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| | ==Thermolysin, SFX unliganded form with oil-based carrier== | | ==Thermolysin, SFX unliganded form with oil-based carrier== |
| - | <StructureSection load='5wr4' size='340' side='right' caption='[[5wr4]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='5wr4' size='340' side='right'caption='[[5wr4]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5wr4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WR4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WR4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5wr4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WR4 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=ZN:ZINC+ION'>ZN</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]] 2.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5wr6|5wr6]], [[5wr5|5wr5]], [[5wr3|5wr3]], [[5wr2|5wr2]]</td></tr>
| + | <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=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nprS, nprM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=5wr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wr4 OCA], [https://pdbe.org/5wr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wr4 RCSB], [https://www.ebi.ac.uk/pdbsum/5wr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wr4 ProSAT]</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=5wr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wr4 OCA], [http://pdbe.org/5wr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wr4 RCSB], [http://www.ebi.ac.uk/pdbsum/5wr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wr4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/THER_GEOSE THER_GEOSE]] Extracellular zinc metalloprotease.<ref>PMID:3149972</ref> | + | [https://www.uniprot.org/uniprot/THER_GEOSE THER_GEOSE] Extracellular zinc metalloprotease.<ref>PMID:3149972</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Thermolysin|Thermolysin]] | + | *[[Thermolysin 3D structures|Thermolysin 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 12980]] | + | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: Thermolysin]] | + | [[Category: Large Structures]] |
| - | [[Category: Kunishima, N]] | + | [[Category: Kunishima N]] |
| - | [[Category: Matsuura, Y]] | + | [[Category: Matsuura Y]] |
| - | [[Category: Naitow, H]] | + | [[Category: Naitow H]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Microcrystal]]
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| - | [[Category: Serial femtosecond crystallography]]
| + | |
| - | [[Category: Structure-based drug design]]
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| - | [[Category: X-ray free-electron laser]]
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| Structural highlights
Function
THER_GEOSE Extracellular zinc metalloprotease.[1]
Publication Abstract from PubMed
Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein-ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.
Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation.,Naitow H, Matsuura Y, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Tanaka R, Tanaka T, Sugahara M, Kobayashi J, Nango E, Iwata S, Kunishima N Acta Crystallogr D Struct Biol. 2017 Aug 1;73(Pt 8):702-709. doi:, 10.1107/S2059798317008919. Epub 2017 Jul 31. PMID:28777085[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kubo M, Imanaka T. Cloning and nucleotide sequence of the highly thermostable neutral protease gene from Bacillus stearothermophilus. J Gen Microbiol. 1988 Jul;134(7):1883-92. PMID:3149972
- ↑ Naitow H, Matsuura Y, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Tanaka R, Tanaka T, Sugahara M, Kobayashi J, Nango E, Iwata S, Kunishima N. Protein-ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation. Acta Crystallogr D Struct Biol. 2017 Aug 1;73(Pt 8):702-709. doi:, 10.1107/S2059798317008919. Epub 2017 Jul 31. PMID:28777085 doi:http://dx.doi.org/10.1107/S2059798317008919
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