6knf: Difference between revisions

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<StructureSection load='6knf' size='340' side='right'caption='[[6knf]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
<StructureSection load='6knf' size='340' side='right'caption='[[6knf]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6knf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KNF FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KNF FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.99&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=6knf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6knf OCA], [https://pdbe.org/6knf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6knf RCSB], [https://www.ebi.ac.uk/pdbsum/6knf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6knf ProSAT]</span></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=6knf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6knf OCA], [https://pdbe.org/6knf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6knf RCSB], [https://www.ebi.ac.uk/pdbsum/6knf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6knf ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cu-containing nitrite reductases (NiRs) are 110 kDa enzymes that play central roles in denitrification. Although the NiRs have been well studied, with over 100 Protein Data Bank entries, such issues as crystal packing, photoreduction, and lack of high pH cases have impeded structural analysis of their catalytic mechanisms. Here we show the cryogenic electron microscopy (cryo-EM) structures of Achromobacter cycloclastes NiR (AcNiR) at pH 6.2 and 8.1. The optimization of 3D-reconstruction parameters achieved 2.99 and 2.85 A resolution. Comprehensive comparisons with cryo-EM and 56 AcNiR crystal structures suggested crystallographic artifacts in residues 185-215 and His255' due to packing and photoreduction, respectively. We used a newly developed map comparison method to detect structural change around the type 2 Cu site. While the theoretical estimation of coordinate errors of cryo-EM structures remains difficult, combined analysis using X-ray and cryo-EM structures will allow deeper insight into the local structural changes of proteins.
2.85 and 2.99 A resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy.,Adachi N, Yamaguchi T, Moriya T, Kawasaki M, Koiwai K, Shinoda A, Yamada Y, Yumoto F, Kohzuma T, Senda T J Struct Biol. 2021 Jul 1;213(3):107768. doi: 10.1016/j.jsb.2021.107768. PMID:34217801<ref>PMID:34217801</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6knf" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Achromobacter cycloclastes]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Adachi, N]]
[[Category: Adachi N]]
[[Category: Kawasaki, M]]
[[Category: Kawasaki M]]
[[Category: Kohzuma, T]]
[[Category: Kohzuma T]]
[[Category: Koiwai, K]]
[[Category: Koiwai K]]
[[Category: Moriya, T]]
[[Category: Moriya T]]
[[Category: Senda, T]]
[[Category: Senda T]]
[[Category: Shinoda, A]]
[[Category: Shinoda A]]
[[Category: Yamada, Y]]
[[Category: Yamada Y]]
[[Category: Yamaguchi, T]]
[[Category: Yamaguchi T]]
[[Category: Yumoto, F]]
[[Category: Yumoto F]]
[[Category: Cu containing nitrite reductase]]
[[Category: Oxidoreductase]]

Latest revision as of 22:27, 29 May 2024

CryoEM map and model of Nitrite Reductase at pH 6.2CryoEM map and model of Nitrite Reductase at pH 6.2

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 2.99Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

6knf, resolution 2.99Å

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