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| | <StructureSection load='1p7g' size='340' side='right'caption='[[1p7g]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='1p7g' size='340' side='right'caption='[[1p7g]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51768 Atcc 51768]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1P7G FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1p7g]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P7G FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></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]] 1.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iks|1iks]]</div></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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [https://pdbe.org/1p7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [https://www.ebi.ac.uk/pdbsum/1p7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7g ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SOD OR PAE0274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13773 ATCC 51768])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Superoxide_dismutase Superoxide dismutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.15.1.1 1.15.1.1] </span></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=1p7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7g OCA], [http://pdbe.org/1p7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p7g RCSB], [http://www.ebi.ac.uk/pdbsum/1p7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7g ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SODF_PYRAE SODF_PYRAE]] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. | + | [https://www.uniprot.org/uniprot/SODF_PYRAE SODF_PYRAE] Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 51768]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Superoxide dismutase]] | + | [[Category: Pyrobaculum aerophilum]] |
| - | [[Category: Eisenberg, D]] | + | [[Category: Eisenberg D]] |
| - | [[Category: Lee, S]] | + | [[Category: Lee S]] |
| - | [[Category: Sawaya, M R]] | + | [[Category: Sawaya MR]] |
| - | [[Category: Alpha-beta]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
SODF_PYRAE Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structure of superoxide dismutase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum was determined by molecular replacement at 1.8 A resolution. The structure determination was made especially challenging by the large number of molecules (24) in the asymmetric unit, the presence of a pseudo-crystallographic twofold operator close to a twinning operator and the inability to detect twinning by conventional means. Molecular replacement proceeded at low resolution in pseudo (apparent) space group P3(2)12 and was facilitated by examination of the self-rotation function and native Patterson map. Refinement, however, stalled at an R factor of 40% when high-resolution data were included. Expanding to the lower symmetry space group P3(2) decreased R (to 22%) and R(free) (to 26%), but not by as much as expected for the quality of data. Finally, despite the apparent lack of evidence from conventional twinning tests [i.e. plots of the second moment of I and N(Z) distributions], a twinning operator was included in the refinement, lowering R and R(free) to 16.2 and 21.7%, respectively. The early detection of twinning appears to have been masked by a deviation in the expected intensity distribution caused by the presence of non-crystallographic translational symmetry. These findings suggest the importance of testing twinning operators in cases where pseudo-translational symmetry can explain negative results from conventional twinning tests. The structure reveals a tetrameric assembly with 222 symmetry, similar to superoxide dismutase structures from other organisms. The current structural model represents the metal-free state of the enzyme.
Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning.,Lee S, Sawaya MR, Eisenberg D Acta Crystallogr D Biol Crystallogr. 2003 Dec;59(Pt 12):2191-9. Epub 2003, Nov 27. PMID:14646077[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lee S, Sawaya MR, Eisenberg D. Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning. Acta Crystallogr D Biol Crystallogr. 2003 Dec;59(Pt 12):2191-9. Epub 2003, Nov 27. PMID:14646077
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