1s61 - Revision history

OCA at 08:28, 14 February 2024

2024-02-14T08:28:31Z

←Older revision		Revision as of 08:28, 14 February 2024
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	<StructureSection load='1s61' size='340' side='right'caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1s61' size='340' side='right'caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1S61 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S61 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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.1Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</div></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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [https://pdbe.org/1s61 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [https://www.ebi.ac.uk/pdbsum/1s61 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s61 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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [~~http~~://pdbe.org/1s61 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1s61 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1s61 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TRHBN_MYCTU TRHBN_MYCTU] Binds oxygen cooperatively with very high affinity (P(50) = 0.013 mmHg at 20 degrees Celsius) because of a fast combination (25 microM(-1).s(-1)) and a slow dissociation (0.2 s(-1)) rate.
	== 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=1s61 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=1s61 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Truncated hemoglobins (trHbs) are small hemoproteins forming a separate cluster within the hemoglobin superfamily; their functional roles in bacteria, plants, and unicellular eukaryotes are marginally understood. Crystallographic investigations have shown that the trHb fold (a two-on-two alpha-helical sandwich related to the globin fold) hosts a protein matrix tunnel system offering a potential path for ligand diffusion to the heme distal site. The tunnel topology is conserved in group I trHbs, although with modulation of its size/structure. Here, we present a crystallographic investigation on trHbs from Mycobacterium tuberculosis, Chlamydomonas eugametos, and Paramecium caudatum, showing that treatment of trHb crystals under xenon pressure leads to binding of xenon atoms at specific (conserved) sites along the protein matrix tunnel. The crystallographic results are in keeping with data from molecular dynamics simulations, where a dioxygen molecule is left free to diffuse within the protein matrix. Modulation of xenon binding over four main sites is related to the structural properties of the tunnel system in the three trHbs and may be connected to their functional roles. In a parallel crystallographic investigation on M. tuberculosis trHbN, we show that butyl isocyanide also binds within the apolar tunnel, in excellent agreement with concepts derived from the xenon binding experiments. These results, together with recent data on atypical CO rebinding kinetics to group I trHbs, underline the potential role of the tunnel system in supporting diffusion, but also accumulation in multiple copies, of low polarity ligands/molecules within group I trHbs.
-
-	Heme-ligand tunneling in group I truncated hemoglobins.,Milani M, Pesce A, Ouellet Y, Dewilde S, Friedman J, Ascenzi P, Guertin M, Bolognesi M J Biol Chem. 2004 May 14;279(20):21520-5. Epub 2004 Mar 11. PMID:15016811<ref>PMID:15016811</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1s61" 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: Ascenzi, P]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Bolognesi, M]]	+	[[Category: Ascenzi P]]
-	[[Category: Dewilde, S]]	+	[[Category: Bolognesi M]]
-	[[Category: Friedman, J]]	+	[[Category: Dewilde S]]
-	[[Category: Guertin, M]]	+	[[Category: Friedman J]]
-	[[Category: Milani, M]]	+	[[Category: Guertin M]]
-	[[Category: Ouellet, Y]]	+	[[Category: Milani M]]
-	[[Category: Pesce, A]]	+	[[Category: Ouellet Y]]
-	~~[[Category: Oxygen storage-transport complex]]~~	+	[[Category: Pesce A]]
-	~~[[Category: Truncated hemoglobin~~]]	+

OCA at 13:41, 16 December 2020

2020-12-16T13:41:58Z

←Older revision		Revision as of 13:41, 16 December 2020
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	==Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide==		==Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide==
-	<StructureSection load='1s61' size='340' side='right' caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1s61' size='340' side='right'caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1S61 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1S61 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=HEC:HEME+C'>HEC~~</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://pdbe.org/1s61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s61 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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://pdbe.org/1s61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s61 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 35:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ascenzi, P]]		[[Category: Ascenzi, P]]
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]

OCA at 07:12, 8 March 2018

2018-03-08T07:12:57Z

←Older revision		Revision as of 07:12, 8 March 2018
Line 1:		Line 1:
		+
	==Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide==		==Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide==
	<StructureSection load='1s61' size='340' side='right' caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1s61' size='340' side='right' caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://pdbe.org/1s61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://pdbe.org/1s61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1s61 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s6/1s61_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s6/1s61_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>
	</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=1s61 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:36, 11 September 2015

2015-09-11T15:36:18Z

←Older revision		Revision as of 15:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1s61' size='340' side='right' caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1s61' size='340' side='right' caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S61 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S61 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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://pdbe.org/1s61 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 1s61" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Ascenzi, P]]		[[Category: Ascenzi, P]]
	[[Category: Bolognesi, M]]		[[Category: Bolognesi, M]]

OCA at 18:28, 25 December 2014

2014-12-25T18:28:47Z

←Older revision		Revision as of 18:28, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S61 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S61 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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 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:
	</StructureSection>		</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Ascenzi, P.]]	+	[[Category: Ascenzi, P]]
-	[[Category: Bolognesi, M.]]	+	[[Category: Bolognesi, M]]
-	[[Category: Dewilde, S.]]	+	[[Category: Dewilde, S]]
-	[[Category: Friedman, J.]]	+	[[Category: Friedman, J]]
-	[[Category: Guertin, M.]]	+	[[Category: Guertin, M]]
-	[[Category: Milani, M.]]	+	[[Category: Milani, M]]
-	[[Category: Ouellet, Y.]]	+	[[Category: Ouellet, Y]]
-	[[Category: Pesce, A.]]	+	[[Category: Pesce, A]]
	[[Category: Oxygen storage-transport complex]]		[[Category: Oxygen storage-transport complex]]
	[[Category: Truncated hemoglobin]]		[[Category: Truncated hemoglobin]]

