3fbd - Revision history

OCA at 15:28, 1 November 2023

2023-11-01T15:28:36Z

← Older revision		Revision as of 15:28, 1 November 2023
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	<StructureSection load='3fbd' size='340' side='right'caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3fbd' size='340' side='right'caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FBD FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</div></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]] 2.9Å</td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">cea, colE7 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [https://pdbe.org/3fbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [https://www.ebi.ac.uk/pdbsum/3fbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbd 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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [https://pdbe.org/3fbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [https://www.ebi.ac.uk/pdbsum/3fbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/CEA7_ECOLX CEA7_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.		[https://www.uniprot.org/uniprot/CEA7_ECOLX CEA7_ECOLX] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.
	== 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=3fbd 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=3fbd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			It is of crucial importance to elucidate the underlying principles that govern the binding affinity and selectivity between proteins and DNA. Here we use the nuclease domain of Colicin E7 (nColE7) as a model system to generate redesigned nucleases with improved DNA-binding affinities. ColE7 is a bacterial toxin, bearing a nonspecific endonuclease domain with a preference for hydrolyzing DNA phosphodiester bonds at the 3'O-side after thymine and adenine; i.e., it prefers Thy and Ade at the -1 site. Using systematic computational screening, six nColE7 mutants were predicted to bind DNA with high affinity. Five of the redesigned single-point mutants were constructed and purified, and four mutants had a 3- to 5-fold higher DNA binding affinity than wild-type nColE7 as measured by fluorescence kinetic assays. Moreover, three of the designed mutants, D493N, D493Q, and D493R, digested DNA with an increased preference for guanine at +3 sites compared to the wild-type enzyme, as shown by DNA footprint assays. X-ray structure determination of the ColE7 mutant D493Q-DNA complex in conjunction with structural and free energy decomposition analyses provides a physical basis for the improved protein-DNA interactions: Replacing D493 at the protein-DNA interface with an amino acid residue that can maintain the native hydrogen bonds removes the unfavorable electrostatic repulsion between the negatively charged carboxylate and DNA phosphate groups. These results show that computational screening combined with biochemical, structural, and free energy analyses provide a useful means for generating redesigned nucleases with a higher DNA-binding affinity and altered sequence preferences in DNA cleavage.

			Redesign of high-affinity nonspecific nucleases with altered sequence preference.,Wang YT, Wright JD, Doudeva LG, Jhang HC, Lim C, Yuan HS J Am Chem Soc. 2009 Dec 2;131(47):17345-53. doi: 10.1021/ja907160r. PMID:19929021<ref>PMID:19929021</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 3fbd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Colicin 3D structures\|Colicin 3D structures]]		*[[Colicin 3D structures\|Colicin 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Doudeva~~, L G~~]]		[[Category: Doudeva LG]]
	[[Category: Wang~~, Y T~~]]		[[Category: Wang YT]]
	[[Category: Yuan~~, H S]]~~		[[Category: Yuan HS]]
	~~[[Category: Antibiotic]]~~
	~~[[Category: Antimicrobial]]~~
	~~[[Category: Bacteriocin]]~~
	~~[[Category: Computational redesign]]~~
	~~[[Category: Dna hydrolysis]]~~
	~~[[Category: Dnase]]~~
	~~[[Category: Endonuclease]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Hydrolase-dna complex]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Nuclease]]~~
	~~[[Category: Plasmid]]~~
	~~[[Category: Protein engineering]]~~
	~~[[Category: Protein-nucleic acid interaction]]~~
	~~[[Category: Zinc~~]]

OCA at 07:38, 10 November 2021

2021-11-10T07:38:34Z

← Older revision		Revision as of 07:38, 10 November 2021
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	==Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA==		==Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA==
	<StructureSection load='3fbd' size='340' side='right' caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3fbd' size='340' side='right'caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FBD FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [~~http~~://pdbe.org/3fbd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fbd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbd 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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [https://pdbe.org/3fbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [https://www.ebi.ac.uk/pdbsum/3fbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/CEA7_ECOLX CEA7_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.		[[https://www.uniprot.org/uniprot/CEA7_ECOLX CEA7_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Colicin\|Colicin]]		*[[Colicin 3D structures\|Colicin 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
			[[Category: Large Structures]]
	[[Category: Doudeva, L G]]		[[Category: Doudeva, L G]]
	[[Category: Wang, Y T]]		[[Category: Wang, Y T]]

OCA at 07:36, 5 December 2018

2018-12-05T07:36:31Z

← Older revision		Revision as of 07:36, 5 December 2018
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	==Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA==		==Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA==
	<StructureSection load='3fbd' size='340' side='right' caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3fbd' size='340' side='right' caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [http://pdbe.org/3fbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [http://www.ebi.ac.uk/pdbsum/3fbd 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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [http://pdbe.org/3fbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [http://www.ebi.ac.uk/pdbsum/3fbd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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/fb/3fbd_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fb/3fbd_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>
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	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Nuclease]]		[[Category: Nuclease]]
			[[Category: Plasmid]]
	[[Category: Protein engineering]]		[[Category: Protein engineering]]
	[[Category: Protein-nucleic acid interaction]]		[[Category: Protein-nucleic acid interaction]]
			[[Category: Zinc]]

