3e79 - Revision history

OCA at 09:45, 21 February 2024

2024-02-21T09:45:20Z

←Older revision		Revision as of 09:45, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3e79' size='340' side='right'caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3e79' size='340' side='right'caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e79]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"asterococcus_hyorhinis"_(switzer_1955)_prevot_1961 "asterococcus~~ hyorhinis~~" (switzer 1955) prevot 1961~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E79 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e79]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesomycoplasma_hyorhinis Mesomycoplasma hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E79 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e78\|3e78]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p37 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2100 "Asterococcus hyorhinis" (Switzer 1955) Prevot 1961])</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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [https://pdbe.org/3e79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [https://www.ebi.ac.uk/pdbsum/3e79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e79 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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [https://pdbe.org/3e79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [https://www.ebi.ac.uk/pdbsum/3e79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e79 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/P37_MESHY P37_MESHY]
	== 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=3e79 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=3e79 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of the Mycoplasma hyorhinis protein Mh-p37 has been solved and refined to 1.9 A resolution. This is the first de novo structure to be determined using the recently described heavy-atom reagent [Beck et al. (2008), Acta Cryst. D64, 1179-1182] 5-amino-2,4,6-triiodoisophthalic acid (I3C), which contains three I atoms arranged in an equilateral triangle, by SIRAS methods. Data collection was performed in-house at room temperature. SHELXD and SHELXE were used to determine the I-atom positions and phase the native protein and PHENIX AutoBuild software was used to automatically fit the amino-acid sequence to the electron-density map. The structure was refined using SHELX97 to an R(cryst) of 18.6% and an R(free) of 24.0%. Mh-p37 is an alpha/beta protein with two well defined domains which are separated by a deep cleft. An unanticipated ligand bound in the center of the molecule at the base of the cleft has been modeled as thiamine pyrophosphate or vitamin B(1). Retrospective attempts to solve the crystal structure by Patterson search methods using either isomorphous or anomalous differences failed. Additionally, attempts to use proteins with the highest structural homology in the Protein Data Bank to phase the data by molecular replacement were unsuccessful, most likely in hindsight because of their poor structural agreement. Therefore, the I3C reagent offers an alternative, quick and inexpensive method for in-house phasing of de novo structures where other methods may not be successful.
-
-	Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37.,Sippel KH, Robbins AH, Reutzel R, Domsic J, Boehlein SK, Govindasamy L, Agbandje-McKenna M, Rosser CJ, McKenna R Acta Crystallogr D Biol Crystallogr. 2008 Nov;64(Pt 11):1172-8. Epub 2008, Oct 18. PMID:19020356<ref>PMID:19020356</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3e79" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Domsic, J]]	+	[[Category: Mesomycoplasma hyorhinis]]
-	[[Category: McKenna, R]]	+	[[Category: Domsic J]]
-	[[Category: Reutzel, R]]	+	[[Category: McKenna R]]
-	[[Category: Robbins~~, A H~~]]	+	[[Category: Reutzel R]]
-	[[Category: Sippel~~, K H]]~~	+	[[Category: Robbins AH]]
-	~~[[Category: Cell membrane]]~~	+	[[Category: Sippel KH]]
-	~~[[Category: Lipoprotein]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Mycoplasma]]~~	+
-	~~[[Category: P37]]~~	+
-	~~[[Category: Palmitate]]~~	+
-	~~[[Category: Tpp]]~~	+
-	~~[[Category: Tpp binding protein]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 11:42, 16 February 2022

2022-02-16T11:42:08Z

←Older revision		Revision as of 11:42, 16 February 2022
Line 1:		Line 1:

	==Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37==		==Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37==
-	<StructureSection load='3e79' size='340' side='right' caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3e79' size='340' side='right'caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e79]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"asterococcus_hyorhinis"_(switzer_1955)_prevot_1961 "asterococcus hyorhinis" (switzer 1955) prevot 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3E79 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e79]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"asterococcus_hyorhinis"_(switzer_1955)_prevot_1961 "asterococcus hyorhinis" (switzer 1955) prevot 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E79 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e78\|3e78]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e78\|3e78]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p37 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2100 "Asterococcus hyorhinis" (Switzer 1955) Prevot 1961])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p37 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2100 "Asterococcus hyorhinis" (Switzer 1955) Prevot 1961])</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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [~~http~~://pdbe.org/3e79 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3e79 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3e79 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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [https://pdbe.org/3e79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [https://www.ebi.ac.uk/pdbsum/3e79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e79 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Domsic, J]]		[[Category: Domsic, J]]
	[[Category: McKenna, R]]		[[Category: McKenna, R]]

