4bww - Revision history

OCA at 11:59, 20 December 2023

2023-12-20T11:59:43Z

←Older revision		Revision as of 11:59, 20 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BWW FirstGlance]. <br>		<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BWW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [https://pdbe.org/4bww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [https://www.ebi.ac.uk/pdbsum/4bww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bww 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=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [https://pdbe.org/4bww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [https://www.ebi.ac.uk/pdbsum/4bww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bww ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AZUR_PSEAE AZUR_PSEAE]] Transfers electrons from cytochrome c551 to cytochrome oxidase.	+	[https://www.uniprot.org/uniprot/AZUR_PSEAE AZUR_PSEAE] Transfers electrons from cytochrome c551 to cytochrome oxidase.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: EPR-based distance measurements between spin labels in proteins have become a valuable tool in structural biology. The direct translation of the experimental distances into structural information is however often impaired by the intrinsic flexibility of the spin labelled side chains. Different algorithms exist that predict the approximate conformation of the spin label either by using pre-computed rotamer libraries of the labelled side chain (rotamer approach) or by simply determining its accessible volume (accessible volume approach). Surprisingly, comparisons with many experimental distances have shown that both approaches deliver the same distance prediction accuracy of about 3 A. RESULTS: Here, instead of comparing predicted and experimental distances, we test the ability of both approaches to predict the actual conformations of spin labels found in a new high-resolution crystal structure of spin labelled azurin (T21R1). Inside the crystal, the label is found in two very different environments which serve as a challenging test for the in silico approaches. CONCLUSIONS: Our results illustrate why simple and more sophisticated programs lead to the same prediciton error. Thus, a more precise treatment of the complete environment of the label and also its interactions with the environment will be needed to increase the accuracy of in silico spin labelling algorithms.
		+
		+	High-resolution crystal structure of spin labelled (T21R1) azurin from Pseudomonas aeruginosa: a challenging structural benchmark for in silico spin labelling algorithms.,Florin N, Schiemann O, Hagelueken G BMC Struct Biol. 2014 May 29;14(1):16. PMID:24884565<ref>PMID:24884565</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4bww" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Azurin 3D structures\|Azurin 3D structures]]		*[[Azurin 3D structures\|Azurin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:14, 7 September 2022

2022-09-07T17:14:16Z

←Older revision		Revision as of 17:14, 7 September 2022
Line 3:		Line 3:
	<StructureSection load='4bww' size='340' side='right'caption='[[4bww]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='4bww' size='340' side='right'caption='[[4bww]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4BWW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4BWW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></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=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [https://pdbe.org/4bww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [https://www.ebi.ac.uk/pdbsum/4bww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4bww 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=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [~~http~~://pdbe.org/4bww PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4bww PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4bww ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AZUR_PSEAE AZUR_PSEAE]] Transfers electrons from cytochrome c551 to cytochrome oxidase.	+	[[https://www.uniprot.org/uniprot/AZUR_PSEAE AZUR_PSEAE]] Transfers electrons from cytochrome c551 to cytochrome oxidase.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	BACKGROUND: EPR-based distance measurements between spin labels in proteins have become a valuable tool in structural biology. The direct translation of the experimental distances into structural information is however often impaired by the intrinsic flexibility of the spin labelled side chains. Different algorithms exist that predict the approximate conformation of the spin label either by using pre-computed rotamer libraries of the labelled side chain (rotamer approach) or by simply determining its accessible volume (accessible volume approach). Surprisingly, comparisons with many experimental distances have shown that both approaches deliver the same distance prediction accuracy of about 3 A. RESULTS: Here, instead of comparing predicted and experimental distances, we test the ability of both approaches to predict the actual conformations of spin labels found in a new high-resolution crystal structure of spin labelled azurin (T21R1). Inside the crystal, the label is found in two very different environments which serve as a challenging test for the in silico approaches. CONCLUSIONS: Our results illustrate why simple and more sophisticated programs lead to the same prediciton error. Thus, a more precise treatment of the complete environment of the label and also its interactions with the environment will be needed to increase the accuracy of in silico spin labelling algorithms.	+
-		+
-	High-resolution crystal structure of spin labelled (T21R1) azurin from Pseudomonas aeruginosa: a challenging structural benchmark for in silico spin labelling algorithms.,Florin N, Schiemann O, Hagelueken G BMC Struct Biol. 2014 May 29;14(1):16. PMID:24884565<ref>PMID:24884565</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4bww" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
-	*[[Azurin\|Azurin]]	+	*[[Azurin 3D structures\|Azurin 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseae~~]]	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	[[Category: Hagelueken, G]]	+	[[Category: Hagelueken G]]
-	~~[[Category: Electron transport~~]]	+

OCA at 13:59, 13 March 2019

2019-03-13T13:59:08Z

←Older revision		Revision as of 13:59, 13 March 2019
Line 1:		Line 1:

