6h6s - Revision history

OCA at 06:30, 21 August 2019

2019-08-21T06:30:53Z

←Older revision		Revision as of 06:30, 21 August 2019
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	==Sad phasing on nickel-substituted human carbonic anhydrase II==		==Sad phasing on nickel-substituted human carbonic anhydrase II==
-	<StructureSection load='6h6s' size='340' side='right' caption='[[6h6s]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='6h6s' size='340' side='right'caption='[[6h6s]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6h6s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H6S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H6S FirstGlance]. <br>		<table><tr><td colspan='2'>[[6h6s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H6S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H6S FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6h6s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6h6s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carbonic anhydrase 3D structures\|Carbonic anhydrase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Calderone, V]]		[[Category: Calderone, V]]
	[[Category: Cerofolini, L]]		[[Category: Cerofolini, L]]

OCA at 08:25, 6 March 2019

2019-03-06T08:25:22Z

←Older revision		Revision as of 08:25, 6 March 2019
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	==Sad phasing on nickel-substituted human carbonic anhydrase II==		==Sad phasing on nickel-substituted human carbonic anhydrase II==
-	<StructureSection load='6h6s' size='340' side='right' caption='[[6h6s]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='6h6s' size='340' side='right' caption='[[6h6s]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6h6s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H6S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H6S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6h6s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H6S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H6S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </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=6h6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h6s OCA], [http://pdbe.org/6h6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h6s RCSB], [http://www.ebi.ac.uk/pdbsum/6h6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h6s 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=6h6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h6s OCA], [http://pdbe.org/6h6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h6s RCSB], [http://www.ebi.ac.uk/pdbsum/6h6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h6s ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
		+	[[Category: Human]]
	[[Category: Calderone, V]]		[[Category: Calderone, V]]
	[[Category: Cerofolini, L]]		[[Category: Cerofolini, L]]

OCA at 06:36, 9 January 2019

2019-01-09T06:36:34Z

←Older revision		Revision as of 06:36, 9 January 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6h6s is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Sad phasing on nickel-substituted human carbonic anhydrase II==
		+	<StructureSection load='6h6s' size='340' side='right' caption='[[6h6s]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6h6s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H6S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6H6S FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </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=6h6s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h6s OCA], [http://pdbe.org/6h6s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h6s RCSB], [http://www.ebi.ac.uk/pdbsum/6h6s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h6s ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[http://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Partial symmetry, i.e., the presence of more than one molecule in the asymmetric unit of a crystal, is a relatively rare phenomenon in small-molecule crystallography, but is quite common in protein crystallography, where it is typically known as non-crystallographic symmetry (NCS). Several papers in literature propose molecular determinants such as crystal contacts, thermal factors, or TLS parameters as an explanation for the phenomenon of intrinsic asymmetry among molecules that are in principle equivalent. Nevertheless, are all of the above determinants the cause or are they rather the effect? In the general frame of the NCS often observed in crystals of biomolecules, this paper deals with nickel(II)-substituted human carbonic anhydrase(II) (hCAII) and its SAD structure determination at the nickel edge. The structure revealed two non-equivalent molecules in the asymmetric unit, the presence of a secondary nickel-binding site at the N-terminus of both molecules (which had never been found before in the nickel-substituted enzyme) and two different coordination geometries of the active site nickel (hexa-coordinated in one molecule and mainly penta-coordinated in the other). The above-mentioned standard molecular crystallographic determinants of this asymmetry are analyzed and presented in detail for this particular case. From these considerations, we speculate on the existence of a fundamental, although yet unknown, common cause for the partial symmetry that is so often encountered in X-ray structures of biomolecules.

-	~~Authors~~: ~~Calderone~~, V., ~~Fragai~~, M., ~~Silva~~, ~~J.P., Luchinat, C.~~, Ravera, E., ~~Geraldes~~, C.F.G.C., ~~Macedo, A~~.~~L., Cerofolini, L., Giuntini, S~~.	+	Non-crystallographic symmetry in proteins: Jahn-Teller-like and Butterfly-like effects?,Silva JM, Giuntini S, Cerofolini L, Geraldes CFGC, Macedo AL, Ravera E, Fragai M, Luchinat C, Calderone V J Biol Inorg Chem. 2018 Nov 23. pii: 10.1007/s00775-018-1630-0. doi:, 10.1007/s00775-018-1630-0. PMID:30470900<ref>PMID:30470900</ref>

-	~~Description: Sad phasing on nickel~~-~~substituted human carbonic anhydrase II~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6h6s" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carbonate dehydratase]]
	[[Category: Calderone, V]]		[[Category: Calderone, V]]
-	[[Category: ~~Giuntini~~, S]]	+	[[Category: Cerofolini, L]]
	[[Category: Fragai, M]]		[[Category: Fragai, M]]
-	[[Category: Geraldes, C.F.G.C]]	+	[[Category: Geraldes, C F.G C]]
-	[[Category: ~~Ravera~~, ~~E]]~~	+	[[Category: Giuntini, S]]
-	~~[[Category: Macedo, A.L~~]]	+
	[[Category: Luchinat, C]]		[[Category: Luchinat, C]]
-	[[Category: ~~Cerofolini~~, L]]	+	[[Category: Macedo, A L]]
-	[[Category: Silva, J.P]]	+	[[Category: Ravera, E]]
		+	[[Category: Silva, J P]]
		+	[[Category: Caii]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nickel]]
		+	[[Category: Sad]]

OCA: Protected "6h6s" [edit=sysop:move=sysop]

2018-08-09T20:04:59Z

Protected "6h6s" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:04, 9 August 2018

OCA: New page: '''Unreleased structure''' The entry 6h6s is ON HOLD until Paper Publication Authors: Calderone, V., Fragai, M., Silva, J.P., Luchinat, C., Ravera, E., Geraldes, C.F.G.C., Macedo, A.L.,...

2018-08-09T20:04:58Z

New page: '''Unreleased structure''' The entry 6h6s is ON HOLD until Paper Publication Authors: Calderone, V., Fragai, M., Silva, J.P., Luchinat, C., Ravera, E., Geraldes, C.F.G.C., Macedo, A.L.,...

New page

'''Unreleased structure'''

The entry 6h6s is ON HOLD until Paper Publication

Authors: Calderone, V., Fragai, M., Silva, J.P., Luchinat, C., Ravera, E., Geraldes, C.F.G.C., Macedo, A.L., Cerofolini, L., Giuntini, S.

Description: Sad phasing on nickel-substituted human carbonic anhydrase II
[[Category: Unreleased Structures]]
[[Category: Calderone, V]]
[[Category: Giuntini, S]]
[[Category: Fragai, M]]
[[Category: Geraldes, C.F.G.C]]
[[Category: Ravera, E]]
[[Category: Macedo, A.L]]
[[Category: Luchinat, C]]
[[Category: Cerofolini, L]]
[[Category: Silva, J.P]]