3IFM

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


Experimental Data Snapshot

  • Method: FIBER DIFFRACTION
  • Resolution: 3.3 Å

wwPDB Validation

Currently 3IFM does not have a wwPDB validation report.


This is version 1.2 of the entry. See complete history

Literature

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, D.A.

(1995) Acta Crystallogr.,Sect.D 51: 792-804

  • DOI: 10.1107/S0907444995003027
  • Primary Citation of Related Structures:  2IFM, 2IFN, 4IFM
  • Also Cited By: 1HGV, 1HGZ, 1HH0, 1QL1, 1QL2, 2XKM

  • PubMed Abstract: 
  • 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 ca ...

    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.


    Related Citations: 
    • Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions
      Marvin, D.A.
      (1989) Int.J.Biol.Macromol. 11: 159
    • Two Forms of Pf1 Inovirus: X-Ray Diffraction Studies on a Structural Phase Transition and a Calculated Libration Normal Mode of the Asymmetric Unit
      Marvin, D.A.,Nave, C.,Bansal, M.,Hale, R.D.,Salje, E.K.H.
      (1992) Phase Transitions 39: 45
    • Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme
      Marvin, D.A.
      (1990) Int.J.Biol.Macromol. 12: 125


    Organizational Affiliation

    Daresbury Laboratory, Warrington, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PF1 FILAMENTOUS BACTERIOPHAGE
A
46Pseudomonas phage Pf1Gene Names: VIII
Find proteins for P03621 (Pseudomonas phage Pf1)
Go to UniProtKB:  P03621
Experimental Data & Validation

Experimental Data

  • Method: FIBER DIFFRACTION
  • Resolution: 3.3 Å
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

Currently 3IFM does not have a wwPDB validation report.



Entry History 

Deposition Data

  • Deposited Date: 1994-01-16 
  • Released Date: 1996-01-01 
  • Deposition Author(s): Marvin, D.A.

Revision History 

  • Version 1.0: 1996-01-01
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance