5ptr - Revision history

OCA at 10:34, 18 February 2026

2026-02-18T10:34:04Z

← Older revision		Revision as of 10:34, 18 February 2026
Line 10:		Line 10:
	== Function ==		== Function ==
	[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>		[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>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5ptr" style="background-color:#fffaf0;"></div>

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

OCA at 13:17, 6 March 2024

2024-03-06T13:17:59Z

← Older revision		Revision as of 13:17, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[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>		[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>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 5ptr" style="background-color:#fffaf0;"></div>~~

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

OCA at 13:13, 17 January 2024

2024-01-17T13:13:17Z

← Older revision		Revision as of 13:13, 17 January 2024
Line 1:		Line 1:

	==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 169)==		==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 169)==
	<StructureSection load='5ptr' size='340' side='right' caption='[[5ptr]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='5ptr' size='340' side='right'caption='[[5ptr]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ptr]] is a 2 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=5PTR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5PTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ptr]] 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=5PTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PTR 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]] 1.52Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~BRD1~~, ~~BRL~~, ~~BRPF2 ([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=NA:SODIUM+ION'>NA</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=5ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ptr OCA], [~~http~~://pdbe.org/5ptr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ptr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ptr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ptr 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=5ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ptr OCA], [https://pdbe.org/5ptr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ptr RCSB], [https://www.ebi.ac.uk/pdbsum/5ptr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ptr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ptr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ptr" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Bromodomain-containing protein 3D structures\|Bromodomain-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: Collins, P]]		[[Category: Brennan PE]]
	[[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: Pearce~~, N M~~]]		[[Category: Pearce NM]]
	[[Category: Renjie, Z]]		[[Category: Renjie Z]]
	[[Category: Sethi, R]]		[[Category: Sethi R]]
	[[Category: Talon, R]]		[[Category: Talon R]]
	[[Category: Wright, N]]		[[Category: Wright N]]
	[[Category: ~~Bromodomain]]~~		[[Category: Von Delft F]]
	~~[[Category: Epigenetic]]~~
	~~[[Category: Gene regulation]]~~
	~~[[Category: Pandda]]~~
	~~[[Category: Sgc - diamond i04-1 fragment screening]]~~
	~~[[Category: Xchemexplorer~~]]

OCA at 14:08, 6 November 2017

2017-11-06T14:08:22Z

← Older revision		Revision as of 14:08, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5ptr' size='340' side='right' caption='[[5ptr]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='5ptr' size='340' side='right' caption='[[5ptr]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ptr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ptr]] is a 2 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=5PTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PTR 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='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>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD1, BRL, BRPF2 ([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=5ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ptr OCA], [http://pdbe.org/5ptr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ptr RCSB], [http://www.ebi.ac.uk/pdbsum/5ptr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ptr 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=5ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ptr OCA], [http://pdbe.org/5ptr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ptr RCSB], [http://www.ebi.ac.uk/pdbsum/5ptr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ptr ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 10:27, 27 September 2017

2017-09-27T10:27:57Z

← Older revision		Revision as of 10:27, 27 September 2017
Line 9:		Line 9:
	== Function ==		== 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>		[[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>
			<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 5ptr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:58, 29 March 2017

2017-03-29T13:58:30Z

← Older revision		Revision as of 13:58, 29 March 2017
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 5ptr ~~is ON HOLD~~		==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 169)==
			<StructureSection load='5ptr' size='340' side='right' caption='[[5ptr]], [[Resolution\|resolution]] 1.52Å' scene=''>
	~~Authors~~: ~~Pearce, N~~.M.~~, Krojer, T~~.~~, Talon, R~~.~~, Bradley, A~~.R.~~, Fairhead, M~~.~~, Sethi, R~~., ~~Wright~~, N.~~, MacLean, E~~.~~, Collins, P~~.~~, Brandao~~-~~Neto, J~~., ~~Douangamath, A~~.~~, Renjie, Z~~.~~, Dias, A~~., ~~Ng, J~~., ~~Brennan, P~~.E.~~, Cox, O~~., ~~Bountra, C~~.~~, Arrowsmith, C~~.H., ~~Edwards, A~~.~~, von Delft, F~~.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5ptr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PTR FirstGlance]. <br>
	~~Description~~: ~~PanDDA analysis group deposition --Crystal Structure~~ of ~~BRD1 after initial refinement with no ligand modelled (structure 169)~~		</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>
	[[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=5ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ptr OCA], [http://pdbe.org/5ptr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ptr RCSB], [http://www.ebi.ac.uk/pdbsum/5ptr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ptr ProSAT]</span></td></tr>
	[[Category: ~~Pearce~~, ~~N.M~~]]		</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>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Arrowsmith, C H]]
			[[Category: Bountra, C]]
			[[Category: Bradley, A R]]
			[[Category: Brandao-Neto, J]]
			[[Category: Brennan, P E]]
	[[Category: Collins, P]]		[[Category: Collins, P]]
	[[Category: Cox, O]]		[[Category: Cox, O]]
	[[Category: ~~Arrowsmith~~, ~~C.H~~]]		[[Category: Delft, F von]]
	[[Category: ~~Brandao-Neto~~, J]]		[[Category: Dias, A]]
			[[Category: Douangamath, A]]
			[[Category: Edwards, A]]
	[[Category: Fairhead, M]]		[[Category: Fairhead, M]]
	[[Category: ~~Von Delft~~, F]]		[[Category: Krojer, T]]
			[[Category: MacLean, E]]
			[[Category: Ng, J]]
			[[Category: Pearce, N M]]
	[[Category: Renjie, Z]]		[[Category: Renjie, Z]]
			[[Category: Sethi, R]]
			[[Category: Talon, R]]
	[[Category: Wright, N]]		[[Category: Wright, N]]
	[[Category: ~~Ng, J~~]]		[[Category: Bromodomain]]
	[[Category: ~~Bradley, A.R~~]]		[[Category: Epigenetic]]
	[[Category: ~~Talon, R~~]]		[[Category: Gene regulation]]
	[[Category: ~~Brennan, P.E~~]]		[[Category: Pandda]]
	[[Category: ~~Edwards, A~~]]		[[Category: Sgc - diamond i04-1 fragment screening]]
	[[Category: ~~Douangamath, A]]~~		[[Category: Xchemexplorer]]
	~~[[Category: Maclean, E]]~~
	~~[[Category: Krojer, T]]~~
	~~[[Category: Dias, A]]~~
	~~[[Category: Sethi, R]]~~
	~~[[Category: Bountra, C~~]]

OCA at 17:52, 15 March 2017

2017-03-15T17:52:33Z

@@ Line 3: / Line 3: @@
 The entry 5ptr is ON HOLD
-Authors: Krojer, T.
+Authors: Pearce, N.M., Krojer, T., Talon, R., Bradley, A.R., Fairhead, M., Sethi, R., Wright, N., MacLean, E., Collins, P., Brandao-Neto, J., Douangamath, A., Renjie, Z., Dias, A., Ng, J., Brennan, P.E., Cox, O., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.
 Description: PanDDA analysis group deposition --Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 169)
 [[Category: Unreleased Structures]]
 [[Category: Krojer, T]]

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

2017-03-09T13:05:46Z

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

← Older revision	Revision as of 13:05, 9 March 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5ptr is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of BRD1 after initial refinement with no liga...

2017-03-09T13:05:45Z

New page: '''Unreleased structure''' The entry 5ptr is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of BRD1 after initial refinement with no liga...

New page

'''Unreleased structure'''

The entry 5ptr is ON HOLD

Authors: Krojer, T.

Description: PanDDA analysis group deposition --Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 169)
[[Category: Unreleased Structures]]
[[Category: Krojer, T]]