2ifn: Difference between revisions

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[[Image:2ifn.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_2ifn", creates the "Structure Box" on the page.
<StructureSection load='2ifn' size='340' side='right'caption='[[2ifn]], [[Resolution|resolution]] 4.00&Aring;' 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'>[[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>
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]] 4&#8491;</td></tr>
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<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>
{{STRUCTURE_2ifn|  PDB=2ifn  |  SCENE= }}
</table>
 
== Function ==
'''PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA'''
[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).
 
__TOC__
 
</StructureSection>
==Overview==
[[Category: Large Structures]]
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: Pseudomonas virus Pf1]]
 
[[Category: Marvin DA]]
==About this Structure==
2IFN 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=2IFN OCA].  
 
==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: Pseudomonas phage pf1]]
[[Category: Single protein]]
[[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 07:26:58 2008''

Latest revision as of 12:02, 21 February 2024

PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATAPF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA

Structural highlights

2ifn is a 1 chain structure with sequence from Pseudomonas virus Pf1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Fiber diffraction, Resolution 4Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).

2ifn, resolution 4.00Å

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