3ifm - Revision history

OCA at 10:05, 21 February 2024

OCA — Wed, 21 Feb 2024 10:05:11 GMT

←Older revision		Revision as of 10:05, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3ifm' size='340' side='right'caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3ifm' size='340' side='right'caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pseudomonas_phage_pf1~~ Pseudomonas ~~phage pf1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_virus_Pf1 Pseudomonas virus Pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IFM 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;'~~>~~[[1ifd\|1ifd]]~~, [[~~1ifm~~\|~~1ifm~~]]~~, [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</div>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Fiber diffraction, [[Resolution\|Resolution]] 3.3Å</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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [https://pdbe.org/3ifm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [https://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm 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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [https://pdbe.org/3ifm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [https://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CAPSD_BPPF1 CAPSD_BPPF1]] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).	+	[https://www.uniprot.org/uniprot/CAPSD_BPPF1 CAPSD_BPPF1] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The filamentous bacteriophage Pf1 is structurally similar to the well known Ff (fd, fl, M13) strains, but it gives much better X-ray diffraction patterns, enabling a more detailed analysis of the molecular structure. The 46-residue protein subunit can be closely approximated by a single gently curved stretch of alpha-helix. The axes of the subunits are at a small angle to the virion axis, and several thousand subunits form an overlapping inter-digitated helical array surrounding a DNA core. We have derived a detailed model of the virion based on X-ray data and stereochemical constraints. We have considered potential sources of error in the diffraction data, and used the improved data to study regions where the protein subunit of Pf1 may deviate from a continuous alpha-helix. We use simulated annealing to escape from local minima, and various kinds of electron-density maps to guide the model building. Refinement of the model shows that the first few residues at the N terminus are non-helical, and there is a slight discontinuity in the alpha-helix near the middle of the sequence. The model is consistent both with general structural principles derived from high-resolution analysis of other proteins, and with specific chemical and spectroscopic data about Pf1. We apply the same refinement techniques to an alternative model with a non-helical surface loop between residues 13 and 19. Comparative analysis of models with and without a loop shows that the loop model is not supported by 3.3 A resolution X-ray diffraction data.	+
-		+
-	Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 A resolution X-ray fibre diffraction data.,Gonzalez A, Nave C, Marvin DA Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):792-804. PMID:15299811<ref>PMID:15299811</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3ifm" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pseudomonas ~~phage pf1~~]]	+	[[Category: Pseudomonas virus Pf1]]
-	[[Category: Marvin~~, D A]]~~	+	[[Category: Marvin DA]]
-	~~[[Category: Helical virus]]~~	+
-	~~[[Category: Virus]]~~	+
-	~~[[Category: Virus coat protein~~]]	+

OCA at 07:46, 29 June 2022

OCA — Wed, 29 Jun 2022 07:46:06 GMT

←Older revision		Revision as of 07:46, 29 June 2022
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	<StructureSection load='3ifm' size='340' side='right'caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3ifm' size='340' side='right'caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3IFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IFM FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</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;'>[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</div></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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [~~http~~://pdbe.org/3ifm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm 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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [https://pdbe.org/3ifm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [https://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CAPSD_BPPF1 CAPSD_BPPF1]] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).	+	[[https://www.uniprot.org/uniprot/CAPSD_BPPF1 CAPSD_BPPF1]] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 11:55, 23 September 2020

OCA — Wed, 23 Sep 2020 11:55:39 GMT

←Older revision		Revision as of 11:55, 23 September 2020
Line 1:		Line 1:

	==PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA==		==PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA==
-	<StructureSection load='3ifm' size='340' side='right' caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='3ifm' size='340' side='right'caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3IFM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://pdbe.org/3ifm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm 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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://pdbe.org/3ifm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pseudomonas phage pf1]]		[[Category: Pseudomonas phage pf1]]
	[[Category: Marvin, D A]]		[[Category: Marvin, D A]]

