3CSZ | pdb_00003csz

Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.225 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail.

Xiang, Y.Morais, M.C.Cohen, D.N.Bowman, V.D.Anderson, D.L.Rossmann, M.G.

(2008) Proc Natl Acad Sci U S A 105: 9552-9557

  • DOI: https://doi.org/10.1073/pnas.0803787105
  • Primary Citation Related Structures: 
    3CSQ, 3CSR, 3CSZ, 3CT0, 3CT1, 3CT5

  • PubMed Abstract: 

    The small bacteriophage phi29 must penetrate the approximately 250-A thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome through its tail into the bacterial cytoplasm. The tail of bacteriophage phi29 is noncontractile and approximately 380 A long. A 1.8-A resolution crystal structure of gene product 13 (gp13) shows that this tail protein has spatially well separated N- and C-terminal domains, whose structures resemble lysozyme-like enzymes and metallo-endopeptidases, respectively. CryoEM reconstructions of the WT bacteriophage and mutant bacteriophages missing some or most of gp13 shows that this enzyme is located at the distal end of the phi29 tail knob. This finding suggests that gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall. Comparisons of the gp13(-) mutants with the phi29 mature and emptied phage structures suggest the sequence of events that occur during the penetration of the tail through the peptidoglycan layer.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.

Macromolecule Content 

  • Total Structure Weight: 19.07 kDa 
  • Atom Count: 1,453 
  • Modeled Residue Count: 159 
  • Deposited Residue Count: 159 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Morphogenesis protein 1159N/AMutation(s): 0 
Gene Names: 13
EC: 3.4 (UniProt), 3.2.1 (UniProt)
UniProt
Find proteins for P15132 (Bacillus phage phi29)
Explore P15132 
Go to UniProtKB:  P15132
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15132
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N/A
Glycosylation Resources
GlyTouCan: G47362BJ
GlyCosmos: G47362BJ
GlyGen: G47362BJ

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.876α = 90
b = 69.35β = 90
c = 70.728γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-02-21
    Changes: Data collection, Database references, Structure summary