2by1: Difference between revisions

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-[[Image:2by1.gif|left|200px]]<br />
-<applet load="2by1" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2by1, resolution 1.55&Aring;" />
-'''IS RADIATION DAMAGE DEPENDENT ON THE DOSE-RATE USED DURING MACROMOLECULAR CRYSTALLOGRAPHY DATA COLLECTION'''<br />
-==Overview==
+==Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection==
-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.
+<StructureSection load='2by1' size='340' side='right'caption='[[2by1]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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.
-==About this Structure==
+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>
-BY1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] with GLC, MG, TRS, TRE and BME as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alpha-amylase Alpha-amylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.1 3.2.1.1] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2BY1 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=16421442 16421442]
+</div>
-[[Category: Alpha-amylase]]
+<div class="pdbe-citations 2by1" style="background-color:#fffaf0;"></div>
-[[Category: Deinococcus radiodurans]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Leiros, H.K.S.]]
+__TOC__
-[[Category: Mcsweeney, S.M.]]
+</StructureSection>
-[[Category: Ravelli, R.B.G.]]
+[[Category: Deinococcus radiodurans R1]]
-[[Category: Timmins, J.]]
+[[Category: Large Structures]]
-[[Category: BME]]
+[[Category: Leiros H-KS]]
-[[Category: GLC]]
+[[Category: McSweeney SM]]
-[[Category: MG]]
+[[Category: Ravelli RBG]]
-[[Category: TRE]]
+[[Category: Timmins J]]
-[[Category: TRS]]
-[[Category: data collection]]
-[[Category: dose-rate]]
-[[Category: hydrolase]]
-[[Category: radiation damage]]
-[[Category: synchrotron radiation]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov  5 14:24:09 2007''