1N7U

THE RECEPTOR-BINDING PROTEIN P2 OF BACTERIOPHAGE PRD1: CRYSTAL FORM I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Receptor Binding Protein P2 of PRD1, a Virus Targeting Antibiotic-Resistant Bacteria, Has a Novel Fold Suggesting Multiple Functions.

Xu, L.Benson, S.D.Butcher, S.J.Bamford, D.H.Burnett, R.M.

(2003) Structure 11: 309-322

  • DOI: 10.1016/s0969-2126(03)00023-6
  • Primary Citation of Related Structures:  
    1N7U, 1N7V

  • PubMed Abstract: 
  • Bacteriophage PRD1 is unusual, with an internal lipid membrane, but has striking resemblances to adenovirus that include receptor binding spikes. The PRD1 vertex complex contains P2, a 590 residue monomer that binds to receptors on antibiotic-resistant strains of E ...

    Bacteriophage PRD1 is unusual, with an internal lipid membrane, but has striking resemblances to adenovirus that include receptor binding spikes. The PRD1 vertex complex contains P2, a 590 residue monomer that binds to receptors on antibiotic-resistant strains of E. coli and so is the functional counterpart to adenovirus fiber. P2 structures from two crystal forms, at 2.2 and 2.4 A resolution, reveal an elongated club-shaped molecule with a novel beta propeller "head" showing pseudo-6-fold symmetry. An extended loop with another novel fold forms a long "tail" containing a protruding proline-rich "fin." The head and fin structures are well suited to recognition and attachment, and the tail is likely to trigger the processes of vertex disassembly, membrane tube formation, and subsequent DNA injection.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of receptor-binding protein P2 of bacteriopahge PRD1
      Xu, L., Butcher, S.J., Benson, S.D., Bamford, D.H., Burnett, R.M.
      (2000) J Struct Biol 131: 159
    • Stable packing of phage PRD1 DNA requires adsorption protein P2, which binds to the IncP plasmid-encoded conjugative transfer complex
      Grahn, A.M., Caldentey, J., Bamford, J.K.H., Bamford, D.H.
      (1999) J Bacteriol 181: 6689
    • Bacteriophage PRD1: a broad host range dsDNA tectivirus with an internal membrane
      Bamford, D.H., Caldentey, J., Bamford, J.K.H.
      (1995) Adv Virus Res 45: 281
    • Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures
      Benson, S.D., Bamford, J.K.H., Bamford, D.H., Burnett, R.M.
      (1999) Cell 98: 825
    • Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex
      Rydman, P.S., Caldentey, J., Butcher, S.J., Fuller, S.D., Rutten, T., Bamford, D.H.
      (1999) J Mol Biol 291: 575
    • A tale of two viruses with therapeutic potential: Structural studies on CELO, an avian adenovirus and the bacteriophage PRD1
      Xu, L.
      (2002) Thesis --: --

    Organizational Affiliation

    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adsorption protein P2A554Enterobacteria phage PRD1Mutation(s): 0 
Gene Names: II
UniProt
Find proteins for P27378 (Enterobacteria phage PRD1)
Explore P27378 
Go to UniProtKB:  P27378
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27378
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.2α = 90
b = 46.5β = 90
c = 136.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence