1xqf - Revision history

OCA at 13:36, 13 March 2024

OCA — Wed, 13 Mar 2024 13:36:53 GMT

←Older revision		Revision as of 13:36, 13 March 2024
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	<StructureSection load='1xqf' size='340' side='right'caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xqf' size='340' side='right'caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XQF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1xqe\|1xqe]]~~, ~~[[1u7g\|1u7g]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [https://pdbe.org/1xqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [https://www.ebi.ac.uk/pdbsum/1xqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqf 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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [https://pdbe.org/1xqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [https://www.ebi.ac.uk/pdbsum/1xqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia.	+	[https://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI] Involved in the uptake of ammonia.
	== 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=1xqf 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=1xqf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ammonium is one of the most important nitrogen sources for bacteria, fungi, and plants, but it is toxic to animals. The ammonium transport proteins (methylamine permeases/ammonium transporters/rhesus) are present in all domains of life; however, functional studies with members of this family have yielded controversial results with respect to the chemical identity (NH(4)(+) or NH(3)) of the transported species. We have solved the structure of wild-type AmtB from Escherichia coli in two crystal forms at 1.8- and 2.1-A resolution, respectively. Substrate transport occurs through a narrow mainly hydrophobic pore located at the center of each monomer of the trimeric AmtB. At the periplasmic entry, a binding site for NH(4)(+) is observed. Two phenylalanine side chains (F107 and F215) block access into the pore from the periplasmic side. Further into the pore, the side chains of two highly conserved histidine residues (H168 and H318) bridged by a H-bond lie adjacent, with their edges pointing into the cavity. These histidine residues may facilitate the deprotonation of an ammonium ion entering the pore. Adiabatic free energy calculations support the hypothesis that an electrostatic barrier between H168 and H318 hinders the permeation of cations but not that of the uncharged NH(3.) The structural data and energetic considerations strongly indicate that the methylamine permeases/ammonium transporters/rhesus proteins are ammonia gas channels. Interestingly, at the cytoplasmic exit of the pore, two different conformational states are observed that might be related to the inactivation mechanism by its regulatory partner.
-
-	The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli.,Zheng L, Kostrewa D, Berneche S, Winkler FK, Li XD Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17090-5. Epub 2004 Nov 24. PMID:15563598<ref>PMID:15563598</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1xqf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ion channels 3D structures\|Ion channels 3D structures]]		*[[Ion channels 3D structures\|Ion channels 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Berneche, S]]	+	[[Category: Berneche S]]
-	[[Category: Kostrewa, D]]	+	[[Category: Kostrewa D]]
-	[[Category: Li, X D]]	+	[[Category: Li X-D]]
-	[[Category: Winkler~~, F K~~]]	+	[[Category: Winkler FK]]
-	[[Category: Zheng, L]]	+	[[Category: Zheng L]]
-	~~[[Category: Ammonia transport]]~~	+
-	~~[[Category: Closed conformation]]~~	+
-	~~[[Category: Transport protein]]~~	+
-	~~[[Category: Wild type~~]]	+

OCA at 09:06, 21 April 2021

OCA — Wed, 21 Apr 2021 09:06:12 GMT

←Older revision		Revision as of 09:06, 21 April 2021
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	<StructureSection load='1xqf' size='340' side='right'caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xqf' size='340' side='right'caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XQF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqe\|1xqe]], [[1u7g\|1u7g]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xqe\|1xqe]], [[1u7g\|1u7g]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [~~http~~://pdbe.org/1xqf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xqf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqf 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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [https://pdbe.org/1xqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [https://www.ebi.ac.uk/pdbsum/1xqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia.	+	[[https://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

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

OCA at 13:41, 17 July 2019

OCA — Wed, 17 Jul 2019 13:41:54 GMT

←Older revision		Revision as of 13:41, 17 July 2019
Line 1:		Line 1:

	==The mechanism of ammonia transport based on the crystal structure of AmtB of E. coli.==		==The mechanism of ammonia transport based on the crystal structure of AmtB of E. coli.==
-	<StructureSection load='1xqf' size='340' side='right' caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1xqf' size='340' side='right'caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQF FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xq/1xqf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xq/1xqf_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 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1xqf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1xqf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels\|Ion channels]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Berneche, S]]		[[Category: Berneche, S]]
	[[Category: Kostrewa, D]]		[[Category: Kostrewa, D]]

OCA at 14:34, 12 October 2017

OCA — Thu, 12 Oct 2017 14:34:21 GMT

←Older revision		Revision as of 14:34, 12 October 2017
Line 1:		Line 1:
		+
	==The mechanism of ammonia transport based on the crystal structure of AmtB of E. coli.==		==The mechanism of ammonia transport based on the crystal structure of AmtB of E. coli.==
	<StructureSection load='1xqf' size='340' side='right' caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xqf' size='340' side='right' caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqe\|1xqe]], [[1u7g\|1u7g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqe\|1xqe]], [[1u7g\|1u7g]]</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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [http://pdbe.org/1xqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [http://www.ebi.ac.uk/pdbsum/1xqf 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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [http://pdbe.org/1xqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [http://www.ebi.ac.uk/pdbsum/1xqf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xqf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1xqf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1xqf" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ion channels\|Ion channels]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:01, 9 February 2016

OCA — Tue, 09 Feb 2016 18:01:37 GMT

←Older revision		Revision as of 18:01, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xqf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:40, 11 September 2015

