5php - Revision history

OCA at 08:49, 18 February 2026

2026-02-18T08:49:23Z

← Older revision		Revision as of 08:49, 18 February 2026
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	== Function ==		== Function ==
	[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>		[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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5php" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 12:55, 6 March 2024

2024-03-06T12:55:08Z

← Older revision		Revision as of 12:55, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[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>		[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®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 5php" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==

OCA at 12:55, 17 January 2024

2024-01-17T12:55:32Z

← Older revision		Revision as of 12:55, 17 January 2024
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	==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 2)==		==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 2)==
	<StructureSection load='5php' size='340' side='right' caption='[[5php]], [[Resolution\|resolution]] 1.72Å' scene=''>		<StructureSection load='5php' size='340' side='right'caption='[[5php]], [[Resolution\|resolution]] 1.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5php]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PHP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5PHP FirstGlance]. <br>		<table><tr><td colspan='2'>[[5php]] 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=5PHP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PHP 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]] 1.72Å</td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KDM4D, JHDM3D, JMJD2D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5php FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5php OCA], [~~http~~://pdbe.org/5php PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5php RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5php PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5php ProSAT]</span></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=5php FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5php OCA], [https://pdbe.org/5php PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5php RCSB], [https://www.ebi.ac.uk/pdbsum/5php PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5php ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5php" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5php" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Jumonji domain-containing protein 3D structures\|Jumonji domain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Arrowsmith~~, C H~~]]		[[Category: Large Structures]]
	[[Category: Bountra, C]]		[[Category: Arrowsmith CH]]
	[[Category: Bradley~~, A R~~]]		[[Category: Bountra C]]
	[[Category: Brandao-Neto, J]]		[[Category: Bradley AR]]
	[[Category: Brennan~~, P E~~]]		[[Category: Brandao-Neto J]]
	[[Category: Burgess-Brown, N]]		[[Category: Brennan PE]]
	[[Category: Collins, P]]		[[Category: Burgess-Brown N]]
	[[Category: Cox, O]]		[[Category: Collins P]]
	~~[[Category: Delft, F von~~]]		[[Category: Cox O]]
	[[Category: Dias, A]]		[[Category: Dias A]]
	[[Category: Douangamath, A]]		[[Category: Douangamath A]]
	[[Category: Edwards, A]]		[[Category: Edwards A]]
	[[Category: Fairhead, M]]		[[Category: Fairhead M]]
	[[Category: Krojer, T]]		[[Category: Krojer T]]
	[[Category: MacLean, E]]		[[Category: MacLean E]]
	[[Category: Ng, J]]		[[Category: Ng J]]
	[[Category: Oppermann, U]]		[[Category: Oppermann U]]
	[[Category: Pearce~~, N M~~]]		[[Category: Pearce NM]]
	[[Category: Renjie, Z]]		[[Category: Renjie Z]]
	[[Category: Sethi, R]]		[[Category: Sethi R]]
	[[Category: Szykowska, A]]		[[Category: Szykowska A]]
	[[Category: Talon, R]]		[[Category: Talon R]]
	[[Category: Vollmar, M]]		[[Category: Vollmar M]]
	[[Category: Wright, N]]		[[Category: Wright N]]
	[[Category: ~~Epigenetic]]~~		[[Category: Von Delft F]]
	~~[[Category: Jmj domain]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Pandda]]~~
	~~[[Category: Sgc - diamond i04-1 fragment screening~~]]

OCA at 13:27, 6 November 2017

2017-11-06T13:27:25Z

← Older revision		Revision as of 13:27, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5php' size='340' side='right' caption='[[5php]], [[Resolution\|resolution]] 1.72Å' scene=''>		<StructureSection load='5php' size='340' side='right' caption='[[5php]], [[Resolution\|resolution]] 1.72Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5php]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PHP FirstGlance]. <br>		<table><tr><td colspan='2'>[[5php]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PHP 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='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>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KDM4D, JHDM3D, JMJD2D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5php FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5php OCA], [http://pdbe.org/5php PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5php RCSB], [http://www.ebi.ac.uk/pdbsum/5php PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5php ProSAT]</span></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=5php FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5php OCA], [http://pdbe.org/5php PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5php RCSB], [http://www.ebi.ac.uk/pdbsum/5php PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5php ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5php" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5php" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Jumonji domain-containing protein\|Jumonji domain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 09:18, 27 September 2017

2017-09-27T09:18:45Z

@@ Line 9: / Line 9: @@
 == 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>
 == References ==
 <references/>

OCA at 21:24, 15 March 2017

2017-03-15T21:24:37Z

@@ Line 1: / Line 1: @@
-The entry 5php is ON HOLD
+==PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 2)==
+<StructureSection load='5php' size='340' side='right' caption='[[5php]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
-Authors: Krojer, T.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5php]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PHP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PHP FirstGlance]. <br>
-Description: PanDDA analysis group deposition --Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 2)
+</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>
-[[Category: Unreleased Structures]]
+<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=5php FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5php OCA], [http://pdbe.org/5php PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5php RCSB], [http://www.ebi.ac.uk/pdbsum/5php PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5php ProSAT]</span></td></tr>
 [[Category: Krojer, T]]

OCA: Protected "5php" [edit=sysop:move=sysop]

2017-03-09T12:41:14Z

Protected "5php" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:41, 9 March 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5php is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of JMJD2D after initial refinement with no li...

2017-03-09T12:41:13Z

New page: '''Unreleased structure''' The entry 5php is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of JMJD2D after initial refinement with no li...

New page

'''Unreleased structure'''

The entry 5php is ON HOLD

Authors: Krojer, T.

Description: PanDDA analysis group deposition --Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 2)
[[Category: Unreleased Structures]]
[[Category: Krojer, T]]