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| | <StructureSection load='4xm2' size='340' side='right'caption='[[4xm2]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='4xm2' size='340' side='right'caption='[[4xm2]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4xm2]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XM2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4xm2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XM2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xlz|4xlz]], [[4xm0|4xm0]], [[4xm1|4xm1]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF0354 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=4xm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xm2 OCA], [https://pdbe.org/4xm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xm2 RCSB], [https://www.ebi.ac.uk/pdbsum/4xm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xm2 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=4xm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xm2 OCA], [http://pdbe.org/4xm2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xm2 RCSB], [http://www.ebi.ac.uk/pdbsum/4xm2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xm2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q8U3V1_PYRFU Q8U3V1_PYRFU] |
| - | Native N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus (Pf-Dac) and its selenomethionine derivative (Se-Pf-Dac) were crystallized and analyzed in the presence and absence of cadmium ion. The four crystal structures fell into three different crystal-packing groups, with the cadmium-free Pf-Dac and Se-Pf-Dac belonging to the same space group, with homologous unit-cell parameters. The crystal structures in the presence of cadmium contained distorted octahedral cadmium complexes coordinated by three chlorides, two O atoms and an S or Se atom from the N-terminal methionine or selenomethionine, respectively. The N-terminal cadmium complex was involved in crystal contacts between symmetry-related molecules through hydrogen bonding to the N-termini. While all six N-termini of Se-Pf-Dac were involved in cadmium-complex formation, only two of the Pf-Dac N-termini participated in complex formation in the Cd-containing crystal, resulting in different crystal forms. These differences are discussed in light of the higher stability of the Cd-Se bond than the Cd-S bond. This work provides an example of the contribution of cadmium towards determining protein crystal quality and packing depending on the use of the native protein or the selenomethionine derivative.
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| - | Multiple crystal forms of N,N'-diacetylchitobiose deacetylase from Pyrococcus furiosus.,Nakamura T, Niiyama M, Hashimoto W, Ida K, Abe M, Morita J, Uegaki K Acta Crystallogr F Struct Biol Commun. 2015 Jun;71(Pt 6):657-62. doi:, 10.1107/S2053230X15005695. Epub 2015 May 20. PMID:26057790<ref>PMID:26057790</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
| + | |
| - | <div class="pdbe-citations 4xm2" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrfu]] | + | [[Category: Pyrococcus furiosus DSM 3638]] |
| - | [[Category: Hashimoto, W]] | + | [[Category: Hashimoto W]] |
| - | [[Category: Ida, K]] | + | [[Category: Ida K]] |
| - | [[Category: Nakamura, T]] | + | [[Category: Nakamura T]] |
| - | [[Category: Niiyama, M]] | + | [[Category: Niiyama M]] |
| - | [[Category: Uegaki, K]] | + | [[Category: Uegaki K]] |
| - | [[Category: Ce-14 deacetylase]]
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| - | [[Category: Metal binding protein]]
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