OCA — Fri, 11 Sep 2015 00:40:40 GMT

←Older revision		Revision as of 00:40, 11 September 2015
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	<StructureSection load='1xqf' size='340' side='right' caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xqf' size='340' side='right' caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqe\|1xqe]], [[1u7g\|1u7g]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqe\|1xqe]], [[1u7g\|1u7g]]</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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [http://www.ebi.ac.uk/pdbsum/1xqf 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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [http://pdbe.org/1xqf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [http://www.ebi.ac.uk/pdbsum/1xqf PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 1xqf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Berneche, S]]		[[Category: Berneche, S]]
	[[Category: Kostrewa, D]]		[[Category: Kostrewa, D]]

OCA at 08:30, 25 December 2014

OCA — Thu, 25 Dec 2014 08:30:55 GMT

←Older revision		Revision as of 08:30, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqe\|1xqe]], [[1u7g\|1u7g]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqe\|1xqe]], [[1u7g\|1u7g]]</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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [http://www.ebi.ac.uk/pdbsum/1xqf 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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [http://www.ebi.ac.uk/pdbsum/1xqf PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMTB_ECOLI AMTB_ECOLI]] Involved in the uptake of ammonia.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Berneche, S.]]	+	[[Category: Berneche, S]]
-	[[Category: Kostrewa, D.]]	+	[[Category: Kostrewa, D]]
-	[[Category: Li, X D.]]	+	[[Category: Li, X D]]
-	[[Category: Winkler, F K.]]	+	[[Category: Winkler, F K]]
-	[[Category: Zheng, L.]]	+	[[Category: Zheng, L]]
	[[Category: Ammonia transport]]		[[Category: Ammonia transport]]
	[[Category: Closed conformation]]		[[Category: Closed conformation]]
	[[Category: Transport protein]]		[[Category: Transport protein]]
	[[Category: Wild type]]		[[Category: Wild type]]

OCA at 21:23, 28 September 2014

OCA — Sun, 28 Sep 2014 21:23:45 GMT

←Older revision		Revision as of 21:23, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xqf.~~png~~\|~~left~~\|200px]]	+	==The mechanism of ammonia transport based on the crystal structure of AmtB of E. coli.==
		+	<StructureSection load='1xqf' size='340' side='right' caption='[[1xqf]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XQF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xqe\|1xqe]], [[1u7g\|1u7g]]</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=1xqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xqf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xqf RCSB], [http://www.ebi.ac.uk/pdbsum/1xqf 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/xq/1xqf_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 ==
		+	Ammonium is one of the most important nitrogen sources for bacteria, fungi, and plants, but it is toxic to animals. The ammonium transport proteins (methylamine permeases/ammonium transporters/rhesus) are present in all domains of life; however, functional studies with members of this family have yielded controversial results with respect to the chemical identity (NH(4)(+) or NH(3)) of the transported species. We have solved the structure of wild-type AmtB from Escherichia coli in two crystal forms at 1.8- and 2.1-A resolution, respectively. Substrate transport occurs through a narrow mainly hydrophobic pore located at the center of each monomer of the trimeric AmtB. At the periplasmic entry, a binding site for NH(4)(+) is observed. Two phenylalanine side chains (F107 and F215) block access into the pore from the periplasmic side. Further into the pore, the side chains of two highly conserved histidine residues (H168 and H318) bridged by a H-bond lie adjacent, with their edges pointing into the cavity. These histidine residues may facilitate the deprotonation of an ammonium ion entering the pore. Adiabatic free energy calculations support the hypothesis that an electrostatic barrier between H168 and H318 hinders the permeation of cations but not that of the uncharged NH(3.) The structural data and energetic considerations strongly indicate that the methylamine permeases/ammonium transporters/rhesus proteins are ammonia gas channels. Interestingly, at the cytoplasmic exit of the pore, two different conformational states are observed that might be related to the inactivation mechanism by its regulatory partner.

-	~~{{STRUCTURE_1xqf\| PDB=1xqf \| SCENE= }}~~	+	The mechanism of ammonia transport based on the crystal structure of AmtB of Escherichia coli.,Zheng L, Kostrewa D, Berneche S, Winkler FK, Li XD Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17090-5. Epub 2004 Nov 24. PMID:15563598<ref>PMID:15563598</ref>

-	~~===The mechanism~~ of ~~ammonia transport based on~~ the ~~crystal structure~~ of ~~AmtB of E~~. ~~coli.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15563598}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1xqf]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA].~~	+

	==See Also==		==See Also==
	*[[Ion channels\|Ion channels]]		*[[Ion channels\|Ion channels]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015563598<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Berneche, S.]]		[[Category: Berneche, S.]]

OCA at 14:39, 20 October 2012

OCA — Sat, 20 Oct 2012 14:39:38 GMT

←Older revision		Revision as of 14:39, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1xqf]] is a 1 chain structure ~~of [[Ion channels]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA].	+	[[1xqf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA].

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

OCA at 18:58, 6 August 2012

OCA — Mon, 06 Aug 2012 18:58:32 GMT

←Older revision		Revision as of 18:58, 6 August 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1xqf]] is a 1 chain structure of ~~[[]] and~~ [[Ion channels]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA].	+	[[1xqf]] is a 1 chain structure of [[Ion channels]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XQF OCA].

	==See Also==		==See Also==
-	*[[\|]]
	*[[Ion channels\|Ion channels]]		*[[Ion channels\|Ion channels]]