4KG2 | pdb_00004kg2

Crystal Structure of AmpC beta-lactamase from E. coli in Complex with Cefotaxime

• PDB DOI: https://doi.org/10.2210/pdb4KG2/pdb

• Classification: Hydrolase/antibiotic
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-28 Released: 2014-10-29 
• Deposition Author(s): Docter, B.E., Baggett, V.L., Powers, R.A., Wallar, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Complexed structures of AmpC beta-lactamase

Docter, B.E., Baggett, V.L., Powers, R.A., Wallar, B.J.

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.35 kDa 
• Atom Count: 5,964 
• Modelled Residue Count: 716 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth B], B [auth A]	358	Escherichia coli K-12	Mutation(s): 0  Gene Names: ampC, ampA, b4150, JW4111 EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12)) Explore P00811  Go to UniProtKB:  P00811

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CEF	F [auth B], H [auth A]	CEFOTAXIME, C3' cleaved, open, bound form C14 H15 N5 O5 S2 NRYMPLKBKFIWQC-YVCCLBOHSA-N
PO4	C [auth B], D [auth B], E [auth B], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.836	α = 90
b = 78.751	β = 115.4
c = 98.095	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Docter, B.E., Baggett, V.L., Powers, R.A., Wallar, B.J.

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 2.0: 2018-09-19
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary