5pv3 - Revision history

OCA at 13:20, 6 March 2024

2024-03-06T13:20:27Z

←Older revision		Revision as of 13:20, 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 5pv3" style="background-color:#fffaf0;"></div>

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

OCA at 13:15, 17 January 2024

2024-01-17T13:15:09Z

←Older revision		Revision as of 13:15, 17 January 2024
Line 1:		Line 1:

	==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 217)==		==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 217)==
-	<StructureSection load='5pv3' size='340' side='right' caption='[[5pv3]], [[Resolution\|resolution]] 1.48Å' scene=''>	+	<StructureSection load='5pv3' size='340' side='right'caption='[[5pv3]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pv3]] 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=5PV3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5PV3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pv3]] 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=5PV3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PV3 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]] 1.48Å</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=5pv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pv3 OCA], [~~http~~://pdbe.org/5pv3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5pv3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5pv3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5pv3 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=5pv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pv3 OCA], [https://pdbe.org/5pv3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pv3 RCSB], [https://www.ebi.ac.uk/pdbsum/5pv3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pv3 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 5pv3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5pv3" 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 14:12, 6 November 2017

2017-11-06T14:12:11Z

←Older revision		Revision as of 14:12, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5pv3' size='340' side='right' caption='[[5pv3]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='5pv3' size='340' side='right' caption='[[5pv3]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pv3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PV3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pv3]] 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=5PV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PV3 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=5pv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pv3 OCA], [http://pdbe.org/5pv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pv3 RCSB], [http://www.ebi.ac.uk/pdbsum/5pv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pv3 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=5pv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pv3 OCA], [http://pdbe.org/5pv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pv3 RCSB], [http://www.ebi.ac.uk/pdbsum/5pv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pv3 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 10:06, 27 September 2017

2017-09-27T10:06:33Z

←Older revision		Revision as of 10:06, 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 5pv3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:01, 29 March 2017

2017-03-29T14:01:25Z

←Older revision		Revision as of 14:01, 29 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5pv3 ~~is ON HOLD~~	+	==PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 217)==
-		+	<StructureSection load='5pv3' size='340' side='right' caption='[[5pv3]], [[Resolution\|resolution]] 1.48Å' 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'>[[5pv3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PV3 FirstGlance]. <br>
-	~~Description~~: ~~PanDDA analysis group deposition --Crystal Structure~~ of ~~BRD1 after initial refinement with no ligand modelled (structure 217)~~	+	</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=5pv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pv3 OCA], [http://pdbe.org/5pv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pv3 RCSB], [http://www.ebi.ac.uk/pdbsum/5pv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pv3 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 17:55, 15 March 2017

2017-03-15T17:55:27Z

←Older revision		Revision as of 17:55, 15 March 2017
Line 3:		Line 3:
	The entry 5pv3 is ON HOLD		The entry 5pv3 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 217)		Description: PanDDA analysis group deposition --Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 217)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Pearce, N.M]]
		+	[[Category: Collins, P]]
		+	[[Category: Cox, O]]
		+	[[Category: Arrowsmith, C.H]]
		+	[[Category: Brandao-Neto, J]]
		+	[[Category: Fairhead, M]]
		+	[[Category: Von Delft, F]]
		+	[[Category: Renjie, Z]]
		+	[[Category: Wright, N]]
		+	[[Category: Ng, J]]
		+	[[Category: Bradley, A.R]]
		+	[[Category: Talon, R]]
		+	[[Category: Brennan, P.E]]
		+	[[Category: Edwards, A]]
		+	[[Category: Douangamath, A]]
		+	[[Category: Maclean, E]]
	[[Category: Krojer, T]]		[[Category: Krojer, T]]
		+	[[Category: Dias, A]]
		+	[[Category: Sethi, R]]
		+	[[Category: Bountra, C]]

OCA: Protected "5pv3" [edit=sysop:move=sysop]

2017-03-09T13:08:06Z

Protected "5pv3" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:08, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5pv3 is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of BRD1 after initial refinement with no liga...

2017-03-09T13:08:05Z

New page: '''Unreleased structure''' The entry 5pv3 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 5pv3 is ON HOLD

Authors: Krojer, T.

Description: PanDDA analysis group deposition --Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 217)
[[Category: Unreleased Structures]]
[[Category: Krojer, T]]