5pfj - Revision history

OCA at 12:51, 6 March 2024

OCA — Wed, 06 Mar 2024 12:51:16 GMT

←Older revision		Revision as of 12:51, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN] May play a role in transcriptional regulation interacting with ISWI.		[https://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN] May play a role in transcriptional regulation interacting with ISWI.
-	<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 5pfj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Bromodomain adjacent to zinc finger 3D structures\|Bromodomain adjacent to zinc finger 3D structures]]		*[[Bromodomain adjacent to zinc finger 3D structures\|Bromodomain adjacent to zinc finger 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:44, 10 January 2024

OCA — Wed, 10 Jan 2024 12:44:36 GMT

←Older revision		Revision as of 12:44, 10 January 2024
Line 1:		Line 1:

	==PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 148)==		==PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 148)==
-	<StructureSection load='5pfj' size='340' side='right' caption='[[5pfj]], [[Resolution\|resolution]] 2.07Å' scene=''>	+	<StructureSection load='5pfj' size='340' side='right'caption='[[5pfj]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pfj]] 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=5PFJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5PFJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pfj]] 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=5PFJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5PFJ 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>~~</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]] 2.07Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~BAZ2B, KIAA1476 ([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></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=5pfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pfj OCA], [~~http~~://pdbe.org/5pfj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5pfj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5pfj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5pfj 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=5pfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pfj OCA], [https://pdbe.org/5pfj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5pfj RCSB], [https://www.ebi.ac.uk/pdbsum/5pfj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5pfj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN]] May play a role in transcriptional regulation interacting with ISWI.	+	[https://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN] May play a role in transcriptional regulation interacting with ISWI.
	<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 5pfj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5pfj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bromodomain adjacent to zinc finger 3D structures\|Bromodomain adjacent to zinc finger 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: Vollmar, M]]	+	[[Category: Vollmar M]]
-	[[Category: Wright, N]]	+	[[Category: Wright N]]
-	[[Category: ~~Bromodomain]]~~	+	[[Category: Von Delft F]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Epigenetic]]~~	+
-	~~[[Category: Pandda]]~~	+
-	~~[[Category: Sgc - diamond i04-1 fragment screening~~]]	+

OCA at 13:21, 6 November 2017

OCA — Mon, 06 Nov 2017 13:21:43 GMT

←Older revision		Revision as of 13:21, 6 November 2017
Line 3:		Line 3:
	<StructureSection load='5pfj' size='340' side='right' caption='[[5pfj]], [[Resolution\|resolution]] 2.07Å' scene=''>		<StructureSection load='5pfj' size='340' side='right' caption='[[5pfj]], [[Resolution\|resolution]] 2.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5pfj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PFJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PFJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5pfj]] 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=5PFJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PFJ 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></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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAZ2B, KIAA1476 ([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=5pfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pfj OCA], [http://pdbe.org/5pfj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pfj RCSB], [http://www.ebi.ac.uk/pdbsum/5pfj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pfj 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=5pfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pfj OCA], [http://pdbe.org/5pfj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pfj RCSB], [http://www.ebi.ac.uk/pdbsum/5pfj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pfj 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 10:21, 27 September 2017

OCA — Wed, 27 Sep 2017 10:21:31 GMT

←Older revision		Revision as of 10:21, 27 September 2017
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN]] May play a role in transcriptional regulation interacting with ISWI.		[[http://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN]] May play a role in transcriptional regulation interacting with ISWI.
		+	<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 5pfj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:34, 22 March 2017

OCA — Wed, 22 Mar 2017 16:34:21 GMT

←Older revision		Revision as of 16:34, 22 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5pfj ~~is ON HOLD~~	+	==PanDDA analysis group deposition -- Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 148)==
-		+	<StructureSection load='5pfj' size='340' side='right' caption='[[5pfj]], [[Resolution\|resolution]] 2.07Å' 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~~., ~~Vollmar, M~~., ~~Ng, J~~.~~, Brennan, P~~.E., ~~Cox, O~~.~~, Bountra, C~~.~~, Arrowsmith, C~~.~~H., Edwards~~, A.~~, von Delft, F~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5pfj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5PFJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5PFJ FirstGlance]. <br>
-	~~Description~~: ~~PanDDA analysis group deposition --Crystal Structure of BAZ2B after initial refinement~~ with ~~no ligand modelled (structure 148)~~	+	</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></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=5pfj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5pfj OCA], [http://pdbe.org/5pfj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5pfj RCSB], [http://www.ebi.ac.uk/pdbsum/5pfj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5pfj ProSAT]</span></td></tr>
-	[[Category: ~~Pearce~~, ~~N.M~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN]] May play a role in transcriptional regulation interacting with ISWI.
		+	__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: ~~Wright~~, ~~N]]~~	+	[[Category: Sethi, R]]
-	~~[[Category: Ng, J]]~~	+
-	~~[[Category: Bradley, A.~~R]]	+
	[[Category: Talon, R]]		[[Category: Talon, R]]
-	[[Category: Brennan, P.E]]
-	[[Category: Edwards, A]]
-	[[Category: Douangamath, A]]
-	[[Category: Maclean, E]]
-	[[Category: Krojer, T]]
-	[[Category: Dias, A]]
-	[[Category: Sethi, R]]
-	[[Category: Bountra, C]]
	[[Category: Vollmar, M]]		[[Category: Vollmar, M]]
		+	[[Category: Wright, N]]
		+	[[Category: Bromodomain]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Epigenetic]]
		+	[[Category: Pandda]]
		+	[[Category: Sgc - diamond i04-1 fragment screening]]

OCA at 17:41, 15 March 2017

OCA — Wed, 15 Mar 2017 17:41:30 GMT

←Older revision		Revision as of 17:41, 15 March 2017
Line 3:		Line 3:
	The entry 5pfj is ON HOLD		The entry 5pfj 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., Vollmar, M., 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 BAZ2B after initial refinement with no ligand modelled (structure 148)		Description: PanDDA analysis group deposition --Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 148)
	[[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]]
		+	[[Category: Vollmar, M]]

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

OCA — Thu, 09 Mar 2017 12:37:29 GMT

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

←Older revision

Revision as of 12:37, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5pfj is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of BAZ2B after initial refinement with no lig...

OCA — Thu, 09 Mar 2017 12:37:27 GMT

New page: '''Unreleased structure''' The entry 5pfj is ON HOLD Authors: Krojer, T. Description: PanDDA analysis group deposition --Crystal Structure of BAZ2B after initial refinement with no lig...

New page

'''Unreleased structure'''

The entry 5pfj is ON HOLD

Authors: Krojer, T.

Description: PanDDA analysis group deposition --Crystal Structure of BAZ2B after initial refinement with no ligand modelled (structure 148)
[[Category: Unreleased Structures]]
[[Category: Krojer, T]]