8HP8 | pdb_00008hp8

Crystal Structure of Engineered Endolysin EC340 derived from Gram-Negative Bacteria targeted Bacteriophage

• PDB DOI: https://doi.org/10.2210/pdb8HP8/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia phage PBEC131
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-12 Released: 2023-05-17 
• Deposition Author(s): Wang, J.M., Yoon, W.S., Seo, M.D.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the engineered endolysin mtEC340M.

Wang, J.M., Seok, S.H., Yoon, W.S., Kim, J.H., Seo, M.D.

(2023) Acta Crystallogr F Struct Biol Commun 79: 105-110

• PubMed: 37132476 
• DOI: https://doi.org/10.1107/S2053230X23002583
• Primary Citation Related Structures: 
  8HP8


• PubMed Abstract: 
  

  Endolysins produced by bacteriophages play essential roles in the release of phage progeny by degrading the peptidoglycan layers of the bacterial cell wall. Bacteriophage-encoded endolysins have emerged as a new class of antibacterial agents to combat surging antibiotic resistance. The crystal structure of mtEC340M, an engineered endolysin EC340 from the PBEC131 phage that infects Escherichia coli, was determined. The crystal structure of mtEC340M at 2.4 Å resolution consists of eight α-helices and two loops. The three active residues of mtEC340M were predicted by structural comparison with peptidoglycan-degrading lysozyme.

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Organizational Affiliation: 
• Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea.
College of Pharmacy and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, Jeju 63243, Republic of Korea.
College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 28160, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.02 kDa 
• Atom Count: 3,886 
• Modeled Residue Count: 481 
• Deposited Residue Count: 483 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin mtEC340M	A, B, C	161	Escherichia phage PBEC131	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.7	α = 90
b = 125.042	β = 114.74
c = 69.237	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Wang, J.M., Yoon, W.S., Seo, M.D.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2020R1A2C300888911

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection