5tim - Revision history

OCA at 14:20, 6 March 2024

2024-03-06T14:20:48Z

← Older revision		Revision as of 14:20, 6 March 2024
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	<StructureSection load='5tim' size='340' side='right'caption='[[5tim]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5tim' size='340' side='right'caption='[[5tim]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tim]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Trybb Trybb~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5TIM FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tim]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TIM FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DTT:2~~,~~3-DIHYDROXY-~~1~~,4-DITHIOBUTANE'>DTT</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]] 1.83Å</td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Triose~~-~~phosphate_isomerase Triose~~-~~phosphate isomerase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info~~/~~php/result_flat.php4?ecno~~=~~5.3.1.1 5.3.1.1]~~ </~~span~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tim OCA], [~~http~~://pdbe.org/5tim PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tim RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tim PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tim 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=5tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tim OCA], [https://pdbe.org/5tim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tim RCSB], [https://www.ebi.ac.uk/pdbsum/5tim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tim ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/TPIS_TRYBB TPIS_TRYBB]
	== 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=5tim 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=5tim ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Triosephosphate isomerase (TIM) is a dimeric glycolytic enzyme. TIM from Trypanosoma brucei brucei has been crystallized at pH 7.0 in 2.4 M-ammonium sulphate. The well-diffracting crystals have one dimer per asymmetric unit. The structure has been refined at 1.83 A resolution with an R-factor of 18.3% for all data between 6 A and 1.83 A (37,568 reflections). The model consists of 3778 protein atoms and 297 solvent atoms. Subunit 1 is involved in considerably more crystal contacts than subunit 2. Correlated with these differences in crystal packing is the observation that only in the active site of subunit 2 is a sulphate ion bound. Furthermore, significant differences with respect to structure and flexibility are observed in three loops near the active site. In particular, there is a 7 A positional difference of the tip of the flexible loop (loop 6) when comparing subunit 1 and subunit 2. Also, the neighbouring loops (loop 5 and loop 7) have significantly different conformations and flexibility. In subunit 1, loop 6 is in an "open" conformation, in subunit 2, loop 6 is in an "almost closed" conformation. Only in the presence of a phosphate-containing ligand, such as glycerol-3-phosphate, does loop 6 take up the "closed" conformation. Loop 6 and loop 7 (and also to some extent loop 5) are rather flexible in the almost closed conformation, but well defined in the open and closed conformations. The closing of loop 6 (167 to 180), as observed in the almost closed conformation, slightly changes the main-chain conformation of the catalytic glutamate, Glu167, leading to a change of the chi 1 angle of this residue from approximately -60 degrees to approximately 60 degrees and the weakening of the hydrogen bonds between its polar side-chain atoms and Ser96. In the closed conformation, in the presence of glycerol-3-phosphate, the main-chain atoms of Glu167 remain in the same position as in the almost closed conformation, but the side-chain has rotated around the CA-CB bond changing chi 1 from approximately 60 degrees to approximately -60 degrees. In this new position the hydrogen bonding to Ser96 is completely lost and also a water-mediated salt bridge between OE2(Glu167) and NE(Arg99) is lost. Comparison of the two independently refined subunits, showed that the root-mean-square deviation for all 249 CA atoms is 0.9 A; for the CA atoms of the beta-strands this is only 0.2 A. The average B-factor for all subunit 1 and subunit 2 atoms is 20 A2 and 25 A2, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)

	Refined 1.83 A structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex.,Wierenga RK, Noble ME, Vriend G, Nauche S, Hol WG J Mol Biol. 1991 Aug 20;220(4):995-1015. PMID:1880808<ref>PMID:1880808</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 5tim" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Triose phosphate isomerase 3D structures\|Triose phosphate isomerase 3D structures]]		*[[Triose phosphate isomerase 3D structures\|Triose phosphate isomerase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Triose-phosphate isomerase]]~~		[[Category: Trypanosoma brucei brucei]]
	~~[[Category: Trybb~~]]		[[Category: Hol WGJ]]
	[[Category: Hol~~, W G.J~~]]		[[Category: Wierenga RK]]
	[[Category: Wierenga~~, R K~~]]

OCA at 12:11, 23 September 2020

2020-09-23T12:11:55Z

← Older revision		Revision as of 12:11, 23 September 2020
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	==REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX==		==REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX==
	<StructureSection load='5tim' size='340' side='right' caption='[[5tim]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5tim' size='340' side='right'caption='[[5tim]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TIM FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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=5tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tim OCA], [http://pdbe.org/5tim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tim RCSB], [http://www.ebi.ac.uk/pdbsum/5tim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tim 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=5tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tim OCA], [http://pdbe.org/5tim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tim RCSB], [http://www.ebi.ac.uk/pdbsum/5tim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tim ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ti/5tim_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ti/5tim_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:

