1f63 - Revision history

OCA at 07:11, 7 February 2024

2024-02-07T07:11:13Z

←Older revision		Revision as of 07:11, 7 February 2024
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	<StructureSection load='1f63' size='340' side='right'caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f63' size='340' side='right'caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Phymc Phymc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F63 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1dxc\|1dxc]]~~, ~~[[1dxd\|1dxd]], [[1f65\|1f65]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [https://pdbe.org/1f63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [https://www.ebi.ac.uk/pdbsum/1f63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f63 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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [https://pdbe.org/1f63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [https://www.ebi.ac.uk/pdbsum/1f63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f63 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.	+	[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1f63 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1f63 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A triple mutant of sperm whale myoglobin (Mb) [Leu(B10) --> Tyr, His(E7) --> Gln, and Thr(E10) --> Arg, called Mb-YQR], investigated by stopped-flow, laser photolysis, crystallography, and molecular dynamics (MD) simulations, proved to be quite unusual. Rebinding of photodissociated NO, O2, and CO from within the protein (in a "geminate" mode) allows us to reach general conclusions about dynamics and cavities in proteins. The 3D structure of oxy Mb-YQR shows that bound O2 makes two H-bonds with Tyr(B10)29 and Gln(E7)64; on deoxygenation, these two residues move toward the space occupied by O2. The bimolecular rate constant for NO binding is the same as for wild-type, but those for CO and O2 binding are reduced 10-fold. While there is no geminate recombination with O2 and CO, geminate rebinding of NO displays an unusually large and very slow component, which is pretty much abolished in the presence of xenon. These results and MD simulations suggest that the ligand migrates in the protein matrix to a major "secondary site," located beneath Tyr(B10)29 and accessible via the motion of Ile(G8)107; this site is different from the "primary site" identified by others who investigated the photolyzed state of wild-type Mb by crystallography. Our hypothesis may rationalize the O2 binding properties of Mb-YQR, and more generally to propose a mechanism of control of ligand binding and dissociation in hemeproteins based on the dynamics of side chains that may (or may not) allow access to and direct temporary sequestration of the dissociated ligand in a docking site within the protein. This interpretation suggests that very fast (picosecond) fluctuations of amino acid side chains may play a crucial role in controlling O2 delivery to tissue at a rate compatible with physiology.
-
-	Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10).,Brunori M, Cutruzzola F, Savino C, Travaglini-Allocatelli C, Vallone B, Gibson QH Biophys J. 1999 Mar;76(3):1259-69. PMID:10049310<ref>PMID:10049310</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1f63" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Myoglobin 3D structures\|Myoglobin 3D structures]]		*[[Myoglobin 3D structures\|Myoglobin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Phymc~~]]	+	[[Category: Physeter catodon]]
-	[[Category: Brunori, M]]	+	[[Category: Brunori M]]
-	[[Category: Cutruzzola, F]]	+	[[Category: Cutruzzola F]]
-	[[Category: Gibson~~, Q H~~]]	+	[[Category: Gibson QH]]
-	[[Category: Savino, C]]	+	[[Category: Savino C]]
-	[[Category: Travaglini-Allocatelli, C]]	+	[[Category: Travaglini-Allocatelli C]]
-	[[Category: Vallone, B]]	+	[[Category: Vallone B]]
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Myoglobin]]~~	+
-	~~[[Category: Oxygen storage-transport complex]]~~	+
-	~~[[Category: Triple mutant~~]]	+

OCA at 15:09, 3 November 2021

2021-11-03T15:09:52Z

←Older revision		Revision as of 15:09, 3 November 2021
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	<StructureSection load='1f63' size='340' side='right'caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f63' size='340' side='right'caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Phycd Phycd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phymc Phymc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F63 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</div></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Phycd~~]]	+	[[Category: Phymc]]
	[[Category: Brunori, M]]		[[Category: Brunori, M]]
	[[Category: Cutruzzola, F]]		[[Category: Cutruzzola, F]]

OCA at 11:08, 28 July 2021

2021-07-28T11:08:56Z

←Older revision		Revision as of 11:08, 28 July 2021
Line 3:		Line 3:
	<StructureSection load='1f63' size='340' side='right'caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f63' size='340' side='right'caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Phycd Phycd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1F63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phycd Phycd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F63 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</div></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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [~~http~~://pdbe.org/1f63 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1f63 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1f63 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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [https://pdbe.org/1f63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [https://www.ebi.ac.uk/pdbsum/1f63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f63 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.	+	[[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Myoglobin\|Myoglobin]]	+	*[[Myoglobin 3D structures\|Myoglobin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:31, 23 October 2019

2019-10-23T08:31:24Z

←Older revision		Revision as of 08:31, 23 October 2019
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	==CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)==		==CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)==
-	<StructureSection load='1f63' size='340' side='right' caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1f63' size='340' side='right'caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phycd Phycd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F63 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phycd Phycd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F63 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1f63" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1f63" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Myoglobin\|Myoglobin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phycd]]		[[Category: Phycd]]
	[[Category: Brunori, M]]		[[Category: Brunori, M]]

