6b68 - Revision history

OCA at 14:20, 13 March 2024

2024-03-13T14:20:33Z

←Older revision		Revision as of 14:20, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6b68' size='340' side='right'caption='[[6b68]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='6b68' size='340' side='right'caption='[[6b68]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b68]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B68 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6B68 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b68]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B68 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6B68 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9F2:Ceftriaxone'>9F2</scene>, <scene name='pdbligand=FZS:(2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>FZS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.15Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6b5x\|6b5x]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9F2:Ceftriaxone'>9F2</scene>, <scene name='pdbligand=FZS:(2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>FZS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaC, blaA, Rv2068c, MTCY49.07c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=6b68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b68 OCA], [https://pdbe.org/6b68 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6b68 RCSB], [https://www.ebi.ac.uk/pdbsum/6b68 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6b68 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/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=6b68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b68 OCA], [~~http~~://pdbe.org/6b68 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6b68 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6b68 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6b68 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/BLAC_MYCTU BLAC_MYCTU]
-	~~BACKGROUND~~: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. RESULTS: Here, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis beta-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s. CONCLUSIONS: MISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.	+
-		+
-	Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.,Olmos JL Jr, Pandey S, Martin-Garcia JM, Calvey G, Katz A, Knoska J, Kupitz C, Hunter MS, Liang M, Oberthuer D, Yefanov O, Wiedorn M, Heyman M, Holl M, Pande K, Barty A, Miller MD, Stern S, Roy-Chowdhury S, Coe J, Nagaratnam N, Zook J, Verburgt J, Norwood T, Poudyal I, Xu D, Koglin J, Seaberg MH, Zhao Y, Bajt S, Grant T, Mariani V, Nelson G, Subramanian G, Bae E, Fromme R, Fung R, Schwander P, Frank M, White TA, Weierstall U, Zatsepin N, Spence J, Fromme P, Chapman HN, Pollack L, Tremblay L, Ourmazd A, Phillips GN Jr, Schmidt M BMC Biol. 2018 May 31;16(1):59. doi: 10.1186/~~s12915-018-0524-5. PMID:29848358<ref>PMID:29848358<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6b68" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]		*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Beta-lactamase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Pandey, S]]	+	[[Category: Pandey S]]
-	[[Category: Schmidt, M]]	+	[[Category: Schmidt M]]
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Hydrolase-antibiotic complex~~]]	+

OCA at 12:46, 25 December 2019

2019-12-25T12:46:28Z

←Older revision		Revision as of 12:46, 25 December 2019
Line 1:		Line 1:

	==Beta-Lactamase, 100ms timepoint, mixed, shards crystal form==		==Beta-Lactamase, 100ms timepoint, mixed, shards crystal form==
-	<StructureSection load='6b68' size='340' side='right' caption='[[6b68]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='6b68' size='340' side='right'caption='[[6b68]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6b68]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B68 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B68 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6b68]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B68 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B68 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9F2:Ceftriaxone'>9F2</scene>, <scene name='pdbligand=FZS:(2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>FZS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9F2:Ceftriaxone'>9F2</scene>, <scene name='pdbligand=FZS:(2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>FZS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6b5x\|6b5x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6b5x\|6b5x]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">blaC, blaA, Rv2068c, MTCY49.07c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=6b68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b68 OCA], [http://pdbe.org/6b68 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b68 RCSB], [http://www.ebi.ac.uk/pdbsum/6b68 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b68 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=6b68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b68 OCA], [http://pdbe.org/6b68 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b68 RCSB], [http://www.ebi.ac.uk/pdbsum/6b68 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b68 ProSAT]</span></td></tr>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6b68" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6b68" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
		+	[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Pandey, S]]		[[Category: Pandey, S]]
	[[Category: Schmidt, M]]		[[Category: Schmidt, M]]
	[[Category: Antibiotic]]		[[Category: Antibiotic]]
	[[Category: Hydrolase-antibiotic complex]]		[[Category: Hydrolase-antibiotic complex]]

