S2059798318008793. Epub 2018 Sep 5. PMID:30198901<ref>PMID:30198901</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6d5t" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Thermolysin|Thermolysin]]
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*[[Thermolysin 3D structures|Thermolysin 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus thermoproteolyticus]]
[[Category: Bacillus thermoproteolyticus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Thermolysin]]
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[[Category: Juers DH]]
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[[Category: Juers, D H]]
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[[Category: Hydrolase]]
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[[Category: Zinc protease]]
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Current revision

Hexagonal thermolysin cryocooled to 100 K with 50% MPD as cryoprotectant

PDB ID 6d5t

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