	==See Also==		==See Also==
	*[[Triose ~~Phosphate Isomerase~~\|Triose ~~Phosphate Isomerase~~]]		*[[Triose phosphate isomerase 3D structures\|Triose phosphate isomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Triose-phosphate isomerase]]		[[Category: Triose-phosphate isomerase]]
	[[Category: Trybb]]		[[Category: Trybb]]
	[[Category: Hol, W G.J]]		[[Category: Hol, W G.J]]
	[[Category: Wierenga, R K]]		[[Category: Wierenga, R K]]

OCA at 09:05, 5 August 2016

2016-08-05T09:05:17Z

← Older revision		Revision as of 09:05, 5 August 2016
Line 1:		Line 1:

	==REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX==		==REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX==
	<StructureSection load='5tim' size='340' side='right' caption='[[5tim]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5tim' size='340' side='right' caption='[[5tim]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Trypanosoma_brucei_brucei Trypanosoma brucei brucei~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TIM FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TIM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</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=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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=5tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5tim RCSB], [http://www.ebi.ac.uk/pdbsum/5tim 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=5tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tim OCA], [http://pdbe.org/5tim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tim RCSB], [http://www.ebi.ac.uk/pdbsum/5tim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tim ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		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=5tim ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		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 5tim" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Triose-phosphate isomerase]]		[[Category: Triose-phosphate isomerase]]
	[[Category: ~~Trypanosoma brucei brucei~~]]		[[Category: Trybb]]
	[[Category: Hol, W G.J]]		[[Category: Hol, W G.J]]
	[[Category: Wierenga, R K]]		[[Category: Wierenga, R K]]

OCA at 08:44, 18 December 2014

2014-12-18T08:44:40Z

← Older revision		Revision as of 08:44, 18 December 2014
Line 1:		Line 1:
	~~{{STRUCTURE_5tim\| PDB=5tim \| SCENE= }}~~		==REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX==
	===REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX===		<StructureSection load='5tim' size='340' side='right' caption='[[5tim]], [[Resolution\|resolution]] 1.83Å' scene=''>
	~~{{ABSTRACT_PUBMED_1880808}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[5tim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TIM FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] </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=5tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tim OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5tim RCSB], [http://www.ebi.ac.uk/pdbsum/5tim 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/ti/5tim_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 ==
			Triosephosphate isomerase (TIM) is a dimeric glycolytic enzyme. TIM from Trypanosoma brucei brucei has been crystallized at pH 7.0 in 2.4 M-ammonium sulphate. The well-diffracting crystals have one dimer per asymmetric unit. The structure has been refined at 1.83 A resolution with an R-factor of 18.3% for all data between 6 A and 1.83 A (37,568 reflections). The model consists of 3778 protein atoms and 297 solvent atoms. Subunit 1 is involved in considerably more crystal contacts than subunit 2. Correlated with these differences in crystal packing is the observation that only in the active site of subunit 2 is a sulphate ion bound. Furthermore, significant differences with respect to structure and flexibility are observed in three loops near the active site. In particular, there is a 7 A positional difference of the tip of the flexible loop (loop 6) when comparing subunit 1 and subunit 2. Also, the neighbouring loops (loop 5 and loop 7) have significantly different conformations and flexibility. In subunit 1, loop 6 is in an "open" conformation, in subunit 2, loop 6 is in an "almost closed" conformation. Only in the presence of a phosphate-containing ligand, such as glycerol-3-phosphate, does loop 6 take up the "closed" conformation. Loop 6 and loop 7 (and also to some extent loop 5) are rather flexible in the almost closed conformation, but well defined in the open and closed conformations. The closing of loop 6 (167 to 180), as observed in the almost closed conformation, slightly changes the main-chain conformation of the catalytic glutamate, Glu167, leading to a change of the chi 1 angle of this residue from approximately -60 degrees to approximately 60 degrees and the weakening of the hydrogen bonds between its polar side-chain atoms and Ser96. In the closed conformation, in the presence of glycerol-3-phosphate, the main-chain atoms of Glu167 remain in the same position as in the almost closed conformation, but the side-chain has rotated around the CA-CB bond changing chi 1 from approximately 60 degrees to approximately -60 degrees. In this new position the hydrogen bonding to Ser96 is completely lost and also a water-mediated salt bridge between OE2(Glu167) and NE(Arg99) is lost. Comparison of the two independently refined subunits, showed that the root-mean-square deviation for all 249 CA atoms is 0.9 A; for the CA atoms of the beta-strands this is only 0.2 A. The average B-factor for all subunit 1 and subunit 2 atoms is 20 A2 and 25 A2, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)

