4epd: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[ | ==Initial Urease Structure for Radiation Damage Experiment at 300 K== | ||
<StructureSection load='4epd' size='340' side='right' caption='[[4epd]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4epd]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacter_aerogenes Enterobacter aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4EPD 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> | |||
<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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ep8|4ep8]], [[4epb|4epb]], [[4epe|4epe]]</td></tr> | |||
<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 Enterobacter aerogenes]), ureB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 Enterobacter aerogenes]), ureA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=548 Enterobacter aerogenes])</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=4epd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4epd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4epd RCSB], [http://www.ebi.ac.uk/pdbsum/4epd PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:22948911</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | |||
*[[Urease|Urease]] | |||
== | == References == | ||
[[ | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Enterobacter aerogenes]] | [[Category: Enterobacter aerogenes]] | ||
[[Category: Urease]] | [[Category: Urease]] | ||
[[Category: Badeau, R | [[Category: Badeau, R]] | ||
[[Category: Hopkins, J B | [[Category: Hopkins, J B]] | ||
[[Category: Thorne, R E | [[Category: Thorne, R E]] | ||
[[Category: Warkentin, M | [[Category: Warkentin, M]] | ||
[[Category: Alpha-beta barrel]] | [[Category: Alpha-beta barrel]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
[[Category: Nickel metalloenzyme]] | [[Category: Nickel metalloenzyme]] | ||
[[Category: Radiation damage]] | [[Category: Radiation damage]] | ||
Revision as of 15:23, 4 January 2015
Initial Urease Structure for Radiation Damage Experiment at 300 KInitial Urease Structure for Radiation Damage Experiment at 300 K
Structural highlights
Publication Abstract from PubMedThe 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 AlsoReferences
|
| ||||||||||||||||||||||||