6knf | pdb_00006knf

CryoEM map and model of Nitrite Reductase at pH 6.2

spinqualitylabelsall models 6knf, resolution 2.99Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6knf is a 3 chain structure with sequence from Achromobacter cycloclastes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CU Activity: Nitrite reductase (NO-forming), with EC number 1.7.2.1 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Nitrite reductase 3D structures

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