	~~==About this Structure==~~		Refined 1.83 A structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate isomerase-glycerol-3-phosphate complex.,Wierenga RK, Noble ME, Vriend G, Nauche S, Hol WG J Mol Biol. 1991 Aug 20;220(4):995-1015. PMID:1880808<ref>PMID:1880808</ref>
	~~[[5tim]] is a~~ 2 ~~chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This~~ structure ~~supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.~~ac.il/oca-bin/send~~-~~pdb?obs=1&id=2tim 2tim]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=5TIM OCA].~~
			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	==See Also==		==See Also==
	*[[Triose Phosphate Isomerase\|Triose Phosphate Isomerase]]		*[[Triose Phosphate Isomerase\|Triose Phosphate Isomerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:001880808<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Triose-phosphate isomerase]]		[[Category: Triose-phosphate isomerase]]
	[[Category: Trypanosoma brucei brucei]]		[[Category: Trypanosoma brucei brucei]]
	[[Category: Hol, W G.J.]]		[[Category: Hol, W G.J]]
	[[Category: Wierenga, R K.]]		[[Category: Wierenga, R K]]

OCA at 09:35, 11 March 2013

2013-03-11T09:35:48Z

← Older revision		Revision as of 09:35, 11 March 2013
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	~~[[Image:5tim.png\|left\|200px]]~~

	{{STRUCTURE_5tim\| PDB=5tim \| SCENE= }}		{{STRUCTURE_5tim\| PDB=5tim \| SCENE= }}

	===REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX===		===REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX===

	{{ABSTRACT_PUBMED_1880808}}		{{ABSTRACT_PUBMED_1880808}}

OCA at 19:28, 20 October 2012

2012-10-20T19:28:47Z

← Older revision		Revision as of 19:28, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[5tim]] is a 2 chain structure ~~of [[Triose Phosphate Isomerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA].		[[5tim]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA].

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

	==Reference==		==Reference==
	<ref group="xtra">PMID:001880808~~</ref><ref group="xtra">PMID:012215419~~</ref><references group="xtra"/>		<ref group="xtra">PMID:001880808</ref><references group="xtra"/>
	[[Category: Triose-phosphate isomerase]]		[[Category: Triose-phosphate isomerase]]
	[[Category: Trypanosoma brucei brucei]]		[[Category: Trypanosoma brucei brucei]]
	[[Category: Hol, W G.J.]]		[[Category: Hol, W G.J.]]
	[[Category: Wierenga, R K.]]		[[Category: Wierenga, R K.]]

OCA at 02:46, 29 August 2012

2012-08-29T02:46:16Z

← Older revision		Revision as of 02:46, 29 August 2012
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	==About this Structure==		==About this Structure==
	[[5tim]] is a 2 chain structure of ~~[[TIM test]] and~~ [[Triose Phosphate Isomerase]] with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA].		[[5tim]] is a 2 chain structure of [[Triose Phosphate Isomerase]] with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA].

	==See Also==		==See Also==
	*[[TIM test\|TIM test]]
	*[[Triose Phosphate Isomerase\|Triose Phosphate Isomerase]]		*[[Triose Phosphate Isomerase\|Triose Phosphate Isomerase]]

OCA: Protected "5tim" [edit=sysop:move=sysop]

2012-07-27T07:28:59Z

Protected "5tim" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:28, 27 July 2012
(No difference)

OCA at 07:28, 27 July 2012

2012-07-27T07:28:58Z

← Older revision		Revision as of 07:28, 27 July 2012
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	~~{{Seed}}~~
	[[Image:5tim.png\|left\|200px]]		[[Image:5tim.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_5tim", 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_5tim\| PDB=5tim \| SCENE= }}		{{STRUCTURE_5tim\| PDB=5tim \| SCENE= }}

	===REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX===		===REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE, CRYSTALLIZED IN THE PRESENCE OF 2.4 M-AMMONIUM SULPHATE. A COMPARISON WITH THE STRUCTURE OF THE TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE-GLYCEROL-3-PHOSPHATE COMPLEX===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_1880808}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 1880808 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_1880808}}		{{ABSTRACT_PUBMED_1880808}}

	==About this Structure==		==About this Structure==
	~~5TIM~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA].		[[5tim]] is a 2 chain structure of [[TIM test]] and [[Triose Phosphate Isomerase]] with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2tim 2tim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TIM OCA].

			==See Also==
			*[[TIM test\|TIM test]]
			*[[Triose Phosphate Isomerase\|Triose Phosphate Isomerase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~1880808~~</ref><references group="xtra"/>		<ref group="xtra">PMID:001880808</ref><ref group="xtra">PMID:012215419</ref><references group="xtra"/>
	[[Category: Triose-phosphate isomerase]]		[[Category: Triose-phosphate isomerase]]
	[[Category: Trypanosoma brucei brucei]]		[[Category: Trypanosoma brucei brucei]]
	[[Category: Hol, W G.J.]]		[[Category: Hol, W G.J.]]
	[[Category: Wierenga, R K.]]		[[Category: Wierenga, R K.]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 16 23:15:12 2010''~~

OCA: New page: {{Seed}} 200px