5gua - Revision history

OCA at 11:42, 2 August 2023

2023-08-02T11:42:41Z

←Older revision		Revision as of 11:42, 2 August 2023
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	==Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) A138Y mutant==		==Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) A138Y mutant==
-	<StructureSection load='5gua' size='340' side='right' caption='[[5gua]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5gua' size='340' side='right'caption='[[5gua]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gua]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gua]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GUA FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5gu8\|5gu8]], [[5gu9\|5gu9]]</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]] 1.5Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">PH1284 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=70601 Pyrococcus horikoshii])~~</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=5gua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gua OCA], [https://pdbe.org/5gua PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gua RCSB], [https://www.ebi.ac.uk/pdbsum/5gua PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gua ProSAT]</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=5gua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gua OCA], [~~http~~://pdbe.org/5gua PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gua RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gua PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gua ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O59021_PYRHO O59021_PYRHO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Large Structures]]
-	[[Category: Fukasawa, Y]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	[[Category: Kunishima, N]]	+	[[Category: Fukasawa Y]]
-	[[Category: Matsuura, Y]]	+	[[Category: Kunishima N]]
-	[[Category: Naitow, H]]	+	[[Category: Matsuura Y]]
-	[[Category: Nakai, K]]	+	[[Category: Naitow H]]
-	[[Category: Tomii, K]]	+	[[Category: Nakai K]]
-	[[Category: Yamada, K]]	+	[[Category: Tomii K]]
-	~~[[Category: Crystal contact engineering]]~~	+	[[Category: Yamada K]]
-	~~[[Category: Crystal packing]]~~	+
-	~~[[Category: Surface engineering]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:33, 6 December 2017

2017-12-06T07:33:58Z

←Older revision		Revision as of 07:33, 6 December 2017
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	<StructureSection load='5gua' size='340' side='right' caption='[[5gua]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5gua' size='340' side='right' caption='[[5gua]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gua]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gua]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUA FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gu8\|5gu8]], [[5gu9\|5gu9]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gu8\|5gu8]], [[5gu9\|5gu9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH1284 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=5gua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gua OCA], [http://pdbe.org/5gua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gua RCSB], [http://www.ebi.ac.uk/pdbsum/5gua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gua ProSAT]</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=5gua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gua OCA], [http://pdbe.org/5gua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gua RCSB], [http://www.ebi.ac.uk/pdbsum/5gua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gua ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	An alternative rational approach to improve protein crystals by using single-site mutation of surface residues is proposed based on the results of a statistical analysis using a compiled data set of 918 independent crystal structures, thereby reflecting not only the entropic effect but also other effects upon protein crystallization. This analysis reveals a clear difference in the crystal-packing propensity of amino acids depending on the secondary-structural class. To verify this result, a systematic crystallization experiment was performed with the biotin carboxyl carrier protein from Pyrococcus horikoshii OT3 (PhBCCP). Six single-site mutations were examined: Ala138 on the surface of a beta-sheet was mutated to Ile, Tyr, Arg, Gln, Val and Lys. In agreement with prediction, it was observed that the two mutants (A138I and A138Y) harbouring the residues with the highest crystal-packing propensities for beta-sheet at position 138 provided better crystallization scores relative to those of other constructs, including the wild type, and that the crystal-packing propensity for beta-sheet provided the best correlation with the ratio of obtaining crystals. Two new crystal forms of these mutants were obtained that diffracted to high resolution, generating novel packing interfaces with the mutated residues (Ile/Tyr). The mutations introduced did not affect the overall structures, indicating that a beta-sheet can accommodate a successful mutation if it is carefully selected so as to avoid intramolecular steric hindrance. A significant negative correlation between the ratio of obtaining amorphous precipitate and the crystal-packing propensity was also found.
		+
		+	Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids.,Yamada KD, Kunishima N, Matsuura Y, Nakai K, Naitow H, Fukasawa Y, Tomii K Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):757-766. doi:, 10.1107/S2059798317010932. Epub 2017 Aug 15. PMID:28876239<ref>PMID:28876239</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5gua" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: Fukasawa, Y]]		[[Category: Fukasawa, Y]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]

