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| | <StructureSection load='5gkn' size='340' side='right'caption='[[5gkn]], [[Resolution|resolution]] 3.20Å' scene=''> | | <StructureSection load='5gkn' size='340' side='right'caption='[[5gkn]], [[Resolution|resolution]] 3.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5gkn]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j7u 3j7u]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GKN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5gkn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j7u 3j7u]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GKN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron crystallography, [[Resolution|Resolution]] 3.2Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkn OCA], [http://pdbe.org/5gkn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gkn RCSB], [http://www.ebi.ac.uk/pdbsum/5gkn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkn 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=5gkn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkn OCA], [https://pdbe.org/5gkn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gkn RCSB], [https://www.ebi.ac.uk/pdbsum/5gkn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkn ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CATA_BOVIN CATA_BOVIN]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. Promotes growth of cells. | + | [https://www.uniprot.org/uniprot/CATA_BOVIN CATA_BOVIN] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. Promotes growth of cells. |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-A and 3.2-A resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.
| + | |
| - | | + | |
| - | Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.,Yonekura K, Kato K, Ogasawara M, Tomita M, Toyoshima C Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3368-73. doi:, 10.1073/pnas.1500724112. Epub 2015 Feb 17. PMID:25730881<ref>PMID:25730881</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 5gkn" style="background-color:#fffaf0;"></div>
| + | |
| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Catalase 3D structures|Catalase 3D structures]] | | *[[Catalase 3D structures|Catalase 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Bos taurus]] | | [[Category: Bos taurus]] |
| - | [[Category: Catalase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Yonekura, K]] | + | [[Category: Yonekura K]] |
| - | [[Category: Heme]]
| + | |
| - | [[Category: Nadph]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