OCA at 07:45, 9 February 2016

2016-02-09T07:45:32Z

← Older revision		Revision as of 07:45, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3fbd' size='340' side='right' caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3fbd' size='340' side='right' caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBD FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [http://www.ebi.ac.uk/pdbsum/3fbd 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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [http://pdbe.org/3fbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [http://www.ebi.ac.uk/pdbsum/3fbd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<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=3fbd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>

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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Doudeva, L G]]		[[Category: Doudeva, L G]]
	[[Category: Wang, Y T]]		[[Category: Wang, Y T]]

OCA at 05:28, 25 December 2014

2014-12-25T05:28:38Z

← Older revision		Revision as of 05:28, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBD FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [http://www.ebi.ac.uk/pdbsum/3fbd 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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [http://www.ebi.ac.uk/pdbsum/3fbd PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/CEA7_ECOLX CEA7_ECOLX]] This plasmid-coded bactericidal protein is an endonuclease active on both single- and double-stranded DNA but with undefined specificity. Colicins are polypeptide toxins produced by and active against E.coli and closely related bacteria.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Doudeva, L G.]]		[[Category: Doudeva, L G]]
	[[Category: Wang, Y T.]]		[[Category: Wang, Y T]]
	[[Category: Yuan, H S.]]		[[Category: Yuan, H S]]
	[[Category: Antibiotic]]		[[Category: Antibiotic]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]
	[[Category: Bacteriocin]]		[[Category: Bacteriocin]]
	[[Category: Computational redesign]]		[[Category: Computational redesign]]
	[[Category: Dna hydrolysis.]]		[[Category: Dna hydrolysis]]
	[[Category: Dnase]]		[[Category: Dnase]]
	[[Category: Endonuclease]]		[[Category: Endonuclease]]

OCA at 13:03, 29 September 2014

2014-09-29T13:03:45Z

← Older revision		Revision as of 13:03, 29 September 2014
Line 1:		Line 1:
	~~[[Image:3fbd.png\|left\|200px]]~~		==Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA==
			<StructureSection load='3fbd' size='340' side='right' caption='[[3fbd]], [[Resolution\|resolution]] 2.90Å' scene=''>
	~~{{STRUCTURE_3fbd\| PDB=3fbd \| SCENE= }}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[3fbd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBD FirstGlance]. <br>
	===Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA===		</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ivh\|2ivh]], [[1zns\|1zns]], [[1pt3\|1pt3]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cea, colE7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3fbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fbd RCSB], [http://www.ebi.ac.uk/pdbsum/3fbd PDBsum]</span></td></tr>
	==~~About this Structure~~==		<table>
	[[3fbd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA].		== 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/fb/3fbd_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>

	==See Also==		==See Also==
	*[[Colicin\|Colicin]]		*[[Colicin\|Colicin]]
			__TOC__
			</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Doudeva, L G.]]		[[Category: Doudeva, L G.]]

OCA at 13:09, 20 October 2012

2012-10-20T13:09:59Z

← Older revision		Revision as of 13:09, 20 October 2012
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
	[[3fbd]] is a 6 chain structure ~~of [[Colicin]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA].		[[3fbd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA].

	==See Also==		==See Also==

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

2012-07-26T11:05:52Z

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

← Older revision	Revision as of 11:05, 26 July 2012
(No difference)

OCA at 11:05, 26 July 2012

2012-07-26T11:05:49Z

← Older revision		Revision as of 11:05, 26 July 2012
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	~~{{Seed}}~~		[[Image:3fbd.png\|left\|200px]]
	[[Image:3fbd.~~jpg~~\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3fbd", 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_3fbd\| PDB=3fbd \| SCENE= }}		{{STRUCTURE_3fbd\| PDB=3fbd \| SCENE= }}

Line 14:		Line 7:

	==About this Structure==		==About this Structure==
	~~3FBD~~ is a 6 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA].		[[3fbd]] is a 6 chain structure of [[Colicin]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBD OCA].

			==See Also==
			*[[Colicin\|Colicin]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Doudeva, L G.]]		[[Category: Doudeva, L G.]]
Line 27:		Line 23:
	[[Category: Endonuclease]]		[[Category: Endonuclease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hydrolase/dna complex]]		[[Category: Hydrolase-dna complex]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Nuclease]]		[[Category: Nuclease]]
	~~[[Category: Plasmid]]~~
	[[Category: Protein engineering]]		[[Category: Protein engineering]]
	[[Category: Protein-nucleic acid interaction]]		[[Category: Protein-nucleic acid interaction]]
	~~[[Category: Zinc]]~~

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 4 10:55:17 2009''~~

OCA at 08:55, 4 November 2009

2009-11-04T08:55:19Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+{{Seed}}
-The entry 3fbd is ON HOLD  until Paper Publication
+<!--
-Authors: Wang, Y.T., Doudeva, L.G., Yuan, H.S.
+===Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA===
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep  3 15:17:00 2009''
+==About this Structure==