3BFC | pdb_00003bfc

class A beta-lactamase SED-G238C complexed with imipenem

• PDB DOI: https://doi.org/10.2210/pdb3BFC/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

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: 114.53 kDa 
• Atom Count: 8,648 
• Modeled 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM2	E [auth A], F [auth B], G [auth C], H [auth D]	(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid C12 H19 N3 O4 S UACUABDJLSUFFC-IWSPIJDZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.436	α = 90
b = 73.399	β = 122.36
c = 105.05	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: 2011-08-24
  Changes: Non-polymer description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.4: 2024-10-30
  Changes: Structure summary