4xm0: Difference between revisions

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New page: '''Unreleased structure''' The entry 4xm0 is ON HOLD Authors: Tsutomu Nakamura, Mayumi Niiyama, Wakana Hashimoto, Kurumi Ida, Koichi Uegaki Description: N,N'-diacetylchitobiose deacety...
 
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'''Unreleased structure'''


The entry 4xm0 is ON HOLD
==N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the absence of cadmium==
<StructureSection load='4xm0' size='340' side='right'caption='[[4xm0]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4xm0]] 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=4XM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XM0 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4xm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xm0 OCA], [https://pdbe.org/4xm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xm0 RCSB], [https://www.ebi.ac.uk/pdbsum/4xm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xm0 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q8U3V1_PYRFU Q8U3V1_PYRFU]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


Authors: Tsutomu Nakamura, Mayumi Niiyama, Wakana Hashimoto, Kurumi Ida, Koichi Uegaki
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>


Description: N,N'-diacetylchitobiose deacetylase (SeMet derivative) from Pyrococcus furiosus in the absence of cadmium
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Tsutomu Nakamura, Mayumi Niiyama, Wakana Hashimoto, Kurumi Ida, Koichi Uegaki]]
<div class="pdbe-citations 4xm0" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus DSM 3638]]
[[Category: Hashimoto W]]
[[Category: Ida K]]
[[Category: Nakamura T]]
[[Category: Niiyama M]]
[[Category: Uegaki K]]
Retrieved from "https://proteopedia.org/4xm0"