3BFD | pdb_00003bfd

Crystal Structure of the Class A beta-lactamase SED-G238C mutant from Citrobacter sedlakii

• PDB DOI: https://doi.org/10.2210/pdb3BFD/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: 2.00 Å
• R-Value Free: 
  0.214 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.188 (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: 114.33 kDa 
• Atom Count: 9,019 
• Modeled Residue Count: 1,052 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class A beta-lactamase Sed1	A, B, C, D	263	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
CAC	E [auth A], F [auth B], G [auth C], H [auth D]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.214 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.642	α = 90
b = 73.2	β = 121.89
c = 103.893	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: Non-polymer description, Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary