8P8E

Crystal structure of endolysin gp46 from Pseudomonas aeruginosa bacteriophage vB_PaeM_KTN6

• PDB DOI: https://doi.org/10.2210/pdb8P8E/pdb

• Classification: HYDROLASE
• Organism(s): Bacteriophage sp.
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-06-01 Released: 2024-05-08 
• Deposition Author(s): van Raaij, M.J., Sanz-Gaitero, M.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.164 
• R-Value Work: 0.126 

Starting Model: experimental

Literature

Structural and Biochemical Characterization of a New Phage-Encoded Muramidase, KTN6 Gp46

Sanz-Gaitero, M., De Maesschalck, V., Patel, A., Longin, H., Van Noort, V., Rodriguez-Rubio, L., van Ryne, M., Danis-Wlodarczyk, K., Drulis-Kawa, Z., Mesnage, S., van Raaij, M., Lavigne, R.

(2024) Phage 

• DOI: https://doi.org/10.1089/phage.2023.0040

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 24.78 kDa 
• Atom Count: 1,959 
• Modelled Residue Count: 218 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family protein	A [auth AAA]	220	Bacteriophage sp.	Mutation(s): 0  Gene Names: IDBGMNHM_00003
UniProt
Find proteins for A0A9E7MJ36 (Pseudomonas phage Ka2) Explore A0A9E7MJ36  Go to UniProtKB:  A0A9E7MJ36

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth EEE], C [auth EaE]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG	D [auth GGG]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.164 
• R-Value Work: 0.126 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M38P8E

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.796	α = 90
b = 43.201	β = 90
c = 126.181	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): van Raaij, M.J., Sanz-Gaitero, M.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	BFU2017-82207-P
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2021-125597NB-I00

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release