1aaj: Difference between revisions

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 ==CRYSTAL STRUCTURE ANALYSIS OF AMICYANIN AND APOAMICYANIN FROM PARACOCCUS DENITRIFICANS AT 2.0 ANGSTROMS AND 1.8 ANGSTROMS RESOLUTION==
-<StructureSection load='1aaj' size='340' side='right' caption='[[1aaj]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='1aaj' size='340' side='right'caption='[[1aaj]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1aaj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AAJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1aaj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AAJ FirstGlance]. <br>
-</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=1aaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aaj OCA], [http://pdbe.org/1aaj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1aaj RCSB], [http://www.ebi.ac.uk/pdbsum/1aaj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1aaj ProSAT]</span></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]] 1.8&#8491;</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=1aaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aaj OCA], [https://pdbe.org/1aaj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aaj RCSB], [https://www.ebi.ac.uk/pdbsum/1aaj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aaj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AMCY_PARDE AMCY_PARDE]] Primary acceptor of electrons from methylamine dehydrogenase. Passes those electrons on either a soluble cytochrome c or to pseudoazurin.
+[https://www.uniprot.org/uniprot/AMCY_PARDE AMCY_PARDE] Primary acceptor of electrons from methylamine dehydrogenase. Passes those electrons on either a soluble cytochrome c or to pseudoazurin.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/aa/1aaj_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/aa/1aaj_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 18: / Line 19: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1aaj ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of amicyanin, a cupredoxin isolated from Paracoccus denitrificans, has been determined by molecular replacement. The structure has been refined at 2.0 A resolution using energy-restrained least-squares procedures to a crystallographic residual of 15.7%. The copper-free protein, apoamicyanin, has also been refined to 1.8 A resolution with residual 15.5%. The protein is found to have a beta-sandwich topology with nine beta-strands forming two mixed beta-sheets. The secondary structure is very similar to that observed in the other classes of cupredoxins, such as plastocyanin and azurin. Amicyanin has approximately 20 residues at the N-terminus that have no equivalents in the other proteins; a portion of these residues forms the first beta-strand of the structure. The copper atom is located in a pocket between the beta-sheets and is found to have four coordinating ligands: two histidine nitrogens, one cysteine sulfur, and, at a longer distance, one methionine sulfur. The geometry of the copper coordination is very similar to that in the plant plastocyanins. Three of the four copper ligands are located in the loop between beta-strands eight and nine. This loop is shorter than that in the other cupredoxins, having only two residues each between the cysteine and histidine and the histidine and methionine ligands. The amicyanin and apoamicyanin structures are very similar; in particular, there is little difference in the positions of the coordinating ligands with or without copper. One of the copper ligands, a histidine, lies close to the protein surface and is surrounded on that surface by seven hydrophobic residues. This hydrophobic patch is thought to be important as an electron transfer site.
-Crystal structure analysis of amicyanin and apoamicyanin from Paracoccus denitrificans at 2.0 A and 1.8 A resolution.,Durley R, Chen L, Lim LW, Mathews FS, Davidson VL Protein Sci. 1993 May;2(5):739-52. PMID:8495197<ref>PMID:8495197</ref>
+==See Also==
+*[[Amicyanin 3D structures|Amicyanin 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1aaj" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 17741]]
+[[Category: Large Structures]]
-[[Category: Chen, L]]
+[[Category: Paracoccus denitrificans]]
-[[Category: Durley, R C.E]]
+[[Category: Chen L]]
-[[Category: Lim, L W]]
+[[Category: Durley RCE]]
-[[Category: Mathews, F S]]
+[[Category: Lim LW]]
-[[Category: Electron transport]]
+[[Category: Mathews FS]]