2by1: Difference between revisions

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{{Seed}}
[[Image:2by1.png|left|200px]]


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==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>
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<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>
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</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]]
2BY1 is a 1 chain 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]]
<ref group="xtra">PMID:16421442</ref><references group="xtra"/>
[[Category: Ravelli RBG]]
[[Category: Alpha-amylase]]
[[Category: Timmins J]]
[[Category: Deinococcus radiodurans]]
[[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 Wed Feb 18 05:25:02 2009''

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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