OCA at 09:23, 27 December 2017

2017-12-27T09:23:21Z

←Older revision		Revision as of 09:23, 27 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)==		==CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)==
	<StructureSection load='1f63' size='340' side='right' caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f63' size='340' side='right' caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://pdbe.org/1f63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://pdbe.org/1f63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f63 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/1f63_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/1f63_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1f63" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1f63" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Myoglobin\|Myoglobin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:54, 7 February 2016

2016-02-07T01:54:31Z

←Older revision		Revision as of 01:54, 7 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1f63 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:34, 9 September 2015

2015-09-09T20:34:04Z

←Older revision		Revision as of 20:34, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1f63' size='340' side='right' caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1f63' size='340' side='right' caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Physeter_catodon Physeter catodon~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phycd Phycd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F63 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://pdbe.org/1f63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1f63" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Physeter catodon~~]]	+	[[Category: Phycd]]
	[[Category: Brunori, M]]		[[Category: Brunori, M]]
	[[Category: Cutruzzola, F]]		[[Category: Cutruzzola, F]]

OCA at 06:50, 24 December 2014

2014-12-24T06:50:32Z

←Older revision		Revision as of 06:50, 24 December 2014
Line 7:		Line 7:
	<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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 18:19, 22 December 2014

2014-12-22T18:19:46Z

←Older revision		Revision as of 18:19, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F63 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F63 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Physeter catodon]]		[[Category: Physeter catodon]]
-	[[Category: Brunori, M.]]	+	[[Category: Brunori, M]]
-	[[Category: Cutruzzola, F.]]	+	[[Category: Cutruzzola, F]]
-	[[Category: Gibson, Q H.]]	+	[[Category: Gibson, Q H]]
-	[[Category: Savino, C.]]	+	[[Category: Savino, C]]
-	[[Category: Travaglini-Allocatelli, C.]]	+	[[Category: Travaglini-Allocatelli, C]]
-	[[Category: Vallone, B.]]	+	[[Category: Vallone, B]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Myoglobin]]		[[Category: Myoglobin]]
	[[Category: Oxygen storage-transport complex]]		[[Category: Oxygen storage-transport complex]]
	[[Category: Triple mutant]]		[[Category: Triple mutant]]

OCA at 08:23, 28 September 2014

2014-09-28T08:23:58Z

←Older revision		Revision as of 08:23, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1f63.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)==
		+	<StructureSection load='1f63' size='340' side='right' caption='[[1f63]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1f63]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F63 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dxc\|1dxc]], [[1dxd\|1dxd]], [[1f65\|1f65]]</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=1f63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f63 RCSB], [http://www.ebi.ac.uk/pdbsum/1f63 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/1f63_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A triple mutant of sperm whale myoglobin (Mb) [Leu(B10) --> Tyr, His(E7) --> Gln, and Thr(E10) --> Arg, called Mb-YQR], investigated by stopped-flow, laser photolysis, crystallography, and molecular dynamics (MD) simulations, proved to be quite unusual. Rebinding of photodissociated NO, O2, and CO from within the protein (in a "geminate" mode) allows us to reach general conclusions about dynamics and cavities in proteins. The 3D structure of oxy Mb-YQR shows that bound O2 makes two H-bonds with Tyr(B10)29 and Gln(E7)64; on deoxygenation, these two residues move toward the space occupied by O2. The bimolecular rate constant for NO binding is the same as for wild-type, but those for CO and O2 binding are reduced 10-fold. While there is no geminate recombination with O2 and CO, geminate rebinding of NO displays an unusually large and very slow component, which is pretty much abolished in the presence of xenon. These results and MD simulations suggest that the ligand migrates in the protein matrix to a major "secondary site," located beneath Tyr(B10)29 and accessible via the motion of Ile(G8)107; this site is different from the "primary site" identified by others who investigated the photolyzed state of wild-type Mb by crystallography. Our hypothesis may rationalize the O2 binding properties of Mb-YQR, and more generally to propose a mechanism of control of ligand binding and dissociation in hemeproteins based on the dynamics of side chains that may (or may not) allow access to and direct temporary sequestration of the dissociated ligand in a docking site within the protein. This interpretation suggests that very fast (picosecond) fluctuations of amino acid side chains may play a crucial role in controlling O2 delivery to tissue at a rate compatible with physiology.

-	~~{{STRUCTURE_1f63\| PDB=1f63 \| SCENE= }}~~	+	Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10).,Brunori M, Cutruzzola F, Savino C, Travaglini-Allocatelli C, Vallone B, Gibson QH Biophys J. 1999 Mar;76(3):1259-69. PMID:10049310<ref>PMID:10049310</ref>

-	~~===CRYSTAL STRUCTURE OF DEOXY SPERM WHALE MYOGLOBIN MUTANT Y(B10)Q(E7)R(E10)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10049310}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1f63]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Physeter_catodon Physeter catodon]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1F63 OCA].~~	+

	==See Also==		==See Also==
	*[[Myoglobin\|Myoglobin]]		*[[Myoglobin\|Myoglobin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010049310<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Physeter catodon]]		[[Category: Physeter catodon]]
	[[Category: Brunori, M.]]		[[Category: Brunori, M.]]