OCA at 22:10, 2 December 2018

2018-12-02T22:10:19Z

←Older revision		Revision as of 22:10, 2 December 2018
Line 1:		Line 1:
		+
	==Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37==		==Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37==
	<StructureSection load='3e79' size='340' side='right' caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3e79' size='340' side='right' caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e78\|3e78]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e78\|3e78]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p37 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2100 "Asterococcus hyorhinis" (Switzer 1955) Prevot 1961])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p37 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2100 "Asterococcus hyorhinis" (Switzer 1955) Prevot 1961])</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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [http://pdbe.org/3e79 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [http://www.ebi.ac.uk/pdbsum/3e79 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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [http://pdbe.org/3e79 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [http://www.ebi.ac.uk/pdbsum/3e79 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3e79 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/e7/3e79_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e7/3e79_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>

OCA at 19:47, 7 February 2016

2016-02-07T19:47:55Z

←Older revision		Revision as of 19:47, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3e79' size='340' side='right' caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3e79' size='340' side='right' caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3e79]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycoplasma_hyorhinis Mycoplasma~~ hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E79 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3e79]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"asterococcus_hyorhinis"_(switzer_1955)_prevot_1961 "asterococcus hyorhinis" (switzer 1955) prevot 1961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E79 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e78\|3e78]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e78\|3e78]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p37 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2100 ~~Mycoplasma~~ hyorhinis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p37 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2100 "Asterococcus hyorhinis" (Switzer 1955) Prevot 1961])</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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [http://www.ebi.ac.uk/pdbsum/3e79 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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [http://pdbe.org/3e79 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [http://www.ebi.ac.uk/pdbsum/3e79 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=3e79 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3e79" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycoplasma hyorhinis]]
	[[Category: Domsic, J]]		[[Category: Domsic, J]]
	[[Category: McKenna, R]]		[[Category: McKenna, R]]

OCA at 14:22, 18 December 2014

2014-12-18T14:22:01Z

←Older revision		Revision as of 14:22, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3e79\| PDB=3e79 \| SCENE= }}~~	+	==Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37==
-	===Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37===	+	<StructureSection load='3e79' size='340' side='right' caption='[[3e79]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19020356}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3e79]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycoplasma_hyorhinis Mycoplasma hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E79 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=I3C:5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC+ACID'>I3C</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e78\|3e78]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">p37 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2100 Mycoplasma hyorhinis])</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=3e79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e79 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e79 RCSB], [http://www.ebi.ac.uk/pdbsum/3e79 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/e7/3e79_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 ==
		+	The crystal structure of the Mycoplasma hyorhinis protein Mh-p37 has been solved and refined to 1.9 A resolution. This is the first de novo structure to be determined using the recently described heavy-atom reagent [Beck et al. (2008), Acta Cryst. D64, 1179-1182] 5-amino-2,4,6-triiodoisophthalic acid (I3C), which contains three I atoms arranged in an equilateral triangle, by SIRAS methods. Data collection was performed in-house at room temperature. SHELXD and SHELXE were used to determine the I-atom positions and phase the native protein and PHENIX AutoBuild software was used to automatically fit the amino-acid sequence to the electron-density map. The structure was refined using SHELX97 to an R(cryst) of 18.6% and an R(free) of 24.0%. Mh-p37 is an alpha/beta protein with two well defined domains which are separated by a deep cleft. An unanticipated ligand bound in the center of the molecule at the base of the cleft has been modeled as thiamine pyrophosphate or vitamin B(1). Retrospective attempts to solve the crystal structure by Patterson search methods using either isomorphous or anomalous differences failed. Additionally, attempts to use proteins with the highest structural homology in the Protein Data Bank to phase the data by molecular replacement were unsuccessful, most likely in hindsight because of their poor structural agreement. Therefore, the I3C reagent offers an alternative, quick and inexpensive method for in-house phasing of de novo structures where other methods may not be successful.

-	~~==About this~~ Structure==	+	Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37.,Sippel KH, Robbins AH, Reutzel R, Domsic J, Boehlein SK, Govindasamy L, Agbandje-McKenna M, Rosser CJ, McKenna R Acta Crystallogr D Biol Crystallogr. 2008 Nov;64(Pt 11):1172-8. Epub 2008, Oct 18. PMID:19020356<ref>PMID:19020356</ref>
-	~~[[3e79]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycoplasma_hyorhinis~~ Mycoplasma hyorhinis]. ~~Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3E79 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:019020356</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mycoplasma hyorhinis]]		[[Category: Mycoplasma hyorhinis]]
-	[[Category: Domsic, J.]]	+	[[Category: Domsic, J]]
-	[[Category: McKenna, R.]]	+	[[Category: McKenna, R]]
-	[[Category: Reutzel, R.]]	+	[[Category: Reutzel, R]]
-	[[Category: Robbins, A H.]]	+	[[Category: Robbins, A H]]
-	[[Category: Sippel, K H.]]	+	[[Category: Sippel, K H]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Lipoprotein]]		[[Category: Lipoprotein]]

OCA at 11:38, 24 July 2013

2013-07-24T11:38:59Z

←Older revision		Revision as of 11:38, 24 July 2013
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-	[[Image:3e79.png\|left\|200px]]
-
	{{STRUCTURE_3e79\| PDB=3e79 \| SCENE= }}		{{STRUCTURE_3e79\| PDB=3e79 \| SCENE= }}
-
	===Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37===		===Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37===
-
	{{ABSTRACT_PUBMED_19020356}}		{{ABSTRACT_PUBMED_19020356}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:019020356</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019020356</ref><references group="xtra"/><references/>
	[[Category: Mycoplasma hyorhinis]]		[[Category: Mycoplasma hyorhinis]]
	[[Category: Domsic, J.]]		[[Category: Domsic, J.]]

