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5pmk

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PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 178)

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 ==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 178)==
-<StructureSection load='5pmk' size='340' side='right' caption='[[5pmk]], [[Resolution|resolution]] 1.44&Aring;' scene=''>
+<StructureSection load='5pmk' size='340' side='right'caption='[[5pmk]], [[Resolution|resolution]] 1.44&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5pmk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PMK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5pmk]] is a 1 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=5PMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PMK 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.44&#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=5pmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pmk OCA], [http://pdbe.org/5pmk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pmk RCSB], [http://www.ebi.ac.uk/pdbsum/5pmk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pmk 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <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=5pmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pmk OCA], [https://pdbe.org/5pmk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pmk RCSB], [https://www.ebi.ac.uk/pdbsum/5pmk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pmk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KDM4D_HUMAN KDM4D_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</ref>
+[https://www.uniprot.org/uniprot/KDM4D_HUMAN KDM4D_HUMAN] Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate.<ref>PMID:16603238</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>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5pmk" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Jumonji domain-containing protein|Jumonji domain-containing protein]]
+*[[Jumonji domain-containing protein 3D structures|Jumonji domain-containing protein 3D structures]]
 == 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: Burgess-Brown, N]]
+[[Category: Brandao-Neto J]]
-[[Category: Collins, P]]
+[[Category: Brennan PE]]
-[[Category: Cox, O]]
+[[Category: Burgess-Brown N]]
-[[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: Oppermann, U]]
+[[Category: Ng J]]
-[[Category: Pearce, N M]]
+[[Category: Oppermann U]]
-[[Category: Renjie, Z]]
+[[Category: Pearce NM]]
-[[Category: Sethi, R]]
+[[Category: Renjie Z]]
-[[Category: Szykowska, A]]
+[[Category: Sethi R]]
-[[Category: Talon, R]]
+[[Category: Szykowska A]]
-[[Category: Vollmar, M]]
+[[Category: Talon R]]
-[[Category: Wright, N]]
+[[Category: Vollmar M]]
-[[Category: Epigenetic]]
+[[Category: Wright N]]
-[[Category: Jmj domain]]
+[[Category: Von Delft F]]
-[[Category: Oxidoreductase]]
-[[Category: Pandda]]
-[[Category: Sgc - diamond i04-1 fragment screening]]

5pmk

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PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 178)

Structural highlights

Function

See Also

References

Contents

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