OCA at 09:33, 19 December 2018

OCA — Wed, 19 Dec 2018 09:33:21 GMT

←Older revision		Revision as of 09:33, 19 December 2018
Line 3:		Line 3:
	<StructureSection load='3ifm' size='340' side='right' caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3ifm' size='340' side='right' caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bppf1 Bppf1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IFM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://pdbe.org/3ifm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm 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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://pdbe.org/3ifm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm ProSAT]</span></td></tr>
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bppf1~~]]	+	[[Category: Pseudomonas phage pf1]]
	[[Category: Marvin, D A]]		[[Category: Marvin, D A]]
	[[Category: Helical virus]]		[[Category: Helical virus]]
	[[Category: Virus]]		[[Category: Virus]]
	[[Category: Virus coat protein]]		[[Category: Virus coat protein]]

OCA at 08:18, 5 August 2016

OCA — Fri, 05 Aug 2016 08:18:42 GMT

←Older revision		Revision as of 08:18, 5 August 2016
Line 1:		Line 1:
		+
	==PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA==		==PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA==
	<StructureSection load='3ifm' size='340' side='right' caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='3ifm' size='340' side='right' caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_phage_pf1 Pseudomonas phage pf1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IFM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bppf1 Bppf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IFM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm 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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://pdbe.org/3ifm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ifm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~COATB_BPPF1 COATB_BPPF1~~]] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).	+	[[http://www.uniprot.org/uniprot/CAPSD_BPPF1 CAPSD_BPPF1]] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 17:
	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 3ifm" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseudomonas phage pf1~~]]	+	[[Category: Bppf1]]
	[[Category: Marvin, D A]]		[[Category: Marvin, D A]]
	[[Category: Helical virus]]		[[Category: Helical virus]]
	[[Category: Virus]]		[[Category: Virus]]
	[[Category: Virus coat protein]]		[[Category: Virus coat protein]]

OCA at 17:12, 25 December 2014

OCA — Thu, 25 Dec 2014 17:12:43 GMT

←Older revision		Revision as of 17:12, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IFM FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IFM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm 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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COATB_BPPF1 COATB_BPPF1]] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Pseudomonas phage pf1]]		[[Category: Pseudomonas phage pf1]]
-	[[Category: Marvin, D A.]]	+	[[Category: Marvin, D A]]
	[[Category: Helical virus]]		[[Category: Helical virus]]
	[[Category: Virus]]		[[Category: Virus]]
	[[Category: Virus coat protein]]		[[Category: Virus coat protein]]

OCA at 06:54, 9 June 2014

OCA — Mon, 09 Jun 2014 06:54:23 GMT

←Older revision		Revision as of 06:54, 9 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3ifm.~~png~~\|~~left~~\|~~200px~~]]	+	==PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA==
		+	<StructureSection load='3ifm' size='340' side='right' caption='[[3ifm]], [[Resolution\|resolution]] 3.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IFM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ifd\|1ifd]], [[1ifm\|1ifm]], [[2ifm\|2ifm]], [[4ifm\|4ifm]], [[1ifi\|1ifi]], [[1ifj\|1ifj]], [[1ifk\|1ifk]], [[1ifl\|1ifl]], [[1ifn\|1ifn]], [[2ifo\|2ifo]]</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=3ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ifm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ifm RCSB], [http://www.ebi.ac.uk/pdbsum/3ifm PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The filamentous bacteriophage Pf1 is structurally similar to the well known Ff (fd, fl, M13) strains, but it gives much better X-ray diffraction patterns, enabling a more detailed analysis of the molecular structure. The 46-residue protein subunit can be closely approximated by a single gently curved stretch of alpha-helix. The axes of the subunits are at a small angle to the virion axis, and several thousand subunits form an overlapping inter-digitated helical array surrounding a DNA core. We have derived a detailed model of the virion based on X-ray data and stereochemical constraints. We have considered potential sources of error in the diffraction data, and used the improved data to study regions where the protein subunit of Pf1 may deviate from a continuous alpha-helix. We use simulated annealing to escape from local minima, and various kinds of electron-density maps to guide the model building. Refinement of the model shows that the first few residues at the N terminus are non-helical, and there is a slight discontinuity in the alpha-helix near the middle of the sequence. The model is consistent both with general structural principles derived from high-resolution analysis of other proteins, and with specific chemical and spectroscopic data about Pf1. We apply the same refinement techniques to an alternative model with a non-helical surface loop between residues 13 and 19. Comparative analysis of models with and without a loop shows that the loop model is not supported by 3.3 A resolution X-ray diffraction data.

