4JZ5 | pdb_00004jz5

High-resolution structure of catalytic domain of endolysin ply40 from bacteriophage P40 of Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb4JZ5/pdb

• Classification: HYDROLASE
• Organism(s): Listeria phage P40
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-02 Released: 2014-04-09 
• Deposition Author(s): Romero-Fernandez, P., Bartual, S.G., Carrasco-lopez, C., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.143 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of catalytic domain of endolysin Ply40

Romero-Fernandez, P., Bartual, S.G., Carrasco-lopez, C., Loessner, M., Hermoso, J.A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 25.08 kDa 
• Atom Count: 2,016 
• Modelled Residue Count: 206 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gp26	A	223	Listeria phage P40	Mutation(s): 0  Gene Names: gp26 EC: 3.2.1.17
UniProt
Find proteins for B6D7J9 (Listeria phage P40) Explore B6D7J9  Go to UniProtKB:  B6D7J9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.143 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.332	α = 90
b = 42.332	β = 90
c = 98.627	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Romero-Fernandez, P., Bartual, S.G., Carrasco-lopez, C., Hermoso, J.A.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description