6G88 | pdb_00006g88

Crystal structure of Enterococcus Faecium D63r Penicillin-Binding protein 5 (PBP5fm)

• PDB DOI: https://doi.org/10.2210/pdb6G88/pdb

• Classification: ANTIBIOTIC
• Organism(s): Enterococcus faecium
• Expression System: Enterococcus faecium
• Mutation(s): No 


• Deposited: 2018-04-08 Released: 2019-04-24 
• Deposition Author(s): Sauvage, E., El Gachi, M., Herman, R., Kerff, F., Charlier, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Structural basis of inactivation of Enterococcus faecium penicillin binding protein 5 by ceftobiprole.

Sauvage, E., El Gachi, M., Kerff, F., Herman, R., Verlaine, O., Amoroso, A., Page, M.G.P., Joris, B., Charlier, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

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: 214.13 kDa 
• Atom Count: 13,913 
• Modeled Residue Count: 1,799 
• Deposited Residue Count: 1,947 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity penicillin-binding protein 5 (PBP5)	A, B, C	649	Enterococcus faecium	Mutation(s): 0  Gene Names: pbp5
UniProt
Find proteins for Q47759 (Enterococcus faecium) Explore Q47759  Go to UniProtKB:  Q47759

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RB6	D [auth A], F [auth B], H [auth C]	(2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid C20 H24 N8 O6 S2 MYAXGJQBOYOEHQ-SWBIIUODSA-N
SO4	E [auth A], G [auth B], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.194	α = 90
b = 128.736	β = 94.04
c = 238.479	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Sauvage, E., El Gachi, M., Herman, R., Kerff, F., Charlier, P.

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary