7l9q - Revision history

OCA at 15:41, 18 October 2023

OCA — Wed, 18 Oct 2023 15:41:42 GMT

←Older revision		Revision as of 15:41, 18 October 2023
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	<StructureSection load='7l9q' size='340' side='right'caption='[[7l9q]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='7l9q' size='340' side='right'caption='[[7l9q]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7l9q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Psef5 Psef5~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L9Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7l9q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_protegens_Pf-5 Pseudomonas protegens Pf-5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L9Q FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>inhA, PFL_4109 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=220664 PSEF5])</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]] 1.149Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cyclohexyl~~-~~isocyanide_hydratase Cyclohexyl-isocyanide hydratase]~~, ~~with EC number~~ [~~https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.~~1.~~103 4.2.1.103] </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=7l9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l9q OCA], [https://pdbe.org/7l9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l9q RCSB], [https://www.ebi.ac.uk/pdbsum/7l9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l9q 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=7l9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l9q OCA], [https://pdbe.org/7l9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l9q RCSB], [https://www.ebi.ac.uk/pdbsum/7l9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l9q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4K977_PSEF5 Q4K977_PSEF5]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cyclohexyl-isocyanide hydratase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Psef5]]~~	+	[[Category: Pseudomonas protegens Pf-5]]
-	~~[[Category: Bedem, H van den~~]]	+	[[Category: Dasgupta M]]
-	[[Category: Dasgupta, M]]	+	[[Category: Mathews II]]
-	[[Category: Mathews~~, I I~~]]	+	[[Category: Poitevin F]]
-	[[Category: Poitevin, F]]	+	[[Category: Su Z]]
-	[[Category: Su, Z]]	+	[[Category: Wall ME]]
-	[[Category: Wall~~, M E~~]]	+	[[Category: Wilson MA]]
-	[[Category: Wilson~~, M A~~]]	+	[[Category: Yoon CH]]
-	[[Category: Yoon~~, C H~~]]	+	[[Category: Van den Bedem H]]
-	[[Category: ~~Diffuse scattering]]~~	+
-	~~[[Category: Dj-1/pfpi superfamily]]~~	+
-	~~[[Category: Isocyanide]]~~	+
-	~~[[Category: Isonitrile]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:51, 28 July 2021

OCA — Wed, 28 Jul 2021 10:51:07 GMT

←Older revision		Revision as of 10:51, 28 July 2021
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	==Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-1) at 274K, Refmac5-refined==		==Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-1) at 274K, Refmac5-refined==
-	<StructureSection load='7l9q' size='340' side='right'caption='[[7l9q]]' scene=''>	+	<StructureSection load='7l9q' size='340' side='right'caption='[[7l9q]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L9Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7l9q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Psef5 Psef5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L9Q FirstGlance]. <br>
-	</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=7l9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l9q OCA], [https://pdbe.org/7l9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l9q RCSB], [https://www.ebi.ac.uk/pdbsum/7l9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l9q ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">inhA, PFL_4109 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220664 PSEF5])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cyclohexyl-isocyanide_hydratase Cyclohexyl-isocyanide hydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.103 4.2.1.103] </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=7l9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l9q OCA], [https://pdbe.org/7l9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l9q RCSB], [https://www.ebi.ac.uk/pdbsum/7l9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l9q ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks-diffuse scattering-is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from different mutants were similar in pairwise comparisons (Pearson correlation coefficient >/=0.8). The data were processed in a manner inspired by previously published methods using custom software with modular design, enabling us to perform an analysis of various data processing choices to determine how to obtain the highest quality data as assessed using unbiased measures of symmetry and reproducibility. The diffuse data were then used to characterize atomic mobility using a liquid-like motions (LLM) model. This characterization was able to discriminate between distinct anisotropic atomic displacement parameter (ADP) models arising from different anisotropic scaling choices that agreed comparably with the Bragg data. Our results emphasize the importance of data reproducibility as a model-free measure of diffuse data quality, illustrate the ability of LLM analysis of diffuse scattering to select among alternative ADP models, and offer insights into the design of successful diffuse scattering experiments.
		+
		+	Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters.,Su Z, Dasgupta M, Poitevin F, Mathews II, van den Bedem H, Wall ME, Yoon CH, Wilson MA Struct Dyn. 2021 Jul 8;8(4):044701. doi: 10.1063/4.0000087. eCollection 2021 Jul. PMID:34258328<ref>PMID:34258328</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7l9q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cyclohexyl-isocyanide hydratase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dasgupta M]]	+	[[Category: Psef5]]
-	[[Category: Mathews II]]	+	[[Category: Bedem, H van den]]
-	[[Category: Poitevin F]]	+	[[Category: Dasgupta, M]]
-	[[Category: Su Z]]	+	[[Category: Mathews, I I]]
-	[[Category: Wall ME]]	+	[[Category: Poitevin, F]]
-	[[Category: Wilson MA]]	+	[[Category: Su, Z]]
-	[[Category: Yoon CH]]	+	[[Category: Wall, M E]]
-	[[Category: ~~Van den Bedem H~~]]	+	[[Category: Wilson, M A]]
		+	[[Category: Yoon, C H]]
		+	[[Category: Diffuse scattering]]
		+	[[Category: Dj-1/pfpi superfamily]]
		+	[[Category: Isocyanide]]
		+	[[Category: Isonitrile]]
		+	[[Category: Lyase]]

OCA: Protected "7l9q" [edit=sysop:move=sysop]

OCA — Wed, 03 Feb 2021 11:13:30 GMT

Protected "7l9q" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:13, 3 February 2021

OCA: New page: ==Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-1) at 274K, Refmac5-refined== == Structural ...

OCA — Wed, 03 Feb 2021 11:13:29 GMT

New page: ==Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-1) at 274K, Refmac5-refined== <StructureSection load='7l9q' size='340' side='right'caption='7l9q' scene=''> == Structural ...

New page

==Wild-type Pseudomonas fluorescens isocyanide hydratase (WT-1) at 274K, Refmac5-refined==
<StructureSection load='7l9q' size='340' side='right'caption='[[7l9q]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L9Q FirstGlance]. <br>
</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=7l9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l9q OCA], [https://pdbe.org/7l9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l9q RCSB], [https://www.ebi.ac.uk/pdbsum/7l9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l9q ProSAT]</span></td></tr>
</table>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Dasgupta M]]
[[Category: Mathews II]]
[[Category: Poitevin F]]
[[Category: Su Z]]
[[Category: Wall ME]]
[[Category: Wilson MA]]
[[Category: Yoon CH]]
[[Category: Van den Bedem H]]