2by2: Difference between revisions

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[[Image:2by2.gif|left|200px]]


{{Structure
==Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection==
|PDB= 2by2 |SIZE=350|CAPTION= <scene name='initialview01'>2by2</scene>, resolution 1.50&Aring;
<StructureSection load='2by2' size='340' side='right'caption='[[2by2]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Chain+A'>AC1</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=GLC:GLUCOSE'>GLC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=TRE:TREHALOSE'>TRE</scene> and <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>
<table><tr><td colspan='2'>[[2by2]] 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=2BY2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BY2 FirstGlance]. <br>
|ACTIVITY= [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]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
|GENE=  
<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=2by2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2by2 OCA], [https://pdbe.org/2by2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2by2 RCSB], [https://www.ebi.ac.uk/pdbsum/2by2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2by2 ProSAT]</span></td></tr>
 
</table>
'''IS RADIATION DAMAGE DEPENDENT ON THE DOSE-RATE USED DURING MACROMOLECULAR CRYSTALLOGRAPHY DATA COLLECTION'''
== Function ==
 
[https://www.uniprot.org/uniprot/TREZ_DEIRA TREZ_DEIRA]  
 
== Evolutionary Conservation ==
==Overview==
[[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/2by2_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2by2 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.
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>
2BY2 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=2BY2 OCA].
 
==Reference==
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: Alpha-amylase]]
[[Category: Deinococcus radiodurans]]
[[Category: Single protein]]
[[Category: Leiros, H K.S.]]
[[Category: Mcsweeney, S M.]]
[[Category: Ravelli, R B.G.]]
[[Category: Timmins, J.]]
[[Category: BME]]
[[Category: GLC]]
[[Category: MG]]
[[Category: TRE]]
[[Category: TRS]]
[[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 Thu Mar 20 16:08:16 2008''
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2by2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Deinococcus radiodurans R1]]
[[Category: Large Structures]]
[[Category: Leiros H-KS]]
[[Category: McSweeney SM]]
[[Category: Ravelli RBG]]
[[Category: Timmins J]]
Retrieved from "https://proteopedia.org/2by2"