This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2by5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "2by5" [edit=sysop:move=sysop])
Current revision (11:24, 22 May 2024) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2by5.png|left|200px]]
 
-
{{STRUCTURE_2by5| PDB=2by5 | SCENE= }}
+
==Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection==
 +
<StructureSection load='2by5' size='340' side='right'caption='[[2by5]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2by5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BY5 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]] 1.3&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2by5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2by5 OCA], [https://pdbe.org/2by5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2by5 RCSB], [https://www.ebi.ac.uk/pdbsum/2by5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2by5 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
 +
== 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/2by5_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=2by5 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>
-
{{ABSTRACT_PUBMED_16421442}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 2by5" style="background-color:#fffaf0;"></div>
-
[[2by5]] is a 1 chain structure of [[Basic Pancreatic Trypsin Inhibitor]] and [[Trypsin]] with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BY5 OCA].
+
==See Also==
==See Also==
-
*[[Basic Pancreatic Trypsin Inhibitor|Basic Pancreatic Trypsin Inhibitor]]
+
*[[BPTI 3D structures|BPTI 3D structures]]
-
*[[Trypsin|Trypsin]]
+
*[[Trypsin 3D structures|Trypsin 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:016421442</ref><references group="xtra"/>
+
__TOC__
 +
</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
-
[[Category: Trypsin]]
+
[[Category: Large Structures]]
-
[[Category: Leiros, H K.S.]]
+
[[Category: Leiros H-KS]]
-
[[Category: Mcsweeney, S M.]]
+
[[Category: McSweeney SM]]
-
[[Category: Ravelli, R B.G.]]
+
[[Category: Ravelli RBG]]
-
[[Category: Timmins, J.]]
+
[[Category: Timmins J]]
-
[[Category: Data collection]]
+
-
[[Category: Dose-rate]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Radiation damage]]
+
-
[[Category: Synchrotron radiation]]
+

Current revision

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

PDB ID 2by5

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2by5"
Personal tools