4jy3 - Revision history

OCA at 08:54, 20 March 2024

2024-03-20T08:54:18Z

←Older revision		Revision as of 08:54, 20 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jy3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ali 3ali] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4h28 4h28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JY3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jy3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ali 3ali] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4h28 4h28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JY3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PR:5-HYDROXY-4-(HYDROXYMETHYL)-6-METHYLPYRIDINE-3-CARBOXYLIC+ACID'>5PR</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.77Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PR:5-HYDROXY-4-(HYDROXYMETHYL)-6-METHYLPYRIDINE-3-CARBOXYLIC+ACID'>5PR</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4jy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jy3 OCA], [https://pdbe.org/4jy3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jy3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jy3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jy3 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=4jy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jy3 OCA], [https://pdbe.org/4jy3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jy3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jy3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jy3 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:30, 30 November 2022

2022-11-30T11:30:34Z

←Older revision		Revision as of 11:30, 30 November 2022
Line 1:		Line 1:

	==Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form==		==Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form==
-	<StructureSection load='4jy3' size='340' side='right' caption='[[4jy3]], [[Resolution\|resolution]] 1.77Å' scene=''>	+	<StructureSection load='4jy3' size='340' side='right'caption='[[4jy3]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jy3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mesorhizobium_loti~~ Mesorhizobium ~~loti~~]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ali 3ali] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4h28 4h28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JY3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JY3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jy3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ali 3ali] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4h28 4h28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JY3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5PR:5-HYDROXY-4-(HYDROXYMETHYL)-6-METHYLPYRIDINE-3-CARBOXYLIC+ACID'>5PR</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PR:5-HYDROXY-4-(HYDROXYMETHYL)-6-METHYLPYRIDINE-3-CARBOXYLIC+ACID'>5PR</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jy2\|4jy2]]</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=4jy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jy3 OCA], [https://pdbe.org/4jy3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jy3 RCSB], [https://www.ebi.ac.uk/pdbsum/4jy3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jy3 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mlr6788 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium loti])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridinecarboxylate_dioxygenase 3-hydroxy-2-methylpyridinecarboxylate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.4 1.14.12.4] </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=4jy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jy3 OCA], [~~http~~://pdbe.org/4jy3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jy3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jy3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jy3 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q988D3_RHILO Q988D3_RHILO]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~3-hydroxy-2-methylpyridinecarboxylate dioxygenase~~]]	+	[[Category: Large Structures]]
-	[[Category: Mesorhizobium ~~loti~~]]	+	[[Category: Mesorhizobium japonicum MAFF 303099]]
-	[[Category: Hayashi, H]]	+	[[Category: Hayashi H]]
-	[[Category: Kamitori, S]]	+	[[Category: Kamitori S]]
-	[[Category: Kobayashi, J]]	+	[[Category: Kobayashi J]]
-	[[Category: Mikami, B]]	+	[[Category: Mikami B]]
-	[[Category: Mizutani, K]]	+	[[Category: Mizutani K]]
-	[[Category: Takahashi, N]]	+	[[Category: Takahashi N]]
-	[[Category: Yagi, T]]	+	[[Category: Yagi T]]
-	[[Category: Yoshida, H]]	+	[[Category: Yoshida H]]
-	~~[[Category: 3-hydroxypyridine-5-carboxylic acid]]~~	+
-	~~[[Category: Fad binding motif]]~~	+
-	~~[[Category: Flavoenzyme]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 12:41, 4 August 2016

2016-08-04T12:41:11Z

←Older revision		Revision as of 12:41, 4 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4jy3\| PDB=4jy3 \| SCENE= }}
-	===Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form===

-	==~~About this Structure~~==	+	==Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form==
-	[[4jy3]] is a 2 chain structure. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4h28 4h28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JY3 OCA].	+	<StructureSection load='4jy3' size='340' side='right' caption='[[4jy3]], [[Resolution\|resolution]] 1.77Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4jy3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ali 3ali] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4h28 4h28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JY3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JY3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5PR:5-HYDROXY-4-(HYDROXYMETHYL)-6-METHYLPYRIDINE-3-CARBOXYLIC+ACID'>5PR</scene>, <scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jy2\|4jy2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mlr6788 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266835 Mesorhizobium loti])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridinecarboxylate_dioxygenase 3-hydroxy-2-methylpyridinecarboxylate dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.4 1.14.12.4] </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=4jy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jy3 OCA], [http://pdbe.org/4jy3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jy3 RCSB], [http://www.ebi.ac.uk/pdbsum/4jy3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jy3 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: 3-hydroxy-2-methylpyridinecarboxylate dioxygenase]]		[[Category: 3-hydroxy-2-methylpyridinecarboxylate dioxygenase]]
-	[[Category: Hayashi, H.]]	+	[[Category: Mesorhizobium loti]]
-	[[Category: Kamitori, S.]]	+	[[Category: Hayashi, H]]
-	[[Category: Kobayashi, J.]]	+	[[Category: Kamitori, S]]
-	[[Category: Mikami, B.]]	+	[[Category: Kobayashi, J]]
-	[[Category: Mizutani, K.]]	+	[[Category: Mikami, B]]
-	[[Category: Takahashi, N.]]	+	[[Category: Mizutani, K]]
-	[[Category: Yagi, T.]]	+	[[Category: Takahashi, N]]
-	[[Category: Yoshida, H.]]	+	[[Category: Yagi, T]]
		+	[[Category: Yoshida, H]]
	[[Category: 3-hydroxypyridine-5-carboxylic acid]]		[[Category: 3-hydroxypyridine-5-carboxylic acid]]
	[[Category: Fad binding motif]]		[[Category: Fad binding motif]]
	[[Category: Flavoenzyme]]		[[Category: Flavoenzyme]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 08:57, 2 April 2014

2014-04-02T08:57:28Z

←Older revision		Revision as of 08:57, 2 April 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4jy3\| PDB=4jy3 \| SCENE= }}
		+	===Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form===

-	~~The entry~~ 4jy3 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==About this Structure==
-		+	[[4jy3]] is a 2 chain structure. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4h28 4h28]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JY3 OCA].
-	~~Authors~~: ~~Kobayashi, J., Yoshida~~, H., Kamitori, S., ~~Hayashi, H~~., Mizutani, K., Takahashi, N.~~, Mikami, B.,~~ Yagi, T.	+	[[Category: 3-hydroxy-2-methylpyridinecarboxylate dioxygenase]]
-		+	[[Category: Hayashi, H.]]
-	~~Description~~: ~~Crystal structure of 2-methyl-~~3-hydroxypyridine-5-carboxylic acid ~~oxygenase, 5-pyridoxic acid bound form~~	+	[[Category: Kamitori, S.]]
		+	[[Category: Kobayashi, J.]]
		+	[[Category: Mikami, B.]]
		+	[[Category: Mizutani, K.]]
		+	[[Category: Takahashi, N.]]
		+	[[Category: Yagi, T.]]
		+	[[Category: Yoshida, H.]]
		+	[[Category: 3-hydroxypyridine-5-carboxylic acid]]
		+	[[Category: Fad binding motif]]
		+	[[Category: Flavoenzyme]]
		+	[[Category: Oxidoreductase]]

OCA at 10:56, 24 April 2013

2013-04-24T10:56:51Z

←Older revision		Revision as of 10:56, 24 April 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4jy3 is ON HOLD	+	The entry 4jy3 is ON HOLD until Paper Publication

	Authors: Kobayashi, J., Yoshida, H., Kamitori, S., Hayashi, H., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T.		Authors: Kobayashi, J., Yoshida, H., Kamitori, S., Hayashi, H., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T.

	Description: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form		Description: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form

OCA: Protected "4jy3" [edit=sysop:move=sysop]

2013-04-04T01:09:28Z

Protected "4jy3" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:09, 4 April 2013

OCA: New page: '''Unreleased structure''' The entry 4jy3 is ON HOLD Authors: Kobayashi, J., Yoshida, H., Kamitori, S., Hayashi, H., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T. Description: Crys...

2013-04-04T01:09:27Z

New page: '''Unreleased structure''' The entry 4jy3 is ON HOLD Authors: Kobayashi, J., Yoshida, H., Kamitori, S., Hayashi, H., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T. Description: Crys...

New page

'''Unreleased structure'''

The entry 4jy3 is ON HOLD

Authors: Kobayashi, J., Yoshida, H., Kamitori, S., Hayashi, H., Mizutani, K., Takahashi, N., Mikami, B., Yagi, T.

Description: Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form