3blm - Revision history

OCA at 09:29, 21 February 2024

2024-02-21T09:29:35Z

← Older revision		Revision as of 09:29, 21 February 2024
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	<StructureSection load='3blm' size='340' side='right'caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3blm' size='340' side='right'caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3BLM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLM FirstGlance]. <br>
	</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>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [~~http~~://pdbe.org/3blm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3blm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3blm 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=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [https://pdbe.org/3blm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [https://www.ebi.ac.uk/pdbsum/3blm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3blm ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/BLAC_STAAU BLAC_STAAU]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3blm ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3blm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The crystal structure of a class A beta-lactamase from Staphylococcus aureus PC1 has been refined at 2.0 A resolution. The resulting crystallographic R-factor (R = sigma h parallel Fo[-]Fc parallel/sigma h[Fo], where [Fo] and [Fc] are the observed and calculated structure factor amplitudes, respectively), is 0.163 for the 17,547 reflections with I greater than or equal to 2 sigma (I) within the 8.0 A to 2.0 A resolution range. The molecule consists of two closely associated domains. One domain is formed by a five-stranded antiparallel beta-sheet with three helices packing against a face of the sheet. The second domain is formed mostly by helices that pack against the second face of the sheet. The active site is located in the interface between the two domains, and many of the residues that form it are conserved in all known sequences of class A beta-lactamases. Similar to the serine proteases, an oxyanion hole is implicated in catalysis. It is formed by two main-chain nitrogen atoms, that of the catalytic seryl residue, Ser70, and that of Gln237 on an edge beta-strand of the major beta-sheet. Ser70 is interacting with another conserved seryl residue, Ser130, located between the two ammonium groups of the functionally important lysine residues, Lys73 and Lys234. Such intricate interactions point to a possible catalytic role for this second seryl residue. Another key catalytic residue is Glu166. There are several unusual structural features associated with the active site. (1) A cis peptide bond has been identified between the catalytic Glu166 and Ile167. (2) Ala69 and Leu220 have strained phi, psi dihedral angles making close contacts that restrict the conformation of the active site beta-strand involved in the formation of the oxyanion hole. (3) A buried aspartate residue, the conserved Asp233, is located next to the active site Lys234. It is interacting with another buried aspartyl residue, Asp246. An internal solvent molecule is also involved, but the rest of its interactions with the protein indicate it is not a cation. (4) Another conserved aspartyl residue that is desolvated is Asp131, adjacent to Ser130. Its charge is stabilized by interactions with four main-chain nitrogen atoms. (5) An internal cavity underneath the active site depression is filled with six solvent molecules. This, and an adjacent cavity occupied by three solvent molecules partially separate the omega-loop associated with the active site from the rest of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)

	~~Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution.,Herzberg O J Mol Biol. 1991 Feb 20;217(4):701-19. PMID:2005620<ref>PMID:2005620</ref>~~

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3blm" 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: ~~Herzberg, O~~]]		[[Category: Staphylococcus aureus]]
	[[Category: ~~Moult, J~~]]		[[Category: Herzberg O]]
	[[Category: ~~Hydrolase~~]]		[[Category: Moult J]]

OCA at 06:18, 5 August 2020

2020-08-05T06:18:37Z

← Older revision		Revision as of 06:18, 5 August 2020
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	==REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0==		==REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0==
	<StructureSection load='3blm' size='340' side='right' caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3blm' size='340' side='right'caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BLM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3BLM FirstGlance]. <br>
	</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>		</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=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://pdbe.org/3blm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3blm ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://pdbe.org/3blm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3blm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Beta-lactamase\|Beta-lactamase]]		*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
			[[Category: Large Structures]]
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]
	[[Category: Moult, J]]		[[Category: Moult, J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 07:58, 31 October 2018

2018-10-31T07:58:13Z

← Older revision		Revision as of 07:58, 31 October 2018
Line 1:		Line 1:

	==REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0==		==REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0==
	<StructureSection load='3blm' size='340' side='right' caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3blm' size='340' side='right' caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLM FirstGlance]. <br>
	</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>		</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=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://pdbe.org/3blm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm 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=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://pdbe.org/3blm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3blm ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blm_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blm_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 02:45, 8 February 2016

2016-02-08T02:45:24Z

← Older revision		Revision as of 02:45, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3blm' size='340' side='right' caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3blm' size='340' side='right' caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus Staphylococcus~~ aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLM FirstGlance]. <br>
	</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>		</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=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm 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=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://pdbe.org/3blm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3blm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3blm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	~~[[Category: Staphylococcus aureus]]~~
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]
	[[Category: Moult, J]]		[[Category: Moult, J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:13, 20 January 2015

2015-01-20T08:13:24Z

← Older revision		Revision as of 08:13, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLM FirstGlance]. <br>
	</td></tr><tr><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>		</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm 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=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Herzberg, O.]]		[[Category: Herzberg, O]]
	[[Category: Moult, J.]]		[[Category: Moult, J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 06:50, 29 September 2014

