4i8k - Revision history

OCA at 08:48, 9 November 2022

OCA — Wed, 09 Nov 2022 08:48:33 GMT

←Older revision		Revision as of 08:48, 9 November 2022
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	<StructureSection load='4i8k' size='340' side='right'caption='[[4i8k]], [[Resolution\|resolution]] 0.85Å' scene=''>		<StructureSection load='4i8k' size='340' side='right'caption='[[4i8k]], [[Resolution\|resolution]] 0.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i8k]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I8K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i8k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I8K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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">[[4i8g\|4i8g]], [[4i8h\|4i8h]], [[4i8j\|4i8j]], [[4i8l\|4i8l]]</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=4i8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8k OCA], [https://pdbe.org/4i8k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i8k RCSB], [https://www.ebi.ac.uk/pdbsum/4i8k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i8k ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=4i8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8k OCA], [~~http~~://pdbe.org/4i8k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i8k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i8k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i8k ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Trypsin\|Trypsin]]	+	*[[Trypsin 3D structures\|Trypsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Trypsin]]~~	+	[[Category: Brzuszkiewicz A]]
-	[[Category: Brzuszkiewicz, A]]	+	[[Category: Dauter M]]
-	[[Category: Dauter, M]]	+	[[Category: Dauter Z]]
-	[[Category: Dauter, Z]]	+	[[Category: Liebschner D]]
-	[[Category: Liebschner, D]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Serine protease~~]]	+

OCA at 05:03, 13 February 2020

OCA — Thu, 13 Feb 2020 05:03:20 GMT

←Older revision		Revision as of 05:03, 13 February 2020
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	==Bovine trypsin at 0.85 resolution==		==Bovine trypsin at 0.85 resolution==
-	<StructureSection load='4i8k' size='340' side='right' caption='[[4i8k]], [[Resolution\|resolution]] 0.85Å' scene=''>	+	<StructureSection load='4i8k' size='340' side='right'caption='[[4i8k]], [[Resolution\|resolution]] 0.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4i8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I8K FirstGlance]. <br>		<table><tr><td colspan='2'>[[4i8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I8K FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 4i8k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4i8k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Trypsin\|Trypsin]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
		+	[[Category: Large Structures]]
	[[Category: Trypsin]]		[[Category: Trypsin]]
	[[Category: Brzuszkiewicz, A]]		[[Category: Brzuszkiewicz, A]]

OCA at 08:51, 15 November 2017

OCA — Wed, 15 Nov 2017 08:51:14 GMT

←Older revision		Revision as of 08:51, 15 November 2017
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	</div>		</div>
	<div class="pdbe-citations 4i8k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4i8k" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Trypsin\|Trypsin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:05, 4 August 2016

OCA — Thu, 04 Aug 2016 17:05:24 GMT

←Older revision		Revision as of 17:05, 4 August 2016
Line 1:		Line 1:
		+
	==Bovine trypsin at 0.85 resolution==		==Bovine trypsin at 0.85 resolution==
	<StructureSection load='4i8k' size='340' side='right' caption='[[4i8k]], [[Resolution\|resolution]] 0.85Å' scene=''>		<StructureSection load='4i8k' size='340' side='right' caption='[[4i8k]], [[Resolution\|resolution]] 0.85Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4i8g\|4i8g]], [[4i8h\|4i8h]], [[4i8j\|4i8j]], [[4i8l\|4i8l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4i8g\|4i8g]], [[4i8h\|4i8h]], [[4i8j\|4i8j]], [[4i8l\|4i8l]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=4i8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i8k RCSB], [http://www.ebi.ac.uk/pdbsum/4i8k 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=4i8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8k OCA], [http://pdbe.org/4i8k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i8k RCSB], [http://www.ebi.ac.uk/pdbsum/4i8k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i8k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 4i8k" style="background-color:#fffaf0;"></div>

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

OCA at 12:16, 21 December 2014

OCA — Sun, 21 Dec 2014 12:16:55 GMT

←Older revision		Revision as of 12:16, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4i8k~~\| ~~PDB~~=4i8k \| ~~SCENE~~= }}	+	==Bovine trypsin at 0.85 resolution==
-	===~~Bovine trypsin at 0~~.~~85 resolution~~===	+	<StructureSection load='4i8k' size='340' side='right' caption='[[4i8k]], [[Resolution\|resolution]] 0.85Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23897468}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4i8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I8K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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">[[4i8g\|4i8g]], [[4i8h\|4i8h]], [[4i8j\|4i8j]], [[4i8l\|4i8l]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=4i8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i8k RCSB], [http://www.ebi.ac.uk/pdbsum/4i8k PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C(alpha) and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5 A and more than one third were conserved within 0.1 A. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.

-	~~==About this Structure==~~	+	On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin.,Liebschner D, Dauter M, Brzuszkiewicz A, Dauter Z Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1447-62. doi:, 10.1107/S0907444913009050. Epub 2013 Jul 17. PMID:23897468<ref>PMID:23897468</ref>
-	~~[[4i8k]] is a 1 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Bos_taurus Bos taurus]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4I8K OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Trypsin\|Trypsin]]		*[[Trypsin\|Trypsin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023897468</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Trypsin]]		[[Category: Trypsin]]
-	[[Category: Brzuszkiewicz, A.]]	+	[[Category: Brzuszkiewicz, A]]
-	[[Category: Dauter, M.]]	+	[[Category: Dauter, M]]
-	[[Category: Dauter, Z.]]	+	[[Category: Dauter, Z]]
-	[[Category: Liebschner, D.]]	+	[[Category: Liebschner, D]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Serine protease]]		[[Category: Serine protease]]

OCA at 03:02, 20 September 2013

OCA — Fri, 20 Sep 2013 03:02:16 GMT

←Older revision		Revision as of 03:02, 20 September 2013
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-	[[Image:4i8k.jpg\|left\|200px]]
-
	{{STRUCTURE_4i8k\| PDB=4i8k \| SCENE= }}		{{STRUCTURE_4i8k\| PDB=4i8k \| SCENE= }}
-
	===Bovine trypsin at 0.85 resolution===		===Bovine trypsin at 0.85 resolution===
-		+	{{ABSTRACT_PUBMED_23897468}}

	==About this Structure==		==About this Structure==
	[[4i8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8K OCA].		[[4i8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8K OCA].
		+
		+	==See Also==
		+	*[[Trypsin\|Trypsin]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023897468</ref><references group="xtra"/><references/>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Trypsin]]		[[Category: Trypsin]]

OCA at 11:39, 19 December 2012

OCA — Wed, 19 Dec 2012 11:39:38 GMT

←Older revision		Revision as of 11:39, 19 December 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4i8k.jpg\|left\|200px]]

-	~~The entry~~ 4i8k ~~is ON HOLD~~	+	{{STRUCTURE_4i8k\| PDB=4i8k \| SCENE= }}

-	~~Authors: Dauter, Z., Liebschner, D., Dauter, M., Brzuszkiewicz, A~~.	+	===Bovine trypsin at 0.85 resolution===

-	~~Description~~: ~~Bovine trypsin at 0~~.~~85 resolution~~	+
		+	==About this Structure==
		+	[[4i8k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8K OCA].
		+	[[Category: Bos taurus]]
		+	[[Category: Trypsin]]
		+	[[Category: Brzuszkiewicz, A.]]
		+	[[Category: Dauter, M.]]
		+	[[Category: Dauter, Z.]]
		+	[[Category: Liebschner, D.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Serine protease]]

OCA: Protected "4i8k" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2012 20:50:40 GMT

Protected "4i8k" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:50, 12 December 2012

OCA: New page: '''Unreleased structure''' The entry 4i8k is ON HOLD Authors: Dauter, Z., Liebschner, D., Dauter, M., Brzuszkiewicz, A. Description: Bovine trypsin at 0.85 resolution

OCA — Wed, 12 Dec 2012 20:50:39 GMT

New page: '''Unreleased structure''' The entry 4i8k is ON HOLD Authors: Dauter, Z., Liebschner, D., Dauter, M., Brzuszkiewicz, A. Description: Bovine trypsin at 0.85 resolution

New page

'''Unreleased structure'''

The entry 4i8k is ON HOLD

Authors: Dauter, Z., Liebschner, D., Dauter, M., Brzuszkiewicz, A.

Description: Bovine trypsin at 0.85 resolution