-	~~{{STRUCTURE_3ifm\| PDB=3ifm \| SCENE= }}~~	+	Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 A resolution X-ray fibre diffraction data.,Gonzalez A, Nave C, Marvin DA Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):792-804. PMID:15299811<ref>PMID:15299811</ref>

-	~~===PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15299811}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3ifm]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015299811<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pseudomonas phage pf1]]		[[Category: Pseudomonas phage pf1]]
	[[Category: Marvin, D A.]]		[[Category: Marvin, D A.]]

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

OCA — Tue, 14 Aug 2012 15:15:09 GMT

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

←Older revision

Revision as of 15:15, 14 August 2012

OCA at 15:15, 14 August 2012

OCA — Tue, 14 Aug 2012 15:15:07 GMT

←Older revision		Revision as of 15:15, 14 August 2012
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-	{{Seed}}
	[[Image:3ifm.png\|left\|200px]]		[[Image:3ifm.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ifm", 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_3ifm\| PDB=3ifm \| SCENE= }}		{{STRUCTURE_3ifm\| PDB=3ifm \| SCENE= }}

	===PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA===		===PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15299811}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15299811 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15299811}}		{{ABSTRACT_PUBMED_15299811}}

	==About this Structure==		==About this Structure==
-	~~3IFM is a~~ [[~~Single protein~~]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA].	+	[[3ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_phage_pf1 Pseudomonas phage pf1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IFM OCA].

	==Reference==		==Reference==
-	Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 A resolution X-ray fibre diffraction data., Gonzalez A, Nave C, Marvin DA, Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):792-804. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~15299811 15299811]~~	+	<ref group="xtra">PMID:015299811</ref><references group="xtra"/>
	[[Category: Pseudomonas phage pf1]]		[[Category: Pseudomonas phage pf1]]
-	[[Category: Single protein]]
	[[Category: Marvin, D A.]]		[[Category: Marvin, D A.]]
	[[Category: Helical virus]]		[[Category: Helical virus]]
		+	[[Category: Virus]]
	[[Category: Virus coat protein]]		[[Category: Virus coat protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 12:50:59 2008''

OCA at 09:51, 3 July 2008

OCA — Thu, 03 Jul 2008 09:51:00 GMT

←Older revision		Revision as of 09:51, 3 July 2008
Line 1:		Line 1:
-	[[Image:3ifm.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3ifm.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_3ifm\| PDB=3ifm \| SCENE= }}		{{STRUCTURE_3ifm\| PDB=3ifm \| SCENE= }}

-	~~'''~~PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA~~'''~~	+	===PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA===


-	~~==Overview==~~	+	<!--
-	The ~~filamentous bacteriophage Pf1 is structurally similar to the well known Ff (fd~~, ~~fl, M13) strains, but it gives much better X-ray diffraction patterns~~, ~~enabling a more detailed analysis of~~ the ~~molecular structure. The 46-residue protein subunit can be closely approximated by a single gently curved stretch of alpha-helix. The axes of the subunits are at a small angle~~ to the ~~virion axis, and several thousand subunits form an overlapping inter-digitated helical array surrounding a DNA core. We have derived a detailed model of the virion based~~ on ~~X-ray data and stereochemical constraints~~. ~~We have considered potential sources of error in the diffraction data~~, ~~and used the improved data to study regions~~ where the protein subunit of Pf1 may deviate from a continuous alpha-helix. We use simulated annealing to escape from local minima, and various kinds of electron-density maps to guide the model building. Refinement of the model shows that the first few residues at the N terminus are non-helical, and there is ~~a slight discontinuity in~~ the ~~alpha-helix near the middle of the sequence~~. ~~The model is consistent both with general structural principles derived from high~~-~~resolution analysis of other proteins, and with specific chemical and spectroscopic data about Pf1. We apply the same refinement techniques to an alternative model with a non~~-~~helical surface loop between residues 13 and 19. Comparative analysis of models with and without a loop shows that the loop model is not supported by 3.3 A resolution X-ray diffraction data.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_15299811}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15299811 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15299811}}

	==About this Structure==		==About this Structure==
Line 25:		Line 29:
	[[Category: Helical virus]]		[[Category: Helical virus]]
	[[Category: Virus coat protein]]		[[Category: Virus coat protein]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:04:38 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 12:50:59 2008''