OCA: Protected "3e79" [edit=sysop:move=sysop]

2013-01-09T09:02:14Z

Protected "3e79" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:02, 9 January 2013

OCA at 09:02, 9 January 2013

2013-01-09T09:02:11Z

←Older revision		Revision as of 09:02, 9 January 2013
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-	{{Seed}}
	[[Image:3e79.png\|left\|200px]]		[[Image:3e79.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3e79", 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_3e79\| PDB=3e79 \| SCENE= }}		{{STRUCTURE_3e79\| PDB=3e79 \| SCENE= }}

	===Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37===		===Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19020356}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19020356 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19020356}}		{{ABSTRACT_PUBMED_19020356}}

	==About this Structure==		==About this Structure==
-	~~3E79~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mycoplasma_hyorhinis Mycoplasma hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA].	+	[[3e79]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycoplasma_hyorhinis Mycoplasma hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19020356~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019020356</ref><references group="xtra"/>
	[[Category: Mycoplasma hyorhinis]]		[[Category: Mycoplasma hyorhinis]]
	[[Category: Domsic, J.]]		[[Category: Domsic, J.]]
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	[[Category: Tpp binding protein]]		[[Category: Tpp binding protein]]
	[[Category: Transport]]		[[Category: Transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:06:38 2009''

OCA at 14:06, 16 February 2009

2009-02-16T14:06:39Z

←Older revision		Revision as of 14:06, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3E79 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Mycoplasma_hyorhinis Mycoplasma hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA].	+	3E79 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mycoplasma_hyorhinis Mycoplasma hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA].

	==Reference==		==Reference==
-	Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37., Sippel KH, Robbins AH, Reutzel R, Domsic J, Boehlein SK, Govindasamy L, Agbandje-McKenna M, Rosser CJ, McKenna R, Acta Crystallogr D Biol Crystallogr. 2008 Nov;64(Pt 11):1172-8. Epub 2008, Oct 18. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19020356 19020356]~~	+	<ref group="xtra">PMID:19020356</ref><references group="xtra"/>
	[[Category: Mycoplasma hyorhinis]]		[[Category: Mycoplasma hyorhinis]]
-	[[Category: ~~Single protein~~]]	+	[[Category: Domsic, J.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: McKenna, R.]]
		+	[[Category: Reutzel, R.]]
		+	[[Category: Robbins, A H.]]
		+	[[Category: Sippel, K H.]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Lipoprotein]]		[[Category: Lipoprotein]]
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	[[Category: Transport]]		[[Category: Transport]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Dec 24 20~~:31:~~09 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:06:38 2009''

OCA at 12:16, 25 December 2008

2008-12-25T12:16:45Z

←Older revision		Revision as of 12:16, 25 December 2008
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	==About this Structure==		==About this Structure==
-	3E79 is a ~~1 chain~~ structure of sequence from [http://en.wikipedia.org/wiki/Mycoplasma_hyorhinis Mycoplasma hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA].	+	3E79 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycoplasma_hyorhinis Mycoplasma hyorhinis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E79 OCA].

	==Reference==		==Reference==
	Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37., Sippel KH, Robbins AH, Reutzel R, Domsic J, Boehlein SK, Govindasamy L, Agbandje-McKenna M, Rosser CJ, McKenna R, Acta Crystallogr D Biol Crystallogr. 2008 Nov;64(Pt 11):1172-8. Epub 2008, Oct 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19020356 19020356]		Structure determination of the cancer-associated Mycoplasma hyorhinis protein Mh-p37., Sippel KH, Robbins AH, Reutzel R, Domsic J, Boehlein SK, Govindasamy L, Agbandje-McKenna M, Rosser CJ, McKenna R, Acta Crystallogr D Biol Crystallogr. 2008 Nov;64(Pt 11):1172-8. Epub 2008, Oct 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19020356 19020356]
	[[Category: Mycoplasma hyorhinis]]		[[Category: Mycoplasma hyorhinis]]
-	[[Category: ~~Domsic, J.~~]]	+	[[Category: Single protein]]
-	[[Category: ~~McKenna~~, ~~R.]]~~	+	[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
-	~~[[Category~~: ~~Reutzel, R.]]~~	+
-	~~[[Category: Robbins, A H.]]~~	+
-	~~[[Category: Sippel, K H~~.]]	+
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Lipoprotein]]		[[Category: Lipoprotein]]
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	[[Category: Transport]]		[[Category: Transport]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 24 11:07:44 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 24 20:31:09 2008''