3HDF

Crystal structure of truncated endolysin R21 from phage 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Regulation of a muralytic enzyme by dynamic membrane topology.

Sun, Q.Kuty, G.F.Arockiasamy, A.Xu, M.Young, R.Sacchettini, J.C.

(2009) Nat.Struct.Mol.Biol. 16: 1192-1194

  • DOI: 10.1038/nsmb.1681
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • R(21), the lysozyme of coliphage 21, has an N-terminal signal-anchor-release (SAR) domain that directs its secretion in a membrane-tethered, inactive form and then its release and activation in the periplasm. Both genetic and crystallographic studies ...

    R(21), the lysozyme of coliphage 21, has an N-terminal signal-anchor-release (SAR) domain that directs its secretion in a membrane-tethered, inactive form and then its release and activation in the periplasm. Both genetic and crystallographic studies show that the SAR domain, once extracted from the bilayer, refolds into the body of the enzyme and effects muralytic activation by repositioning one residue of the canonical lysozyme catalytic triad.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A, B
140Enterobacteria phage P21Mutation(s): 0 
Gene Names: R
EC: 3.2.1.17
Find proteins for P27359 (Enterobacteria phage P21)
Go to UniProtKB:  P27359
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.190α = 90.00
b = 109.673β = 90.00
c = 45.015γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
HKL-2000data reduction
SHELXDphasing
HKL-2000data collection
PHENIXrefinement
SCALEPACKdata scaling
SHELXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description