1dwh: Difference between revisions

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-{{Seed}}
-[[Image:1dwh.png|left|200px]]
-<!--
+==Study on radiation damage on a cryocooled crystal. Part 4: Structure after irradiation with 27.2*10e15 photons/mm2==
-The line below this paragraph, containing "STRUCTURE_1dwh", creates the "Structure Box" on the page.
+<StructureSection load='1dwh' size='340' side='right'caption='[[1dwh]], [[Resolution|resolution]] 2.00&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'>[[1dwh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sinapis_alba Sinapis alba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DWH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DWH 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]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1dwh|  PDB=1dwh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dwh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dwh OCA], [https://pdbe.org/1dwh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dwh RCSB], [https://www.ebi.ac.uk/pdbsum/1dwh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dwh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MYRA_SINAL MYRA_SINAL] Degradation of glucosinolates (glucose residue linked by a thioglucoside bound to an amino acid derivative) to glucose, sulfate and any of the products: thiocyanates, isothiocyanates, nitriles, epithionitriles or oxazolidine-2-thiones.
+== 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/dw/1dwh_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=1dwh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The high intensity of third-generation X-ray sources, along with the development of cryo-cooling of protein crystals at temperatures around 100 K, have made it possible to extend the diffraction limit of crystals and to reduce their size. However, even with cryo-cooled crystals, radiation damage becomes a limiting factor. So far, the radiation damage has manifested itself in the form of a loss of overall diffracted intensity and an increase in the temperature factor. The structure of a protein (myrosinase) after exposure to different doses of X-rays in the region of 20 x 10(15) photons mm(-2) has been studied. The changes in the structure owing to radiation damage were analysed using Fourier difference maps and occupancy refinement for the first time. Damage was obvious in the form of breakage of disulfide bonds, decarboxylation of aspartate and glutamate residues, a loss of hydroxyl groups from tyrosine and of the methylthio group of methionine. The susceptibility to radiation damage of individual groups of the same kind varies within the protein. The quality of the model resulting from structure determination might be compromised owing to the presence of radiolysis in the crystal after an excessive radiation dose. Radiation-induced structural changes may interfere with the interpretation of ligand-binding studies or MAD data. The experiments reported here suggest that there is an intrinsic limit to the amount of data which can be extracted from a sample of a given size.
-===STUDY ON RADIATION DAMAGE ON A CRYOCOOLED CRYSTAL. PART 4: STRUCTURE AFTER IRRADIATION WITH 27.2*10E15 PHOTONS/MM2===
+Structural changes in a cryo-cooled protein crystal owing to radiation damage.,Burmeister WP Acta Crystallogr D Biol Crystallogr. 2000 Mar;56(Pt 3):328-41. PMID:10713520<ref>PMID:10713520</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_10713520}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1dwh" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 10713520 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10713520}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-DWH is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Sinapis_alba Sinapis alba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DWH OCA].
-==Reference==
-<ref group="xtra">PMID:10713520</ref><ref group="xtra">PMID:9195886</ref><references group="xtra"/>
 [[Category: Sinapis alba]]
-[[Category: Thioglucosidase]]
+[[Category: Burmeister WP]]
-[[Category: Burmeister, W P.]]
-[[Category: Cryo-cooled]]
-[[Category: Glycosidase]]
-[[Category: Hydrolase]]
-[[Category: Irradiation]]
-[[Category: Myrosinase]]
-[[Category: Radiation damage]]
-[[Category: Radiolysis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun  3 10:09:34 2009''