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[[Image:2by1.gif|left|200px]]


{{Structure
==Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection==
|PDB= 2by1 |SIZE=350|CAPTION= <scene name='initialview01'>2by1</scene>, resolution 1.55&Aring;
<StructureSection load='2by1' size='340' side='right'caption='[[2by1]], [[Resolution|resolution]] 1.55&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'>[[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>
|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]] 1.55&#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=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>
'''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/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.
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>
2BY1 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].
 
==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 16:08:15 2008''
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2by1" 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]]

Latest revision as of 14:24, 22 May 2024

Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collectionIs radiation damage dependent on the dose-rate used during macromolecular crystallography data collection

Structural highlights

2by1 is a 1 chain structure with sequence from Deinococcus radiodurans R1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.55Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TREZ_DEIRA

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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?,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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Leiros HK, Timmins J, Ravelli RB, McSweeney SM. Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection? Acta Crystallogr D Biol Crystallogr. 2006 Feb;62(Pt 2):125-32. Epub 2006, Jan 18. PMID:16421442 doi:http://dx.doi.org/10.1107/S0907444905033627

2by1, resolution 1.55Å

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