8C5B

Crystal Structure of Penicillin-binding Protein 3 (PBP3) from Staphylococcus Epidermidis

• PDB DOI: https://doi.org/10.2210/pdb8C5B/pdb

• Classification: PENICILLIN-BINDING PROTEIN
• Organism(s): Staphylococcus epidermidis RP62A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-06 Released: 2023-12-13 
• Deposition Author(s): Schwinzer, M., Brognaro, H., Rohde, H., Betzel, C.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.257 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Structure and Dynamics of the Penicillin-Binding Protein 3 from Staphylococcus Epidermidis Native and in Complex with Cefotaxime and Vaborbactam

Schwinzer, M., Brognaro, H., Rohde, H., Betzel, C.

(2023) Int J Appl Biol Pharm 

• DOI: https://doi.org/10.26502/ijabpt.202127

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.93 kDa 
• Atom Count: 4,870 
• Modelled Residue Count: 632 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 3	A	668	Staphylococcus epidermidis RP62A	Mutation(s): 0  Gene Names: pbp3, SERP1117
UniProt
Find proteins for Q5HNZ7 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A)) Explore Q5HNZ7  Go to UniProtKB:  Q5HNZ7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.257 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.442	α = 90
b = 83.442	β = 90
c = 307.155	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
STARANISO	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Schwinzer, M., Brognaro, H., Rohde, H., Betzel, C.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release