1rb7: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1rb7.gif|left|200px]]<br /><applet load="1rb7" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1rb7, resolution 2.10&Aring;" />
-'''Yeast cytosine deaminase crystal form p212121 with sodium acetate.'''<br />
-==Overview==
+==Yeast cytosine deaminase crystal form p212121 with sodium acetate.==
-A crystallization strategy termed 'microseed matrix screening' is, described where the optimal conditions for nucleation versus extended, lattice growth are not compatible. This method is an extension of, conventional seeding techniques in which microseeds from the nucleation, step are systematically seeded into new conditions where all components of, the drop are allowed to vary to screen for subsequent growth of well, ordered specimens. The structure of a crystal form of yeast cytosine, deaminase produced by streak-seeding using a single condition for both, nucleation and growth is compared with the structure of a related crystal, form produced by separating nucleation and growth conditions. The, resulting structural comparison demonstrates that differential chelation, patterns of cations by acidic surface residues of proteins within crystal, lattice contacts is a critical parameter of crystal nucleation and growth.
+<StructureSection load='1rb7' size='340' side='right'caption='[[1rb7]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rb7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RB7 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]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1rb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rb7 OCA], [https://pdbe.org/1rb7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rb7 RCSB], [https://www.ebi.ac.uk/pdbsum/1rb7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rb7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FCY1_YEAST FCY1_YEAST] Converts cytosine to uracil or 5-methylcytosine to thymine by deaminating carbon number 4.
+== 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/rb/1rb7_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=1rb7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A crystallization strategy termed 'microseed matrix screening' is described where the optimal conditions for nucleation versus extended lattice growth are not compatible. This method is an extension of conventional seeding techniques in which microseeds from the nucleation step are systematically seeded into new conditions where all components of the drop are allowed to vary to screen for subsequent growth of well ordered specimens. The structure of a crystal form of yeast cytosine deaminase produced by streak-seeding using a single condition for both nucleation and growth is compared with the structure of a related crystal form produced by separating nucleation and growth conditions. The resulting structural comparison demonstrates that differential chelation patterns of cations by acidic surface residues of proteins within crystal lattice contacts is a critical parameter of crystal nucleation and growth.
-==About this Structure==
+Microseed matrix screening to improve crystals of yeast cytosine deaminase.,Ireton GC, Stoddard BL Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):601-5. Epub 2004, Feb 25. PMID:14993707<ref>PMID:14993707</ref>
-RB7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Cytosine_deaminase Cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.1 3.5.4.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RB7 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Microseed matrix screening to improve crystals of yeast cytosine deaminase., Ireton GC, Stoddard BL, Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):601-5. Epub 2004, Feb 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14993707 14993707]
+</div>
-[[Category: Cytosine deaminase]]
+<div class="pdbe-citations 1rb7" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Deaminase 3D structures|Deaminase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Ireton GC]]
-[[Category: Ireton, G.C.]]
+[[Category: Stoddard BL]]
-[[Category: Stoddard, B.L.]]
-[[Category: ZN]]
-[[Category: amino hydrolase]]
-[[Category: cytosine deaminase]]
-[[Category: streak seeding]]
-[[Category: zinc bound]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:25:43 2007''