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| - | [[Image:2ifm.gif|left|200px]] | |
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| - | <!--
| + | ==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, containing "STRUCTURE_2ifm", creates the "Structure Box" on the page.
| + | <StructureSection load='2ifm' size='340' side='right'caption='[[2ifm]], [[Resolution|resolution]] 3.30Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2ifm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_phage_Xf Xanthomonas phage Xf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IFM FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </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=2ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ifm OCA], [https://pdbe.org/2ifm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ifm RCSB], [https://www.ebi.ac.uk/pdbsum/2ifm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ifm ProSAT]</span></td></tr> |
| - | {{STRUCTURE_2ifm| PDB=2ifm | SCENE= }}
| + | </table> |
| | + | == 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). |
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| - | '''PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA'''
| + | ==See Also== |
| - | | + | *[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview==
| + | </StructureSection> |
| - | 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.
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Xanthomonas phage Xf]] |
| - | ==About this Structure== | + | [[Category: Marvin DA]] |
| - | 2IFM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Xanthomonas_phage_xf Xanthomonas phage xf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IFM OCA].
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| - | | + | |
| - | ==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]
| + | |
| - | [[Category: Single protein]] | + | |
| - | [[Category: Xanthomonas phage xf]] | + | |
| - | [[Category: Marvin, D A.]] | + | |
| - | [[Category: Helical virus]]
| + | |
| - | [[Category: Virus coat protein]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 07:26:56 2008''
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