OCA at 05:33, 27 June 2018

2018-06-27T05:33:53Z

←Older revision		Revision as of 05:33, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6b68 is ~~ON HOLD until Paper~~ Publication	+	==Beta-Lactamase, 100ms timepoint, mixed, shards crystal form==
		+	<StructureSection load='6b68' size='340' side='right' caption='[[6b68]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6b68]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6B68 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6B68 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9F2:Ceftriaxone'>9F2</scene>, <scene name='pdbligand=FZS:(2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic+acid'>FZS</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6b5x\|6b5x]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=6b68 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6b68 OCA], [http://pdbe.org/6b68 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6b68 RCSB], [http://www.ebi.ac.uk/pdbsum/6b68 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6b68 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. RESULTS: Here, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis beta-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s. CONCLUSIONS: MISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.

-	~~Authors:~~ Pandey, S., ~~Schmidt~~, M.	+	Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.,Olmos JL Jr, Pandey S, Martin-Garcia JM, Calvey G, Katz A, Knoska J, Kupitz C, Hunter MS, Liang M, Oberthuer D, Yefanov O, Wiedorn M, Heyman M, Holl M, Pande K, Barty A, Miller MD, Stern S, Roy-Chowdhury S, Coe J, Nagaratnam N, Zook J, Verburgt J, Norwood T, Poudyal I, Xu D, Koglin J, Seaberg MH, Zhao Y, Bajt S, Grant T, Mariani V, Nelson G, Subramanian G, Bae E, Fromme R, Fung R, Schwander P, Frank M, White TA, Weierstall U, Zatsepin N, Spence J, Fromme P, Chapman HN, Pollack L, Tremblay L, Ourmazd A, Phillips GN Jr, Schmidt M BMC Biol. 2018 May 31;16(1):59. doi: 10.1186/s12915-018-0524-5. PMID:29848358<ref>PMID:29848358</ref>

-	~~Description: Beta-Lactamase~~, ~~100ms timepoint, mixed, shards crystal form~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Schmidt, M~~]]	+	<div class="pdbe-citations 6b68" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Beta-lactamase]]
	[[Category: Pandey, S]]		[[Category: Pandey, S]]
		+	[[Category: Schmidt, M]]
		+	[[Category: Antibiotic]]
		+	[[Category: Hydrolase-antibiotic complex]]

OCA at 03:57, 16 May 2018

2018-05-16T03:57:08Z

←Older revision		Revision as of 03:57, 16 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6b68 is ON HOLD	+	The entry 6b68 is ON HOLD until Paper Publication

	Authors: Pandey, S., Schmidt, M.		Authors: Pandey, S., Schmidt, M.

OCA at 04:47, 9 May 2018

2018-05-09T04:47:51Z

←Older revision		Revision as of 04:47, 9 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6b68 is ON HOLD ~~until Paper Publication~~	+	The entry 6b68 is ON HOLD

	Authors: Pandey, S., Schmidt, M.		Authors: Pandey, S., Schmidt, M.

OCA at 05:45, 25 October 2017

2017-10-25T05:45:54Z

←Older revision		Revision as of 05:45, 25 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6b68 is ON HOLD	+	The entry 6b68 is ON HOLD until Paper Publication

	Authors: Pandey, S., Schmidt, M.		Authors: Pandey, S., Schmidt, M.

OCA: Protected "6b68" [edit=sysop:move=sysop]

2017-10-11T05:31:24Z

Protected "6b68" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:31, 11 October 2017

OCA: New page: '''Unreleased structure''' The entry 6b68 is ON HOLD Authors: Pandey, S., Schmidt, M. Description: Beta-Lactamase, 100ms timepoint, mixed, shards crystal form [[Category: Unreleased St...

2017-10-11T05:31:23Z

New page: '''Unreleased structure''' The entry 6b68 is ON HOLD Authors: Pandey, S., Schmidt, M. Description: Beta-Lactamase, 100ms timepoint, mixed, shards crystal form [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6b68 is ON HOLD

Authors: Pandey, S., Schmidt, M.

Description: Beta-Lactamase, 100ms timepoint, mixed, shards crystal form
[[Category: Unreleased Structures]]
[[Category: Schmidt, M]]
[[Category: Pandey, S]]