2014-09-29T06:50:05Z

← Older revision		Revision as of 06:50, 29 September 2014
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	[[Image:~~3blm~~.~~png~~\|~~left~~\|~~200px~~]]		==REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0==
			<StructureSection load='3blm' size='340' side='right' caption='[[3blm]], [[Resolution\|resolution]] 2.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BLM FirstGlance]. <br>
			</td></tr><tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3blm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3blm RCSB], [http://www.ebi.ac.uk/pdbsum/3blm PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blm_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The crystal structure of a class A beta-lactamase from Staphylococcus aureus PC1 has been refined at 2.0 A resolution. The resulting crystallographic R-factor (R = sigma h parallel Fo[-]Fc parallel/sigma h[Fo], where [Fo] and [Fc] are the observed and calculated structure factor amplitudes, respectively), is 0.163 for the 17,547 reflections with I greater than or equal to 2 sigma (I) within the 8.0 A to 2.0 A resolution range. The molecule consists of two closely associated domains. One domain is formed by a five-stranded antiparallel beta-sheet with three helices packing against a face of the sheet. The second domain is formed mostly by helices that pack against the second face of the sheet. The active site is located in the interface between the two domains, and many of the residues that form it are conserved in all known sequences of class A beta-lactamases. Similar to the serine proteases, an oxyanion hole is implicated in catalysis. It is formed by two main-chain nitrogen atoms, that of the catalytic seryl residue, Ser70, and that of Gln237 on an edge beta-strand of the major beta-sheet. Ser70 is interacting with another conserved seryl residue, Ser130, located between the two ammonium groups of the functionally important lysine residues, Lys73 and Lys234. Such intricate interactions point to a possible catalytic role for this second seryl residue. Another key catalytic residue is Glu166. There are several unusual structural features associated with the active site. (1) A cis peptide bond has been identified between the catalytic Glu166 and Ile167. (2) Ala69 and Leu220 have strained phi, psi dihedral angles making close contacts that restrict the conformation of the active site beta-strand involved in the formation of the oxyanion hole. (3) A buried aspartate residue, the conserved Asp233, is located next to the active site Lys234. It is interacting with another buried aspartyl residue, Asp246. An internal solvent molecule is also involved, but the rest of its interactions with the protein indicate it is not a cation. (4) Another conserved aspartyl residue that is desolvated is Asp131, adjacent to Ser130. Its charge is stabilized by interactions with four main-chain nitrogen atoms. (5) An internal cavity underneath the active site depression is filled with six solvent molecules. This, and an adjacent cavity occupied by three solvent molecules partially separate the omega-loop associated with the active site from the rest of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)

	~~{{STRUCTURE_3blm\| PDB=3blm \| SCENE= }}~~		Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution.,Herzberg O J Mol Biol. 1991 Feb 20;217(4):701-19. PMID:2005620<ref>PMID:2005620</ref>

	~~===REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_2005620}}~~

	~~==About this Structure==~~
	~~[[3blm]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.~~il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA].~~

	==See Also==		==See Also==
	*[[Beta-lactamase\|Beta-lactamase]]		*[[Beta-lactamase\|Beta-lactamase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:002005620<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]

OCA at 08:38, 20 October 2012

2012-10-20T08:38:18Z

← Older revision		Revision as of 08:38, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[3blm]] is a 1 chain structure ~~of [[Beta-lactamase]]~~ with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA].		[[3blm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA].

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
	<ref group="xtra">PMID:002005620~~</ref><ref group="xtra">PMID:011514231~~</ref><references group="xtra"/>		<ref group="xtra">PMID:002005620</ref><references group="xtra"/>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]

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

2012-07-25T20:15:39Z

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

← Older revision	Revision as of 20:15, 25 July 2012
(No difference)

OCA at 20:15, 25 July 2012

2012-07-25T20:15:37Z

← Older revision		Revision as of 20:15, 25 July 2012
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	~~{{Seed}}~~
	[[Image:3blm.png\|left\|200px]]		[[Image:3blm.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3blm", 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_3blm\| PDB=3blm \| SCENE= }}		{{STRUCTURE_3blm\| PDB=3blm \| SCENE= }}

	===REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0===		===REFINED CRYSTAL STRUCTURE OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1 AT 2.0===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_2005620}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 2005620 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_2005620}}		{{ABSTRACT_PUBMED_2005620}}

	==About this Structure==		==About this Structure==
	~~3BLM~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA].		[[3blm]] is a 1 chain structure of [[Beta-lactamase]] with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA].

			==See Also==
			*[[Beta-lactamase\|Beta-lactamase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~2005620~~</ref><references group="xtra"/>		<ref group="xtra">PMID:002005620</ref><ref group="xtra">PMID:011514231</ref><references group="xtra"/>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
Line 29:		Line 20:
	[[Category: Moult, J.]]		[[Category: Moult, J.]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:14:23 2009''~~

OCA at 16:14, 16 February 2009

2009-02-16T16:14:25Z

← Older revision		Revision as of 16:14, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	3BLM is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA].		3BLM is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1blm 1blm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLM OCA].

	==Reference==		==Reference==
	~~Refined crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.0 A resolution., Herzberg O, J Mol Biol. 1991 Feb 20;217(4):701-19.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/2005620 2005620]~~		<ref group="xtra">PMID:2005620</ref><references group="xtra"/>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	~~[[Category: Single protein]]~~
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Herzberg, O.]]		[[Category: Herzberg, O.]]
Line 31:		Line 30:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 21~~:53:~~52 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:14:23 2009''