3BFF

class A beta-lactamase SED-G238C complexed with faropenem

• PDB DOI: https://doi.org/10.2210/pdb3BFF/pdb

• Classification: HYDROLASE
• Organism(s): Citrobacter sedlakii
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2007-11-21 Released: 2007-12-18 
• Deposition Author(s): Pernot, L., Petrella, S., Sougakoff, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

acyl-intermediate structures of the class A beta-lactamase SED-G238C

Pernot, L., Petrella, S., Sougakoff, W.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 115.17 kDa 
• Atom Count: 9,194 
• Modelled Residue Count: 1,048 
• Deposited Residue Count: 1,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class A beta-lactamase Sed1	A, B, C, D	262	Citrobacter sedlakii	Mutation(s): 1  Gene Names: bla-SED-1 EC: 3.5.2.6
UniProt
Find proteins for Q93PQ0 (Citrobacter sedlakii) Explore Q93PQ0  Go to UniProtKB:  Q93PQ0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFR	F [auth A], J [auth B], M [auth C], O [auth D]	(2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid C12 H17 N O6 S CGJDLFMMMJEANA-DAGMQNCNSA-N
FPM	L [auth C]	(5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid C12 H15 N O5 S HGGAKXAHAYOLDJ-FHZUQPTBSA-N
SCN	E [auth A], G [auth B], H [auth B], I [auth B], K [auth C], N [auth D]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 
• R-Value Observed: 0.189 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.116	α = 90
b = 73.244	β = 121.69
c = 103.504	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
MOLREP	phasing
CNS	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Pernot, L., Petrella, S., Sougakoff, W.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary