5pv0: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
 ==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 214)==
-<StructureSection load='5pv0' size='340' side='right' caption='[[5pv0]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
+<StructureSection load='5pv0' size='340' side='right'caption='[[5pv0]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5pv0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PV0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PV0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5pv0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PV0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.76&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5pv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pv0 OCA], [http://pdbe.org/5pv0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pv0 RCSB], [http://www.ebi.ac.uk/pdbsum/5pv0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pv0 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5pv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pv0 OCA], [https://pdbe.org/5pv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pv0 RCSB], [https://www.ebi.ac.uk/pdbsum/5pv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pv0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BRD1_HUMAN BRD1_HUMAN]] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity.<ref>PMID:16387653</ref> <ref>PMID:21880731</ref>
+[https://www.uniprot.org/uniprot/BRD1_HUMAN BRD1_HUMAN] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity.<ref>PMID:16387653</ref> <ref>PMID:21880731</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-In macromolecular crystallography, the rigorous detection of changed states (for example, ligand binding) is difficult unless signal is strong. Ambiguous ('weak' or 'noisy') density is experimentally common, since molecular states are generally only fractionally present in the crystal. Existing methodologies focus on generating maximally accurate maps whereby minor states become discernible; in practice, such map interpretation is disappointingly subjective, time-consuming and methodologically unsound. Here we report the PanDDA method, which automatically reveals clear electron density for the changed state-even from inaccurate maps-by subtracting a proportion of the confounding 'ground state'; changed states are objectively identified from statistical analysis of density distributions. The method is completely general, implying new best practice for all changed-state studies, including the routine collection of multiple ground-state crystals. More generally, these results demonstrate: the incompleteness of atomic models; that single data sets contain insufficient information to model them fully; and that accuracy requires further map-deconvolution approaches.
-A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.,Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F Nat Commun. 2017 Apr 24;8:15123. doi: 10.1038/ncomms15123. PMID:28436492<ref>PMID:28436492</ref>
+==See Also==
+*[[Bromodomain-containing protein 3D structures|Bromodomain-containing protein 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5pv0" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Arrowsmith, C H]]
+[[Category: Homo sapiens]]
-[[Category: Bountra, C]]
+[[Category: Large Structures]]
-[[Category: Bradley, A R]]
+[[Category: Arrowsmith CH]]
-[[Category: Brandao-Neto, J]]
+[[Category: Bountra C]]
-[[Category: Brennan, P E]]
+[[Category: Bradley AR]]
-[[Category: Collins, P]]
+[[Category: Brandao-Neto J]]
-[[Category: Cox, O]]
+[[Category: Brennan PE]]
-[[Category: Delft, F von]]
+[[Category: Collins P]]
-[[Category: Dias, A]]
+[[Category: Cox O]]
-[[Category: Douangamath, A]]
+[[Category: Dias A]]
-[[Category: Edwards, A]]
+[[Category: Douangamath A]]
-[[Category: Fairhead, M]]
+[[Category: Edwards A]]
-[[Category: Krojer, T]]
+[[Category: Fairhead M]]
-[[Category: MacLean, E]]
+[[Category: Krojer T]]
-[[Category: Ng, J]]
+[[Category: MacLean E]]
-[[Category: Pearce, N M]]
+[[Category: Ng J]]
-[[Category: Renjie, Z]]
+[[Category: Pearce NM]]
-[[Category: Sethi, R]]
+[[Category: Renjie Z]]
-[[Category: Talon, R]]
+[[Category: Sethi R]]
-[[Category: Wright, N]]
+[[Category: Talon R]]
-[[Category: Bromodomain]]
+[[Category: Wright N]]
-[[Category: Epigenetic]]
+[[Category: Von Delft F]]
-[[Category: Gene regulation]]
-[[Category: Pandda]]
-[[Category: Sgc - diamond i04-1 fragment screening]]
-[[Category: Xchemexplorer]]