2by1: Difference between revisions

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-{{Seed}}
-[[Image:2by1.png|left|200px]]
-<!--
+==Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection==
-The line below this paragraph, containing "STRUCTURE_2by1", creates the "Structure Box" on the page.
+<StructureSection load='2by1' size='340' side='right'caption='[[2by1]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2by1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BY1 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PRD_900006:trehalose'>PRD_900006</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-{{STRUCTURE_2by1|  PDB=2by1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2by1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2by1 OCA], [https://pdbe.org/2by1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2by1 RCSB], [https://www.ebi.ac.uk/pdbsum/2by1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2by1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TREZ_DEIRA TREZ_DEIRA]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/2by1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2by1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+This paper focuses on the radiation-damage effects when applying the same total X-ray dose to protein crystals at different dose rates. These experiments have been performed on both a selenomethionated protein and on bovine trypsin using dose rates that span nearly two orders of magnitude. The results show no clear dose-rate effect on the global indicators of radiation damage, but a small measurable dose-rate effect could be found when studying specific radiation damage. It is hypothesized that this observed dose-rate effect relates to differences in the steady-state free-radical concentration.
-===IS RADIATION DAMAGE DEPENDENT ON THE DOSE-RATE USED DURING MACROMOLECULAR CRYSTALLOGRAPHY DATA COLLECTION===
+Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection?,Leiros HK, Timmins J, Ravelli RB, McSweeney SM Acta Crystallogr D Biol Crystallogr. 2006 Feb;62(Pt 2):125-32. Epub 2006, Jan 18. PMID:16421442<ref>PMID:16421442</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16421442}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2by1" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16421442 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16421442}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Deinococcus radiodurans R1]]
-BY1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BY1 OCA].
+[[Category: Large Structures]]
+[[Category: Leiros H-KS]]
-==Reference==
+[[Category: McSweeney SM]]
-Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection?, Leiros HK, Timmins J, Ravelli RB, McSweeney SM, Acta Crystallogr D Biol Crystallogr. 2006 Feb;62(Pt 2):125-32. Epub 2006, Jan 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16421442 16421442]
+[[Category: Ravelli RBG]]
-[[Category: Alpha-amylase]]
+[[Category: Timmins J]]
-[[Category: Deinococcus radiodurans]]
-[[Category: Single protein]]
-[[Category: Leiros, H K.S.]]
-[[Category: Mcsweeney, S M.]]
-[[Category: Ravelli, R B.G.]]
-[[Category: Timmins, J.]]
-[[Category: Data collection]]
-[[Category: Dose-rate]]
-[[Category: Hydrolase]]
-[[Category: Radiation damage]]
-[[Category: Synchrotron radiation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 12:06:22 2008''