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| [[Image:2ifn.gif|left|200px]]<br /><applet load="2ifn" size="350" color="white" frame="true" align="right" spinBox="true"
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| caption="2ifn, resolution 4.Å" />
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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'''<br />
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| ==Overview== | | ==PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA== |
| 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.
| | <StructureSection load='2ifn' size='340' side='right'caption='[[2ifn]], [[Resolution|resolution]] 4.00Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[2ifn]] 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=2IFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IFN FirstGlance]. <br> |
| 2IFN is a [http://en.wikipedia.org/wiki/Single_protein 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=2IFN OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Fiber diffraction, [[Resolution|Resolution]] 4Å</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=2ifn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ifn OCA], [https://pdbe.org/2ifn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ifn RCSB], [https://www.ebi.ac.uk/pdbsum/2ifn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ifn ProSAT]</span></td></tr> |
| ==Reference== | | </table> |
| 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15299811 15299811]
| | == Function == |
| [[Category: Pseudomonas phage pf1]] | | [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). |
| [[Category: Single protein]] | | __TOC__ |
| [[Category: Marvin, D A.]] | | </StructureSection> |
| [[Category: helical virus]] | | [[Category: Large Structures]] |
| [[Category: virus coat protein]] | | [[Category: Pseudomonas virus Pf1]] |
| | | [[Category: Marvin DA]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:52:09 2008''
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