2ZJ9 | pdb_00002zj9

X-ray crystal structure of AmpC beta-Lactamase (AmpC(D)) from an Escherichia coli with a Tripeptide Deletion (Gly286 Ser287 Asp288) on the H10 Helix

• PDB DOI: https://doi.org/10.2210/pdb2ZJ9/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-29 Released: 2009-03-10 
• Deposition Author(s): Yamaguchi, Y., Sato, G., Yamagata, Y., Wachino, J., Arakawa, Y., Kurosaki, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Structure of AmpC beta-lactamase (AmpCD) from an Escherichia coli clinical isolate with a tripeptide deletion (Gly286-Ser287-Asp288) in the H10 helix

Yamaguchi, Y., Sato, G., Yamagata, Y., Doi, Y., Wachino, J., Arakawa, Y., Matsuda, K., Kurosaki, H.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 540-543

• PubMed: 19478427 
• DOI: https://doi.org/10.1107/S1744309109014249
• Primary Citation of Related Structures:  
  2ZJ9


• PubMed Abstract: 
  

  The X-ray crystal structure of AmpC beta-lactamase (AmpC(D)) with a tripeptide deletion (Gly286-Ser287-Asp288) produced by Escherichia coli HKY28, a ceftazidime-resistant strain, was determined at a resolution of 1.7 A. The structure of AmpC(D) suggests that the tripeptide deletion at positions 286-288 located in the H10 helix causes a structural change of the Asn289-Asn294 region from the alpha-helix present in the native AmpC beta-lactamase of E. coli to a loop structure, which results in a widening of the substrate-binding site.

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Organizational Affiliation: 

Environmental Safety Center, Kumamoto University, Kumamoto, Japan. [e-mail]

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)

Macromolecule Content

• Total Structure Weight: 79.02 kDa 
• Atom Count: 6,417 
• Modelled Residue Count: 710 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmpC	A, B	355	Escherichia coli	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for Q76DI4 (Escherichia coli) Explore Q76DI4  Go to UniProtKB:  Q76DI4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	D [auth A], F [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
NA	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.065	α = 82.62
b = 47.381	β = 80.91
c = 81.461	γ = 65.4

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Yamaguchi, Y., Sato, G., Yamagata, Y., Wachino, J., Arakawa, Y., