3rj8 - Revision history

OCA at 14:57, 20 September 2023

OCA — Wed, 20 Sep 2023 14:57:36 GMT

←Older revision		Revision as of 14:57, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [https://pdbe.org/3rj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [https://www.ebi.ac.uk/pdbsum/3rj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rj8 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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [https://pdbe.org/3rj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [https://www.ebi.ac.uk/pdbsum/3rj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rj8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:49, 22 February 2023

OCA — Wed, 22 Feb 2023 12:49:56 GMT

←Older revision		Revision as of 12:49, 22 February 2023
Line 3:		Line 3:
	<StructureSection load='3rj8' size='340' side='right'caption='[[3rj8]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3rj8' size='340' side='right'caption='[[3rj8]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Fusarium_nivale Fusarium~~ nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rja\|3rja]]</div></td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Fusarium nivale])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [https://pdbe.org/3rj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [https://www.ebi.ac.uk/pdbsum/3rj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rj8 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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [https://pdbe.org/3rj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [https://www.ebi.ac.uk/pdbsum/3rj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rj8 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/MNCO_MICNN MNCO_MICNN] Catalyzes the selective oxidation of C1 hydroxyl moieties on mono-, oligo- and polysaccharides with concomitant reduction of molecular oxygen to hydrogen peroxide. This results in the formation of the corresponding lactones, which typically undergo spontaneous hydrolysis. Carbohydrate oxidase is able to oxidize a variety of substrates including D-glucose, D-galactose, D-xylose, D-maltose, D-cellobiose, and lactose. In addition, among various oligosaccharides, the enzyme preferred tetrameric dextrins, indicating a favorable interaction of four linked glucose units with the substrate binding pocket.<ref>PMID:11179980</ref> [PROSITE-ProRule:PRU00718]<ref>PMID:11179980</ref>
-	~~Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized~~. ~~The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions~~. ~~Several different crystal forms were obtained using~~ the ~~hanging-drop vapour-diffusion method, two~~ of ~~which were used for diffraction measurements. Hexagon~~-~~shaped crystals (form I) diffracted to 2.66 A resolution~~, ~~with unit~~-~~cell parameters a = b = 55.7, c = 610.4 A~~ and ~~apparent space group P6(2)22. Analysis~~ of ~~the data quality showed almost perfect twinning of the crystals~~. ~~Attempts to solve~~ the ~~structure by molecular replacement did not give satisfactory results. Recently, clusters~~ of ~~rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to~~ the ~~monoclinic system C2~~, ~~with unit-cell parameters a = 132~~.~~9, b = 56.6, c = 86.5 A, beta = 95.7 degrees . Data sets were collected~~ to a ~~resolution~~ of ~~2.4 A. The structure was solved by the molecular~~-~~replacement method. Model refinement is currently in progress.~~	+
-		+
-	~~Crystallization of carbohydrate oxidase from Microdochium nivale.~~,~~Duskova J~~, ~~Dohnalek J~~, ~~Skalova T~~, ~~Ostergaard LH~~, ~~Fuglsang CC~~, ~~Kolenko P~~, ~~Stepankova A~~, ~~Hasek J Acta Crystallogr Sect F Struct Biol Cryst Commun~~. ~~2009 Jun 1;65(Pt 6):638-40., Epub 2009 May 23. PMID:19478452~~<ref>PMID:~~19478452~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3rj8" style="background-color~~:~~#fffaf0;">~~</~~div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Fusarium nivale]]
-	[[Category: Glucose oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dohnalek, J]]	+	[[Category: Microdochium nivale]]
-	[[Category: Duskova, J]]	+	[[Category: Dohnalek J]]
-	[[Category: Fuglsang~~, C C~~]]	+	[[Category: Duskova J]]
-	[[Category: Hasek, J]]	+	[[Category: Fuglsang CC]]
-	[[Category: Kolenko, P]]	+	[[Category: Hasek J]]
-	[[Category: Koval, T]]	+	[[Category: Kolenko P]]
-	[[Category: Ostergaard~~, L H~~]]	+	[[Category: Koval T]]
-	[[Category: Skalova, T]]	+	[[Category: Ostergaard LH]]
-	[[Category: Stepankova, A]]	+	[[Category: Skalova T]]
-	~~[[Category: Berberine and berberine-like domain]]~~	+	[[Category: Stepankova A]]
-	~~[[Category: Carbohydrate/sugar binding]]~~	+
-	~~[[Category: Extracellular]]~~	+
-	~~[[Category: Fad binding]]~~	+
-	~~[[Category: Fad binding domain]]~~	+
-	~~[[Category: Glucooligosaccharide oxidase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:12, 22 June 2022

OCA — Wed, 22 Jun 2022 10:12:55 GMT

←Older revision		Revision as of 10:12, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of carbohydrate oxidase from Microdochium nivale==		==Crystal structure of carbohydrate oxidase from Microdochium nivale==
-	<StructureSection load='3rj8' size='340' side='right' caption='[[3rj8]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3rj8' size='340' side='right'caption='[[3rj8]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Fusarium_nivale Fusarium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_nivale Fusarium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K~~</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG~~</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rja\|3rja]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rja\|3rja]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Fusarium nivale])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Fusarium nivale])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [~~http~~://pdbe.org/3rj8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rj8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rj8 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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [https://pdbe.org/3rj8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [https://www.ebi.ac.uk/pdbsum/3rj8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rj8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	[[Category: Fusarium nivale]]		[[Category: Fusarium nivale]]
	[[Category: Glucose oxidase]]		[[Category: Glucose oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Dohnalek, J]]		[[Category: Dohnalek, J]]
	[[Category: Duskova, J]]		[[Category: Duskova, J]]

OCA at 11:51, 6 November 2017

OCA — Mon, 06 Nov 2017 11:51:59 GMT

←Older revision		Revision as of 11:51, 6 November 2017
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fusarium_nivale Fusarium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fusarium_nivale Fusarium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN~~</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rja\|3rja]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rja\|3rja]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Fusarium nivale])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Fusarium nivale])</td></tr>

OCA at 12:36, 11 August 2016

OCA — Thu, 11 Aug 2016 12:36:26 GMT

←Older revision		Revision as of 12:36, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of carbohydrate oxidase from Microdochium nivale==		==Crystal structure of carbohydrate oxidase from Microdochium nivale==
	<StructureSection load='3rj8' size='340' side='right' caption='[[3rj8]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3rj8' size='340' side='right' caption='[[3rj8]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Microdochium_nivale Microdochium~~ nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fusarium_nivale Fusarium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rja\|3rja]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rja\|3rja]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 ~~Microdochium~~ nivale])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Fusarium nivale])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [http://www.ebi.ac.uk/pdbsum/3rj8 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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [http://pdbe.org/3rj8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [http://www.ebi.ac.uk/pdbsum/3rj8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rj8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 3rj8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Fusarium nivale]]
	[[Category: Glucose oxidase]]		[[Category: Glucose oxidase]]
-	[[Category: Microdochium nivale]]
	[[Category: Dohnalek, J]]		[[Category: Dohnalek, J]]
	[[Category: Duskova, J]]		[[Category: Duskova, J]]

OCA at 09:23, 4 January 2015

OCA — Sun, 04 Jan 2015 09:23:29 GMT

←Older revision		Revision as of 09:23, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rja\|3rja]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rja\|3rja]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Microdochium nivale])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Microdochium nivale])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </span></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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [http://www.ebi.ac.uk/pdbsum/3rj8 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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [http://www.ebi.ac.uk/pdbsum/3rj8 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 15:
	Crystallization of carbohydrate oxidase from Microdochium nivale.,Duskova J, Dohnalek J, Skalova T, Ostergaard LH, Fuglsang CC, Kolenko P, Stepankova A, Hasek J Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt 6):638-40., Epub 2009 May 23. PMID:19478452<ref>PMID:19478452</ref>		Crystallization of carbohydrate oxidase from Microdochium nivale.,Duskova J, Dohnalek J, Skalova T, Ostergaard LH, Fuglsang CC, Kolenko P, Stepankova A, Hasek J Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt 6):638-40., Epub 2009 May 23. PMID:19478452<ref>PMID:19478452</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 23:		Line 23:
	[[Category: Glucose oxidase]]		[[Category: Glucose oxidase]]
	[[Category: Microdochium nivale]]		[[Category: Microdochium nivale]]
-	[[Category: Dohnalek, J.]]	+	[[Category: Dohnalek, J]]
-	[[Category: Duskova, J.]]	+	[[Category: Duskova, J]]
-	[[Category: Fuglsang, C C.]]	+	[[Category: Fuglsang, C C]]
-	[[Category: Hasek, J.]]	+	[[Category: Hasek, J]]
-	[[Category: Kolenko, P.]]	+	[[Category: Kolenko, P]]
-	[[Category: Koval, T.]]	+	[[Category: Koval, T]]
-	[[Category: Ostergaard, L H.]]	+	[[Category: Ostergaard, L H]]
-	[[Category: Skalova, T.]]	+	[[Category: Skalova, T]]
-	[[Category: Stepankova, A.]]	+	[[Category: Stepankova, A]]
	[[Category: Berberine and berberine-like domain]]		[[Category: Berberine and berberine-like domain]]
	[[Category: Carbohydrate/sugar binding]]		[[Category: Carbohydrate/sugar binding]]

