4EVX | pdb_00004evx

Crystal structure of putative phage endolysin from S. enterica

• PDB DOI: https://doi.org/10.2210/pdb4EVX/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-26 Released: 2012-05-23 
• Deposition Author(s): Michalska, K., Li, H., Jedrzejczak, R., Brown, R.N., Cort, J.R., Heffron, F., Nakayasu, E.S., Adkins, J.N., Joachimiak, A., Program for the Characterization of Secreted Effector Proteins (PCSEP), Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Crystal structure of putative phage endolysin from S. enterica

Michalska, K., Jedrzejczak, R., Li, H., Brown, R.N., Cort, J.R., Heffron, F., Nakayasu, E.S., Adkins, J.N., Joachimiak, A., Program for the Characterization of Secreted Effector Proteins (PCSEP), Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.52 kDa 
• Atom Count: 1,699 
• Modeled Residue Count: 191 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phage endolysin	A, B	106	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: STM3605 EC: 3.2.1.17
UniProt
Find proteins for Q8ZLC6 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZLC6  Go to UniProtKB:  Q8ZLC6

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MLY	A, B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.215 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34EVX

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.4	α = 90
b = 54.4	β = 90
c = 261.09	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
Coot	model building
BUSTER	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Michalska, K., Li, H., Jedrzejczak, R., Brown, R.N., Cort, J.R., Heffron, F., Nakayasu, E.S., Adkins, J.N., Joachimiak, A., Program for the Characterization of Secreted Effector Proteins (PCSEP), Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary