2lhb - Revision history

OCA at 09:04, 21 February 2024

OCA — Wed, 21 Feb 2024 09:04:57 GMT

←Older revision		Revision as of 09:04, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2lhb' size='340' side='right'caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2lhb' size='340' side='right'caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Petma Petma~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LHB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</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">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</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=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [https://pdbe.org/2lhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [https://www.ebi.ac.uk/pdbsum/2lhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lhb 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=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [https://pdbe.org/2lhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [https://www.ebi.ac.uk/pdbsum/2lhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lhb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GLB5_PETMA GLB5_PETMA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		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=2lhb 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=2lhb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A molecular model for the protein and ambient solvent of the complex of cyanide with methemoglobin V from the sea lamprey Petromyzon marinus yields an R-factor of 0.142 against X-ray diffraction data to 2.0 A resolution. The root-mean-square discrepancies from ideal bond length and angle are, respectively, 0.014 A and 1.5 degrees. Atoms that belong to planar groups deviate by 0.012 A from planes determined by a least-squares procedure. The average standard deviation for chiral volumes, peptide torsion angle and torsion angles of side-chains are 0.150 A3, 2.0 degrees and 19.4 degrees, respectively. The root-mean-square variation in the thermal parameters of bonded atoms of the polypeptide backbone is 1.21 A2; the variation in thermal parameters for side-chain atoms is 2.13 A2. The model includes multiple conformations for 11 side-chains of the 149 amino acid residues of the protein. We identify 231 locations as sites of water molecules in full or partial occupancy. The sum of occupancy factors for these sites is approximately 154, representing 28% of the 550 molecules of water within the crystallographic asymmetric unit. The environment of the heme in the cyanide complex of lamprey methemoglobin resembles the deoxy state of the mammalian tetramer. In particular, the bond between atom NE2 of the proximal histidine and the Fe lies 5.1 degrees from the normal of the heme plane. In deoxy- and carbonmonoxyhemoglobins, the deviations from the normal to the heme plane are 7 to 8 degrees and 1 degree, respectively. Furthermore, the inequality in the distance of atom CD2 of the proximal histidine from the pyrrole nitrogen of ring-C of the heme (distance = 3.29 A) and CE1 from the pyrrole nitrogen of ring-A (distance = 3.06 A) is characteristic of deoxyhemoglobin, not carbonmonoxyhemoglobin, where these distances are equal. Finally, a hydrogen bond exists between carbonyl 111 and the hydroxyl of tyrosine 149. The corresponding hydrogen link in the mammalian tetramer is central to the T to R state transition and is present in deoxyhemoglobin but absent in carbonmonoxyhemoglobin. We suggest that the low affinity of oxygen for lamprey hemoglobin may be a consequence of these T-state geometries.
-
-	Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus.,Honzatko RB, Hendrickson WA, Love WE J Mol Biol. 1985 Jul 5;184(1):147-64. PMID:4032476<ref>PMID:4032476</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2lhb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]		*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: PDB Pioneers]]		[[Category: PDB Pioneers]]
-	[[Category: ~~Petma~~]]	+	[[Category: Petromyzon marinus]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: Hendrickson~~, W A~~]]	+	[[Category: Hendrickson WA]]
-	[[Category: Honzatko~~, R B~~]]	+	[[Category: Honzatko RB]]
-	[[Category: Love~~, W E]]~~	+	[[Category: Love WE]]
-	~~[[Category: Oxygen transport~~]]	+

OCA at 20:48, 20 October 2021

OCA — Wed, 20 Oct 2021 20:48:09 GMT

←Older revision		Revision as of 20:48, 20 October 2021
Line 3:		Line 3:
	<StructureSection load='2lhb' size='340' side='right'caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2lhb' size='340' side='right'caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Petma Petma]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2LHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Petma Petma]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LHB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</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=CYN:CYANIDE+ION'>CYN</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [~~http~~://pdbe.org/2lhb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2lhb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2lhb 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=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [https://pdbe.org/2lhb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [https://www.ebi.ac.uk/pdbsum/2lhb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lhb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 14:27, 18 December 2019

OCA — Wed, 18 Dec 2019 14:27:54 GMT

←Older revision		Revision as of 14:27, 18 December 2019
Line 1:		Line 1:

	==REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETROMYZON MARINUS==		==REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETROMYZON MARINUS==
-	<StructureSection load='2lhb' size='340' side='right' caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='2lhb' size='340' side='right'caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petma Petma]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petma Petma]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>
Line 11:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lh/2lhb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lh/2lhb_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 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: PDB Pioneers]]		[[Category: PDB Pioneers]]
	[[Category: Petma]]		[[Category: Petma]]

OCA at 07:08, 29 November 2017

OCA — Wed, 29 Nov 2017 07:08:29 GMT

←Older revision		Revision as of 07:08, 29 November 2017
Line 1:		Line 1:
		+
	==REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETROMYZON MARINUS==		==REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETROMYZON MARINUS==
	<StructureSection load='2lhb' size='340' side='right' caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2lhb' size='340' side='right' caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petma Petma]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petma Petma]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</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=CYN:CYANIDE+ION'>CYN</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [http://pdbe.org/2lhb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [http://www.ebi.ac.uk/pdbsum/2lhb 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=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [http://pdbe.org/2lhb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [http://www.ebi.ac.uk/pdbsum/2lhb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lhb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 15:47, 8 February 2016

OCA — Mon, 08 Feb 2016 15:47:58 GMT

←Older revision		Revision as of 15:47, 8 February 2016
Line 14:		Line 14:
	<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=2lhb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:06, 10 September 2015

OCA — Thu, 10 Sep 2015 13:06:21 GMT

←Older revision		Revision as of 13:06, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2lhb' size='340' side='right' caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='2lhb' size='340' side='right' caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Petromyzon_marinus Petromyzon marinus~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petma Petma]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</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=CYN:CYANIDE+ION'>CYN</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [http://www.ebi.ac.uk/pdbsum/2lhb 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=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [http://pdbe.org/2lhb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [http://www.ebi.ac.uk/pdbsum/2lhb PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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 2lhb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: PDB Pioneers]]		[[Category: PDB Pioneers]]
-	[[Category: ~~Petromyzon marinus~~]]	+	[[Category: Petma]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Hendrickson, W A]]		[[Category: Hendrickson, W A]]

OCA at 18:41, 19 January 2015

OCA — Mon, 19 Jan 2015 18:41:25 GMT

←Older revision		Revision as of 18:41, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</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=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [http://www.ebi.ac.uk/pdbsum/2lhb 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=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [http://www.ebi.ac.uk/pdbsum/2lhb 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 34:		Line 34:
	[[Category: Petromyzon marinus]]		[[Category: Petromyzon marinus]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
-	[[Category: Hendrickson, W A.]]	+	[[Category: Hendrickson, W A]]
-	[[Category: Honzatko, R B.]]	+	[[Category: Honzatko, R B]]
-	[[Category: Love, W E.]]	+	[[Category: Love, W E]]
	[[Category: Oxygen transport]]		[[Category: Oxygen transport]]

OCA at 10:09, 3 October 2014

OCA — Fri, 03 Oct 2014 10:09:09 GMT

←Older revision		Revision as of 10:09, 3 October 2014
Line 1:		Line 1:
-	[[~~Image~~:2lhb.~~png\|left~~\|200px]]	+	==REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETROMYZON MARINUS==
		+	<StructureSection load='2lhb' size='340' side='right' caption='[[2lhb]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LHB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<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=2lhb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lhb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lhb RCSB], [http://www.ebi.ac.uk/pdbsum/2lhb 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/lh/2lhb_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 molecular model for the protein and ambient solvent of the complex of cyanide with methemoglobin V from the sea lamprey Petromyzon marinus yields an R-factor of 0.142 against X-ray diffraction data to 2.0 A resolution. The root-mean-square discrepancies from ideal bond length and angle are, respectively, 0.014 A and 1.5 degrees. Atoms that belong to planar groups deviate by 0.012 A from planes determined by a least-squares procedure. The average standard deviation for chiral volumes, peptide torsion angle and torsion angles of side-chains are 0.150 A3, 2.0 degrees and 19.4 degrees, respectively. The root-mean-square variation in the thermal parameters of bonded atoms of the polypeptide backbone is 1.21 A2; the variation in thermal parameters for side-chain atoms is 2.13 A2. The model includes multiple conformations for 11 side-chains of the 149 amino acid residues of the protein. We identify 231 locations as sites of water molecules in full or partial occupancy. The sum of occupancy factors for these sites is approximately 154, representing 28% of the 550 molecules of water within the crystallographic asymmetric unit. The environment of the heme in the cyanide complex of lamprey methemoglobin resembles the deoxy state of the mammalian tetramer. In particular, the bond between atom NE2 of the proximal histidine and the Fe lies 5.1 degrees from the normal of the heme plane. In deoxy- and carbonmonoxyhemoglobins, the deviations from the normal to the heme plane are 7 to 8 degrees and 1 degree, respectively. Furthermore, the inequality in the distance of atom CD2 of the proximal histidine from the pyrrole nitrogen of ring-C of the heme (distance = 3.29 A) and CE1 from the pyrrole nitrogen of ring-A (distance = 3.06 A) is characteristic of deoxyhemoglobin, not carbonmonoxyhemoglobin, where these distances are equal. Finally, a hydrogen bond exists between carbonyl 111 and the hydroxyl of tyrosine 149. The corresponding hydrogen link in the mammalian tetramer is central to the T to R state transition and is present in deoxyhemoglobin but absent in carbonmonoxyhemoglobin. We suggest that the low affinity of oxygen for lamprey hemoglobin may be a consequence of these T-state geometries.

-	~~{{STRUCTURE_2lhb\| PDB=2lhb \| SCENE= }}~~	+	Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus.,Honzatko RB, Hendrickson WA, Love WE J Mol Biol. 1985 Jul 5;184(1):147-64. PMID:4032476<ref>PMID:4032476</ref>

-	~~===REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETROMYZON MARINUS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_4032476}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2lhb]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1~~&~~id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule~~ of the ~~Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx~~.~~doi~~.~~org/10~~.~~2210~~/~~rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA].~~	+

	==See Also==		==See Also==
-	*[[Hemoglobin\|Hemoglobin]]	+	*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:004032476<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: PDB Pioneers]]		[[Category: PDB Pioneers]]
	[[Category: Petromyzon marinus]]		[[Category: Petromyzon marinus]]

OCA at 10:39, 20 October 2012

OCA — Sat, 20 Oct 2012 10:39:26 GMT

←Older revision		Revision as of 10:39, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2lhb]] is a 1 chain structure ~~of [[Hemoglobin]]~~ with sequence from [http://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA].	+	[[2lhb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lhb 1lhb]. The October 2011 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''PDB Pioneers'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2011_10 10.2210/rcsb_pdb/mom_2011_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LHB OCA].

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:004032476~~</ref><ref group="xtra">PMID:007729532~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:004032476</ref><references group="xtra"/>
	[[Category: PDB Pioneers]]		[[Category: PDB Pioneers]]
	[[Category: Petromyzon marinus]]		[[Category: Petromyzon marinus]]

OCA: Protected "2lhb" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 02:50:40 GMT

Protected "2lhb" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:50, 26 July 2012