OCA at 23:35, 28 September 2014

2014-09-28T23:35:37Z

←Older revision		Revision as of 23:35, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1s61.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide==
		+	<StructureSection load='1s61' size='340' side='right' caption='[[1s61]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1s61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1S61 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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NBN:N-BUTYL+ISOCYANIDE'>NBN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s56\|1s56]], [[1idr\|1idr]], [[1rte\|1rte]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GLBN, RV1542C, MT1594, MTCY48.23, MB1569C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</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=1s61 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s61 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1s61 RCSB], [http://www.ebi.ac.uk/pdbsum/1s61 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/s6/1s61_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 ==
		+	Truncated hemoglobins (trHbs) are small hemoproteins forming a separate cluster within the hemoglobin superfamily; their functional roles in bacteria, plants, and unicellular eukaryotes are marginally understood. Crystallographic investigations have shown that the trHb fold (a two-on-two alpha-helical sandwich related to the globin fold) hosts a protein matrix tunnel system offering a potential path for ligand diffusion to the heme distal site. The tunnel topology is conserved in group I trHbs, although with modulation of its size/structure. Here, we present a crystallographic investigation on trHbs from Mycobacterium tuberculosis, Chlamydomonas eugametos, and Paramecium caudatum, showing that treatment of trHb crystals under xenon pressure leads to binding of xenon atoms at specific (conserved) sites along the protein matrix tunnel. The crystallographic results are in keeping with data from molecular dynamics simulations, where a dioxygen molecule is left free to diffuse within the protein matrix. Modulation of xenon binding over four main sites is related to the structural properties of the tunnel system in the three trHbs and may be connected to their functional roles. In a parallel crystallographic investigation on M. tuberculosis trHbN, we show that butyl isocyanide also binds within the apolar tunnel, in excellent agreement with concepts derived from the xenon binding experiments. These results, together with recent data on atypical CO rebinding kinetics to group I trHbs, underline the potential role of the tunnel system in supporting diffusion, but also accumulation in multiple copies, of low polarity ligands/molecules within group I trHbs.

-	~~{{STRUCTURE_1s61\| PDB=1s61 \| SCENE= }}~~	+	Heme-ligand tunneling in group I truncated hemoglobins.,Milani M, Pesce A, Ouellet Y, Dewilde S, Friedman J, Ascenzi P, Guertin M, Bolognesi M J Biol Chem. 2004 May 14;279(20):21520-5. Epub 2004 Mar 11. PMID:15016811<ref>PMID:15016811</ref>

-	~~===Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis~~, ~~Soaked with Butyl-isocyanide===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15016811}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1s61]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA].~~	+

	==See Also==		==See Also==
-	*[[Hemoglobin\|Hemoglobin]]	+	*[[Hemoglobin 3D structures\|Hemoglobin 3D structures]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015016811<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Ascenzi, P.]]		[[Category: Ascenzi, P.]]

OCA at 19:59, 20 October 2012

2012-10-20T19:59:45Z

←Older revision		Revision as of 19:59, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1s61]] is a 2 chain structure ~~of [[Hemoglobin]]~~ with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA].	+	[[1s61]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA].

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

OCA: Protected "1s61" [edit=sysop:move=sysop]

2012-07-27T09:06:24Z

Protected "1s61" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:06, 27 July 2012

OCA at 09:06, 27 July 2012

2012-07-27T09:06:22Z

←Older revision		Revision as of 09:06, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1s61.png\|left\|200px]]		[[Image:1s61.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1s61", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1s61\| PDB=1s61 \| SCENE= }}		{{STRUCTURE_1s61\| PDB=1s61 \| SCENE= }}

	===Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide===		===Crystal Structure of "Truncated" Hemoglobin N (HbN) from Mycobacterium tuberculosis, Soaked with Butyl-isocyanide===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15016811}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15016811 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15016811}}		{{ABSTRACT_PUBMED_15016811}}

	==About this Structure==		==About this Structure==
-	~~1S61~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA].	+	[[1s61]] is a 2 chain structure of [[Hemoglobin]] with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA].
		+
		+	==See Also==
		+	*[[Hemoglobin\|Hemoglobin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15016811~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015016811</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Ascenzi, P.]]		[[Category: Ascenzi, P.]]
Line 33:		Line 24:
	[[Category: Ouellet, Y.]]		[[Category: Ouellet, Y.]]
	[[Category: Pesce, A.]]		[[Category: Pesce, A.]]
		+	[[Category: Oxygen storage-transport complex]]
	[[Category: Truncated hemoglobin]]		[[Category: Truncated hemoglobin]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:28:27 2009''

OCA at 00:28, 18 February 2009

2009-02-18T00:28:27Z

←Older revision		Revision as of 00:28, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1S61 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA].	+	1S61 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S61 OCA].

	==Reference==		==Reference==
-	~~Heme-ligand tunneling in~~ group ~~I truncated hemoglobins., Milani M, Pesce A, Ouellet Y, Dewilde S, Friedman J, Ascenzi P, Guertin M, Bolognesi M, J Biol Chem. 2004 May 14;279(20):21520-5. Epub 2004 Mar 11.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15016811 15016811]~~	+	<ref group="xtra">PMID:15016811</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Single protein]]
	[[Category: Ascenzi, P.]]		[[Category: Ascenzi, P.]]
	[[Category: Bolognesi, M.]]		[[Category: Bolognesi, M.]]
Line 36:		Line 35:
	[[Category: Truncated hemoglobin]]		[[Category: Truncated hemoglobin]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 09~~:05:~~55 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:28:27 2009''