2blx: Difference between revisions

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-[[Image:2blx.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2blx", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2blx|  PDB=2blx  |  SCENE=  }}
-'''HEWL BEFORE A HIGH DOSE X-RAY "BURN"'''
+==HEWL before a high dose x-ray "burn"==
+<StructureSection load='2blx' size='340' side='right'caption='[[2blx]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2blx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BLX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BLX 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]] 1.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=2blx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2blx OCA], [https://pdbe.org/2blx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2blx RCSB], [https://www.ebi.ac.uk/pdbsum/2blx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2blx ProSAT]</span></td></tr>
+</table>
+== 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/bl/2blx_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=2blx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.
-==Overview==
+Improving radiation-damage substructures for RIP.,Nanao MH, Sheldrick GM, Ravelli RB Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37. Epub 2005, Aug 16. PMID:16131756<ref>PMID:16131756</ref>
-Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-BLX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BLX OCA].
+</div>
+<div class="pdbe-citations 2blx" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Improving radiation-damage substructures for RIP., Nanao MH, Sheldrick GM, Ravelli RB, Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37. Epub 2005, Aug 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16131756 16131756]
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Nanao MH]]
-[[Category: Nanao, M H.]]
+[[Category: Ravelli RB]]
-[[Category: Ravelli, R B.]]
-[[Category: Bacteriolytic enzyme]]
-[[Category: Direct protein sequencing]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Phasing]]
-[[Category: Radiation damage]]
-[[Category: Rip]]
-[[Category: Synchrotron]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 20:28:16 2008''