3ZG9 | pdb_00003zg9

Crystal Structure of Penicillin-Binding Protein 4 from Listeria monocytogenes in the Cefuroxime bound form

• PDB DOI: https://doi.org/10.2210/pdb3ZG9/pdb

• Classification: PENICILLIN-BINDING PROTEIN
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-17 Released: 2014-01-15 
• Deposition Author(s): Jeong, J.H., Kim, Y.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal Structures of Penicillin-Binding Protein 4 from Listeria Monocytogenes

Jeong, J.H., Kim, Y.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.94 kDa 
• Atom Count: 4,046 
• Modeled Residue Count: 497 
• Deposited Residue Count: 584 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PENICILLIN-BINDING PROTEIN 4	A	47	Listeria monocytogenes	Mutation(s): 0
UniProt
Find proteins for Q8Y547 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y547  Go to UniProtKB:  Q8Y547

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PENICILLIN-BINDING PROTEIN 4	B	537	Listeria monocytogenes	Mutation(s): 0
UniProt
Find proteins for Q8Y547 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y547  Go to UniProtKB:  Q8Y547

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DXF	C [auth A]	(2R)-5-[(carbamoyloxy)methyl]-2-[(1R)-1-{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}-2-oxoethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid C16 H18 N4 O8 S RUUDYXYLGTZCPN-VRVPSKPHSA-N
GOL	D [auth B], E [auth B], F [auth B], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.57	α = 90
b = 78.157	β = 90
c = 128.914	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Jeong, J.H., Kim, Y.G.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary