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| | ==Final Urease Structure for Radiation Damage Experiment at 300 K== | | ==Final Urease Structure for Radiation Damage Experiment at 300 K== |
| - | <StructureSection load='4epe' size='340' side='right' caption='[[4epe]], [[Resolution|resolution]] 2.05Å' scene=''> | + | <StructureSection load='4epe' size='340' side='right'caption='[[4epe]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4epe]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_aerogenes"_hormaeche_and_edwards_1958 "aerobacter aerogenes" hormaeche and edwards 1958]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EPE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EPE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4epe]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EPE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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=4epe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4epe OCA], [https://pdbe.org/4epe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4epe RCSB], [https://www.ebi.ac.uk/pdbsum/4epe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4epe ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ep8|4ep8]], [[4epb|4epb]], [[4epd|4epd]]</td></tr>
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| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ureC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 "Aerobacter aerogenes" Hormaeche and Edwards 1958]), ureB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 "Aerobacter aerogenes" Hormaeche and Edwards 1958]), ureA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 "Aerobacter aerogenes" Hormaeche and Edwards 1958])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Urease Urease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.5 3.5.1.5] </span></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=4epe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4epe OCA], [http://pdbe.org/4epe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4epe RCSB], [http://www.ebi.ac.uk/pdbsum/4epe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4epe ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [[https://www.uniprot.org/uniprot/URE1_KLEAE URE1_KLEAE]] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Urease|Urease]] | + | *[[Urease 3D structures|Urease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aerobacter aerogenes hormaeche and edwards 1958]] | + | [[Category: Klebsiella aerogenes]] |
| - | [[Category: Urease]] | + | [[Category: Large Structures]] |
| - | [[Category: Badeau, R]] | + | [[Category: Badeau R]] |
| - | [[Category: Hopkins, J B]] | + | [[Category: Hopkins JB]] |
| - | [[Category: Thorne, R E]] | + | [[Category: Thorne RE]] |
| - | [[Category: Warkentin, M]] | + | [[Category: Warkentin M]] |
| - | [[Category: Alpha-beta barrel]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Nickel metalloenzyme]]
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| - | [[Category: Radiation damage]]
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| Structural highlights
Function
[URE1_KLEAE]
Publication Abstract from PubMed
The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.
Spatial distribution of radiation damage to crystalline proteins at 25-300 K.,Warkentin M, Badeau R, Hopkins JB, Thorne RE Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1108-17. doi:, 10.1107/S0907444912021361. Epub 2012 Aug 18. PMID:22948911[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Warkentin M, Badeau R, Hopkins JB, Thorne RE. Spatial distribution of radiation damage to crystalline proteins at 25-300 K. Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1108-17. doi:, 10.1107/S0907444912021361. Epub 2012 Aug 18. PMID:22948911 doi:http://dx.doi.org/10.1107/S0907444912021361
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