	==Crystal structure of spin labelled azurin T21R1.==		==Crystal structure of spin labelled azurin T21R1.==
-	<StructureSection load='4bww' size='340' side='right' caption='[[4bww]], [[Resolution\|resolution]] 1.48Å' scene=''>	+	<StructureSection load='4bww' size='340' side='right'caption='[[4bww]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BWW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BWW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></td></tr>
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pseae]]
	[[Category: Hagelueken, G]]		[[Category: Hagelueken, G]]
	[[Category: Electron transport]]		[[Category: Electron transport]]

OCA at 05:09, 5 August 2016

2016-08-05T05:09:34Z

←Older revision		Revision as of 05:09, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of spin labelled azurin T21R1.==		==Crystal structure of spin labelled azurin T21R1.==
	<StructureSection load='4bww' size='340' side='right' caption='[[4bww]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='4bww' size='340' side='right' caption='[[4bww]], [[Resolution\|resolution]] 1.48Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</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=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [http://www.ebi.ac.uk/pdbsum/4bww PDBsum]</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=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [http://pdbe.org/4bww PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [http://www.ebi.ac.uk/pdbsum/4bww PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4bww ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4bww" style="background-color:#fffaf0;"></div>

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

OCA at 16:01, 25 December 2014

2014-12-25T16:01:03Z

←Older revision		Revision as of 16:01, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BWW FirstGlance]. <br>		<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BWW FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [http://www.ebi.ac.uk/pdbsum/4bww PDBsum]</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=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [http://www.ebi.ac.uk/pdbsum/4bww PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AZUR_PSEAE AZUR_PSEAE]] Transfers electrons from cytochrome c551 to cytochrome oxidase.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+
		+	==See Also==
		+	*[[Azurin\|Azurin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Hagelueken, G.]]	+	[[Category: Hagelueken, G]]
	[[Category: Electron transport]]		[[Category: Electron transport]]

OCA at 08:48, 11 June 2014

2014-06-11T08:48:04Z

←Older revision		Revision as of 08:48, 11 June 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of spin labelled azurin T21R1.==
		+	<StructureSection load='4bww' size='340' side='right' caption='[[4bww]], [[Resolution\|resolution]] 1.48Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4bww]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BWW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4BWW FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=R1A:3-{[(2,2,5,5-TETRAMETHYL-1-OXO-2,5-DIHYDRO-1H-PYRROLIUM-3-YL)METHYL]DISULFANYL}-D-ALANINE'>R1A</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4bww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4bww OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4bww RCSB], [http://www.ebi.ac.uk/pdbsum/4bww PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: EPR-based distance measurements between spin labels in proteins have become a valuable tool in structural biology. The direct translation of the experimental distances into structural information is however often impaired by the intrinsic flexibility of the spin labelled side chains. Different algorithms exist that predict the approximate conformation of the spin label either by using pre-computed rotamer libraries of the labelled side chain (rotamer approach) or by simply determining its accessible volume (accessible volume approach). Surprisingly, comparisons with many experimental distances have shown that both approaches deliver the same distance prediction accuracy of about 3 A. RESULTS: Here, instead of comparing predicted and experimental distances, we test the ability of both approaches to predict the actual conformations of spin labels found in a new high-resolution crystal structure of spin labelled azurin (T21R1). Inside the crystal, the label is found in two very different environments which serve as a challenging test for the in silico approaches. CONCLUSIONS: Our results illustrate why simple and more sophisticated programs lead to the same prediciton error. Thus, a more precise treatment of the complete environment of the label and also its interactions with the environment will be needed to increase the accuracy of in silico spin labelling algorithms.

-	~~The entry 4bww is ON HOLD~~	+	High-resolution crystal structure of spin labelled (T21R1) azurin from Pseudomonas aeruginosa: a challenging structural benchmark for in silico spin labelling algorithms.,Florin N, Schiemann O, Hagelueken G BMC Struct Biol. 2014 May 29;14(1):16. PMID:24884565<ref>PMID:24884565</ref>

-	~~Authors~~: Hagelueken, G.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of spin labelled azurin T21R1.~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hagelueken, G.]]
		+	[[Category: Electron transport]]

OCA: Protected "4bww" [edit=sysop:move=sysop]

2013-07-10T14:46:52Z

Protected "4bww" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:46, 10 July 2013

OCA: New page: '''Unreleased structure''' The entry 4bww is ON HOLD Authors: Hagelueken, G. Description: Crystal structure of spin labelled azurin T21R1.

2013-07-10T14:46:51Z

New page: '''Unreleased structure''' The entry 4bww is ON HOLD Authors: Hagelueken, G. Description: Crystal structure of spin labelled azurin T21R1.

New page

'''Unreleased structure'''

The entry 4bww is ON HOLD

Authors: Hagelueken, G.

Description: Crystal structure of spin labelled azurin T21R1.