1cq2 - Revision history

OCA at 06:44, 7 February 2024

OCA — Wed, 07 Feb 2024 06:44:32 GMT

←Older revision		Revision as of 06:44, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='1cq2' size='340' side='right'caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1cq2' size='340' side='right'caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>~~, ~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Neutron Diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height~~: ~~3em;~~'>~~[[2mb5\|2mb5]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [https://pdbe.org/1cq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [https://www.ebi.ac.uk/pdbsum/1cq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cq2 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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [https://pdbe.org/1cq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [https://www.ebi.ac.uk/pdbsum/1cq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cq2 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]]
Line 20:		Line 20:
	</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=1cq2 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=1cq2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Although hydrogens comprise half of the atoms in a protein molecule and are of great importance chemically and structurally, direct visualization of them by using crystallography is difficult. Neutron crystallography is capable of directly revealing the position of hydrogens, but its use on unlabeled samples faces certain technical difficulties: the large incoherent scattering of hydrogen results in background scattering that greatly reduces the signal to noise of the experiment. Moreover, whereas the scattering lengths of C, N, and O are positive, that of hydrogen is negative and about half the magnitude. This results in density for hydrogens being half as strong and close to the threshold of detection at 2.0-A resolution. Also, because of its opposite sign, there is a partial cancellation of the hydrogen density with that from neighboring atoms, which can lead to ambiguities in interpretation at medium resolution. These difficulties can be overcome by the use of deuterated protein, and we present here a neutron structure of fully deuterated myoglobin. The structure reveals a wealth of chemical information about the molecule, including the geometry of hydrogen bonding, states of protonation of histidines, and the location and geometry of water molecules at the surface of the protein. The structure also should be of broader interest because it will serve as a benchmark for molecular dynamics and energy minimization calculations and for comparison with NMR studies.
-
-	Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin.,Shu F, Ramakrishnan V, Schoenborn BP Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3872-7. PMID:10725379<ref>PMID:10725379</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1cq2" 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: ~~Phycd~~]]	+	[[Category: Physeter catodon]]
-	[[Category: Ramakrishnan, V]]	+	[[Category: Ramakrishnan V]]
-	[[Category: Schoenborn~~, B P~~]]	+	[[Category: Schoenborn BP]]
-	[[Category: Shu, F]]	+	[[Category: Shu F]]
-	~~[[Category: All-hydrogen containing structure]]~~	+
-	~~[[Category: Globular]]~~	+
-	~~[[Category: Helical]]~~	+
-	~~[[Category: Oxygen storage-transport complex~~]]	+

OCA at 11:27, 30 March 2022

OCA — Wed, 30 Mar 2022 11:27:52 GMT

←Older revision		Revision as of 11:27, 30 March 2022
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	<StructureSection load='1cq2' size='340' side='right'caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1cq2' size='340' side='right'caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2mb5\|2mb5]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [~~http~~://pdbe.org/1cq2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1cq2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1cq2 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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [https://pdbe.org/1cq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [https://www.ebi.ac.uk/pdbsum/1cq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cq2 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]]

OCA at 07:28, 25 June 2020

OCA — Thu, 25 Jun 2020 07:28:36 GMT

←Older revision		Revision as of 07:28, 25 June 2020
Line 1:		Line 1:

	==NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 ANGSTROM==		==NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 ANGSTROM==
-	<StructureSection load='1cq2' size='340' side='right' caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1cq2' size='340' side='right'caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://pdbe.org/1cq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1cq2 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://pdbe.org/1cq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1cq2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Myoglobin\|Myoglobin]]	+	*[[Myoglobin 3D structures\|Myoglobin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Phycd]]		[[Category: Phycd]]
	[[Category: Ramakrishnan, V]]		[[Category: Ramakrishnan, V]]

OCA at 20:42, 19 September 2018

OCA — Wed, 19 Sep 2018 20:42:50 GMT

←Older revision		Revision as of 20:42, 19 September 2018
Line 3:		Line 3:
	<StructureSection load='1cq2' size='340' side='right' caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1cq2' size='340' side='right' caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1cq2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</td></tr>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cq/1cq2_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cq/1cq2_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 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Phycd]]
	[[Category: Ramakrishnan, V]]		[[Category: Ramakrishnan, V]]
	[[Category: Schoenborn, B P]]		[[Category: Schoenborn, B P]]

OCA at 11:26, 15 December 2016

OCA — Thu, 15 Dec 2016 11:26:02 GMT

←Older revision		Revision as of 11:26, 15 December 2016
Line 1:		Line 1:
-	==NEUTRON ~~STRUTURE~~ OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 ANGSTROM==	+
		+	==NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 ANGSTROM==
	<StructureSection load='1cq2' size='340' side='right' caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1cq2' size='340' side='right' caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1cq2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://pdbe.org/1cq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://pdbe.org/1cq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1cq2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=1cq2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Phycd]]
	[[Category: Ramakrishnan, V]]		[[Category: Ramakrishnan, V]]
	[[Category: Schoenborn, B P]]		[[Category: Schoenborn, B P]]

OCA at 09:07, 11 September 2015

OCA — Fri, 11 Sep 2015 09:07:44 GMT

←Older revision		Revision as of 09:07, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1cq2' size='340' side='right' caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1cq2' size='340' side='right' caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://pdbe.org/1cq2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 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 1cq2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Physeter catodon~~]]	+	[[Category: Phycd]]
	[[Category: Ramakrishnan, V]]		[[Category: Ramakrishnan, V]]
	[[Category: Schoenborn, B P]]		[[Category: Schoenborn, B P]]

OCA at 14:16, 25 December 2014

OCA — Thu, 25 Dec 2014 14:16:09 GMT

←Older revision		Revision as of 14:16, 25 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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 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 23:30, 22 December 2014

OCA — Mon, 22 Dec 2014 23:30:59 GMT

←Older revision		Revision as of 23:30, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 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: Ramakrishnan, V.]]	+	[[Category: Ramakrishnan, V]]
-	[[Category: Schoenborn, B P.]]	+	[[Category: Schoenborn, B P]]
-	[[Category: Shu, F.]]	+	[[Category: Shu, F]]
	[[Category: All-hydrogen containing structure]]		[[Category: All-hydrogen containing structure]]
	[[Category: Globular]]		[[Category: Globular]]
	[[Category: Helical]]		[[Category: Helical]]
	[[Category: Oxygen storage-transport complex]]		[[Category: Oxygen storage-transport complex]]

OCA at 09:18, 27 August 2014

OCA — Wed, 27 Aug 2014 09:18:23 GMT

←Older revision		Revision as of 09:18, 27 August 2014
Line 1:		Line 1:
-	[[~~Image:~~1cq2.~~png~~\|~~left~~\|200px]]	+	==NEUTRON STRUTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 ANGSTROM==
		+	<StructureSection load='1cq2' size='340' side='right' caption='[[1cq2]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1cq2]] 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=1CQ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CQ2 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2mb5\|2mb5]]</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=1cq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cq2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cq2 RCSB], [http://www.ebi.ac.uk/pdbsum/1cq2 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/cq/1cq2_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 ==
		+	Although hydrogens comprise half of the atoms in a protein molecule and are of great importance chemically and structurally, direct visualization of them by using crystallography is difficult. Neutron crystallography is capable of directly revealing the position of hydrogens, but its use on unlabeled samples faces certain technical difficulties: the large incoherent scattering of hydrogen results in background scattering that greatly reduces the signal to noise of the experiment. Moreover, whereas the scattering lengths of C, N, and O are positive, that of hydrogen is negative and about half the magnitude. This results in density for hydrogens being half as strong and close to the threshold of detection at 2.0-A resolution. Also, because of its opposite sign, there is a partial cancellation of the hydrogen density with that from neighboring atoms, which can lead to ambiguities in interpretation at medium resolution. These difficulties can be overcome by the use of deuterated protein, and we present here a neutron structure of fully deuterated myoglobin. The structure reveals a wealth of chemical information about the molecule, including the geometry of hydrogen bonding, states of protonation of histidines, and the location and geometry of water molecules at the surface of the protein. The structure also should be of broader interest because it will serve as a benchmark for molecular dynamics and energy minimization calculations and for comparison with NMR studies.

-	~~{{STRUCTURE_1cq2\| PDB=1cq2 \| SCENE= }}~~	+	Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin.,Shu F, Ramakrishnan V, Schoenborn BP Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3872-7. PMID:10725379<ref>PMID:10725379</ref>

-	~~===NEUTRON STRUTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 ANGSTROM===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10725379}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1cq2]] 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=1CQ2 OCA].~~	+

	==See Also==		==See Also==
	*[[Myoglobin\|Myoglobin]]		*[[Myoglobin\|Myoglobin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010725379<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Physeter catodon]]		[[Category: Physeter catodon]]
	[[Category: Ramakrishnan, V.]]		[[Category: Ramakrishnan, V.]]

OCA at 17:42, 20 October 2012

OCA — Sat, 20 Oct 2012 17:42:51 GMT

←Older revision		Revision as of 17:42, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1cq2]] is a 1 chain structure ~~of [[Myoglobin]]~~ 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=1CQ2 OCA].	+	[[1cq2]] 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=1CQ2 OCA].

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