4epb: Difference between revisions
New page: '''Unreleased structure''' The entry 4epb is ON HOLD Authors: Warkentin, M., Badeau, R., Hopkins, J.B., Thorne, R.E. Description: Final Urease Structure for Radiation Damage Experiment... |
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The | ==Final Urease Structure for Radiation Damage Experiment at 100 K== | ||
<StructureSection load='4epb' size='340' side='right'caption='[[4epb]], [[Resolution|resolution]] 1.75Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4epb]] 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=4EPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EPB FirstGlance]. <br> | |||
</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4epb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4epb OCA], [https://pdbe.org/4epb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4epb RCSB], [https://www.ebi.ac.uk/pdbsum/4epb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4epb ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/URE1_KLEAE URE1_KLEAE]] | |||
<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> | |||
<div class="pdbe-citations 4epb" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Urease 3D structures|Urease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Klebsiella aerogenes]] | |||
[[Category: Large Structures]] | |||
[[Category: Badeau R]] | |||
[[Category: Hopkins JB]] | |||
[[Category: Thorne RE]] | |||
[[Category: Warkentin M]] | |||
Latest revision as of 10:21, 28 September 2022
Final Urease Structure for Radiation Damage Experiment at 100 KFinal Urease Structure for Radiation Damage Experiment at 100 K
Structural highlights
FunctionPublication 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
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