3wa3: Difference between revisions
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<StructureSection load='3wa3' size='340' side='right'caption='[[3wa3]], [[Resolution|resolution]] 1.55Å' scene=''> | <StructureSection load='3wa3' size='340' side='right'caption='[[3wa3]], [[Resolution|resolution]] 1.55Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3wa3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3wa3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WA3 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HDZ:NITROGEN+MOLECULE'>HDZ</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HDZ:NITROGEN+MOLECULE'>HDZ</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=TPQ:5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE'>TPQ</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=3wa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wa3 OCA], [https://pdbe.org/3wa3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wa3 RCSB], [https://www.ebi.ac.uk/pdbsum/3wa3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wa3 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=3wa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wa3 OCA], [https://pdbe.org/3wa3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wa3 RCSB], [https://www.ebi.ac.uk/pdbsum/3wa3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wa3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/PAOX_ARTGO PAOX_ARTGO] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Arthrobacter globiformis]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Hayashi H]] | |||
[[Category: Hayashi | [[Category: Kurihara K]] | ||
[[Category: Kurihara | [[Category: Kuroki R]] | ||
[[Category: Kuroki | [[Category: Murakawa T]] | ||
[[Category: Murakawa | [[Category: Okajima T]] | ||
[[Category: Okajima | [[Category: Sunami T]] | ||
[[Category: Sunami | [[Category: Suzuki M]] | ||
[[Category: Suzuki | [[Category: Tamada T]] | ||
[[Category: Tamada | [[Category: Tanizawa K]] | ||
[[Category: Tanizawa | |||
Latest revision as of 16:01, 8 November 2023
Crystal structure of copper amine oxidase from arthrobacter globiformis in N2 conditionCrystal structure of copper amine oxidase from arthrobacter globiformis in N2 condition
Structural highlights
FunctionPublication Abstract from PubMedThe crystal structure of a copper amine oxidase from Arthrobacter globiformis was determined at 1.08 A resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight approximately 200) as a cryoprotectant. The final crystallographic R factor and Rfree were 13.0 and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior, including the active site, which resulted in a marked reduction in the overall B factor and consequently led to a subatomic resolution structure for a relatively large protein with a monomer molecular weight of approximately 70 000. About 40% of the presumed H atoms were observed as clear electron densities in the Fo - Fc difference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site, which contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely to be molecular oxygen, are bound to the protein, one of which is located in a region that had previously been proposed as an entry route for the dioxygen substrate from the central cavity of the dimer interface to the active site. High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2.,Murakawa T, Hayashi H, Sunami T, Kurihara K, Tamada T, Kuroki R, Suzuki M, Tanizawa K, Okajima T Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2483-94. doi:, 10.1107/S0907444913023196. Epub 2013 Nov 19. PMID:24311589[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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