4DXZ | pdb_00004dxz

crystal structure of a PliG-Ec mutant, a periplasmic lysozyme inhibitor of g-type lysozyme from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb4DXZ/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-02-28 Released: 2012-06-20 
• Deposition Author(s): Leysen, S., Vanheuverzwijn, S., Van Asten, K., Vanderkelen, L., Michiels, C.W., Strelkov, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

crystal structure of a PliG-Ec mutant, a periplasmic lysozyme inhibitor of g-type lysozyme from Escherichia coli

Leysen, S., Vandekelen, L., Michiels, C.W., Strelkov, S.V.

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: 12.83 kDa 
• Atom Count: 1,200 
• Modeled Residue Count: 111 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor of g-type lysozyme	A	111	Escherichia coli K-12	Mutation(s): 2  Gene Names: pliG, ycgK, b1178, JW1167
UniProt
Find proteins for P76002 (Escherichia coli (strain K12)) Explore P76002  Go to UniProtKB:  P76002

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	B [auth A], C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.316	α = 90
b = 80.316	β = 90
c = 31.098	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
Auto-Rickshaw	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Leysen, S., Vanheuverzwijn, S., Van Asten, K., Vanderkelen, L., Michiels, C.W., Strelkov, S.V.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary