6HX0 | pdb_00006hx0

Cell wall binding domain of endolysin from Listeria phage A500.

• PDB DOI: https://doi.org/10.2210/pdb6HX0/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Listeria phage A500
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-15 Released: 2019-10-30 
• Deposition Author(s): Dunne, M., Taylor, N.M.I., Shen, Y., Loessner, M.J., Leiman, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Shen, Y., Kalograiaki, I., Prunotto, A., Dunne, M., Bulous, S., Taylor, N.M., Sumrall, E., Eugster, M.R., Martin, R., Julian-Rodero, A., Gerber, B., Leiman, P.G., Menendez, M., dal Peraro, M., Canada, F.J., Loessner, M.J.

(2020) Chem Sci 

• DOI: https://doi.org/10.1039/D0SC04394J

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry, gel filtration

Macromolecule Content

• Total Structure Weight: 19.62 kDa 
• Atom Count: 1,747 
• Modelled Residue Count: 137 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-alanyl-D-glutamate peptidase	A	163	Listeria phage A500	Mutation(s): 0  Gene Names: ply, ply500 EC: 3.4.24
UniProt
Find proteins for Q37979 (Listeria phage A500) Explore Q37979  Go to UniProtKB:  Q37979

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.579	α = 90
b = 49.579	β = 90
c = 63.766	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Dunne, M., Taylor, N.M.I., Shen, Y., Loessner, M.J., Leiman, P.G.

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Funding Organization	Location	Grant Number
	Switzerland	--

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2020-11-11
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description