OCA at 14:33, 5 September 2017

2017-09-05T14:33:46Z

←Older revision		Revision as of 14:33, 5 September 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5gua ~~is ON HOLD~~	+	==Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) A138Y mutant==
-		+	<StructureSection load='5gua' size='340' side='right' caption='[[5gua]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~Authors~~: ~~Yamada, K~~., ~~Kunishima, N~~., ~~Matsuura, Y~~., ~~Nakai, K~~., ~~Naitow, H~~., ~~Fukasawa, Y~~., ~~Tomii, K~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5gua]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GUA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GUA FirstGlance]. <br>
-	~~Description: Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) A138Y mutant~~	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gu8\|5gu8]], [[5gu9\|5gu9]]</td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5gua FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gua OCA], [http://pdbe.org/5gua PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gua RCSB], [http://www.ebi.ac.uk/pdbsum/5gua PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gua ProSAT]</span></td></tr>
-	[[Category: ~~Yamada~~, K]]	+	</table>
-	[[Category: ~~Tomii~~, K]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Fukasawa, Y]]
		+	[[Category: Kunishima, N]]
		+	[[Category: Matsuura, Y]]
	[[Category: Naitow, H]]		[[Category: Naitow, H]]
-	[[Category: Fukasawa, Y]]
	[[Category: Nakai, K]]		[[Category: Nakai, K]]
-	[[Category: ~~Matsuura~~, Y]]	+	[[Category: Tomii, K]]
-	[[Category: ~~Kunishima~~, N]]	+	[[Category: Yamada, K]]
		+	[[Category: Crystal contact engineering]]
		+	[[Category: Crystal packing]]
		+	[[Category: Surface engineering]]
		+	[[Category: Transferase]]

OCA at 09:07, 9 March 2017

2017-03-09T09:07:46Z

←Older revision		Revision as of 09:07, 9 March 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yamada, K]]		[[Category: Yamada, K]]
-	[[Category: Matsuura, Y]]
-	[[Category: Kunishima, N]]
	[[Category: Tomii, K]]		[[Category: Tomii, K]]
	[[Category: Naitow, H]]		[[Category: Naitow, H]]
	[[Category: Fukasawa, Y]]		[[Category: Fukasawa, Y]]
	[[Category: Nakai, K]]		[[Category: Nakai, K]]
		+	[[Category: Matsuura, Y]]
		+	[[Category: Kunishima, N]]

OCA at 10:29, 14 September 2016

2016-09-14T10:29:17Z

←Older revision		Revision as of 10:29, 14 September 2016
Line 5:		Line 5:
	Authors: Yamada, K., Kunishima, N., Matsuura, Y., Nakai, K., Naitow, H., Fukasawa, Y., Tomii, K.		Authors: Yamada, K., Kunishima, N., Matsuura, Y., Nakai, K., Naitow, H., Fukasawa, Y., Tomii, K.

-	Description: ~~STRUCTURE OF BIOTIN CARBOXYL CARRIER PROTEIN FROM PYROCOCCUS HORIKOSHI~~ OT3 (~~DELTA~~ N79) A138Y ~~MUTANT~~	+	Description: Structure of biotin carboxyl carrier protein from pyrococcus horikoshi OT3 (delta N79) A138Y mutant
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yamada, K]]		[[Category: Yamada, K]]

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

2016-09-09T12:05:17Z

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

←Older revision

Revision as of 12:05, 9 September 2016

OCA: New page: '''Unreleased structure''' The entry 5gua is ON HOLD Authors: Yamada, K., Kunishima, N., Matsuura, Y., Nakai, K., Naitow, H., Fukasawa, Y., Tomii, K. Description: STRUCTURE OF BIOTIN C...

2016-09-09T12:05:16Z

New page: '''Unreleased structure''' The entry 5gua is ON HOLD Authors: Yamada, K., Kunishima, N., Matsuura, Y., Nakai, K., Naitow, H., Fukasawa, Y., Tomii, K. Description: STRUCTURE OF BIOTIN C...

New page

'''Unreleased structure'''

The entry 5gua is ON HOLD

Authors: Yamada, K., Kunishima, N., Matsuura, Y., Nakai, K., Naitow, H., Fukasawa, Y., Tomii, K.

Description: STRUCTURE OF BIOTIN CARBOXYL CARRIER PROTEIN FROM PYROCOCCUS HORIKOSHI OT3 (DELTA N79) A138Y MUTANT
[[Category: Unreleased Structures]]
[[Category: Yamada, K]]
[[Category: Matsuura, Y]]
[[Category: Kunishima, N]]
[[Category: Tomii, K]]
[[Category: Naitow, H]]
[[Category: Fukasawa, Y]]
[[Category: Nakai, K]]