OCA at 04:47, 5 June 2014

OCA — Thu, 05 Jun 2014 04:47:28 GMT

←Older revision		Revision as of 04:47, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3rj8.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of carbohydrate oxidase from Microdochium nivale==
		+	<StructureSection load='3rj8' size='340' side='right' caption='[[3rj8]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RJ8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rja\|3rja]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MnCO ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5520 Microdochium nivale])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_oxidase Glucose oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.4 1.1.3.4] </span></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=3rj8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rj8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rj8 RCSB], [http://www.ebi.ac.uk/pdbsum/3rj8 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Microdochium nivale carbohydrate oxidase was produced by heterologous recombinant expression in Aspergillus oryzae, purified and crystallized. The enzyme crystallizes with varying crystal morphologies depending on the crystallization conditions. Several different crystal forms were obtained using the hanging-drop vapour-diffusion method, two of which were used for diffraction measurements. Hexagon-shaped crystals (form I) diffracted to 2.66 A resolution, with unit-cell parameters a = b = 55.7, c = 610.4 A and apparent space group P6(2)22. Analysis of the data quality showed almost perfect twinning of the crystals. Attempts to solve the structure by molecular replacement did not give satisfactory results. Recently, clusters of rod-shaped crystals (form II) were grown in a solution containing PEG MME 550. These crystals belonged to the monoclinic system C2, with unit-cell parameters a = 132.9, b = 56.6, c = 86.5 A, beta = 95.7 degrees . Data sets were collected to a resolution of 2.4 A. The structure was solved by the molecular-replacement method. Model refinement is currently in progress.

-	~~<!--~~	+	Crystallization of carbohydrate oxidase from Microdochium nivale.,Duskova J, Dohnalek J, Skalova T, Ostergaard LH, Fuglsang CC, Kolenko P, Stepankova A, Hasek J Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Jun 1;65(Pt 6):638-40., Epub 2009 May 23. PMID:19478452<ref>PMID:19478452</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3rj8"~~, ~~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_3rj8\| PDB=3rj8 \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~carbohydrate oxidase from Microdochium nivale===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_19478452}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 19478452 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_19478452}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3rj8]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019478452<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Glucose oxidase]]		[[Category: Glucose oxidase]]
	[[Category: Microdochium nivale]]		[[Category: Microdochium nivale]]

OCA at 07:55, 18 April 2012

OCA — Wed, 18 Apr 2012 07:55:40 GMT

←Older revision		Revision as of 07:55, 18 April 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3rj8.jpg\|left\|200px]]

-	The ~~entry 3rj8~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rj8", 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_3rj8\| PDB=3rj8 \| SCENE= }}

-	~~Authors: Duskova, J., Skalova, T., Stepankova, A., Koval, T., Hasek, J., Ostergaard, L.H., Fuglsang, C.C., Kolenko, P., Dohnalek, J.~~	+	===Crystal structure of carbohydrate oxidase from Microdochium nivale===

-	~~Description~~: ~~Crystal~~ structure ~~of carbohydrate oxidase~~ from Microdochium nivale	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19478452}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19478452 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19478452}}
		+
		+	==About this Structure==
		+	[[3rj8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Microdochium_nivale Microdochium nivale]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RJ8 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:019478452</ref><references group="xtra"/>
		+	[[Category: Glucose oxidase]]
		+	[[Category: Microdochium nivale]]
		+	[[Category: Dohnalek, J.]]
		+	[[Category: Duskova, J.]]
		+	[[Category: Fuglsang, C C.]]
		+	[[Category: Hasek, J.]]
		+	[[Category: Kolenko, P.]]
		+	[[Category: Koval, T.]]
		+	[[Category: Ostergaard, L H.]]
		+	[[Category: Skalova, T.]]
		+	[[Category: Stepankova, A.]]
		+	[[Category: Berberine and berberine-like domain]]
		+	[[Category: Carbohydrate/sugar binding]]
		+	[[Category: Extracellular]]
		+	[[Category: Fad binding]]
		+	[[Category: Fad binding domain]]
		+	[[Category: Glucooligosaccharide oxidase]]
		+	[[Category: Oxidoreductase]]

OCA at 05:21, 1 June 2011

OCA — Wed, 01 Jun 2011 05:21:27 GMT

←Older revision		Revision as of 05:21, 1 June 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rj8 is ON HOLD	+	The entry 3rj8 is ON HOLD until Paper Publication

	Authors: Duskova, J., Skalova, T., Stepankova, A., Koval, T., Hasek, J., Ostergaard, L.H., Fuglsang, C.C., Kolenko, P., Dohnalek, J.		Authors: Duskova, J., Skalova, T., Stepankova, A., Koval, T., Hasek, J., Ostergaard, L.H., Fuglsang, C.C., Kolenko, P., Dohnalek, J.

	Description: Crystal structure of carbohydrate oxidase from Microdochium nivale		Description: Crystal structure of carbohydrate oxidase from Microdochium nivale

OCA: Protected "3rj8" [edit=sysop:move=sysop]

OCA — Wed, 27 Apr 2011 06:56:39 GMT

Protected "3rj8" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:56, 27 April 2011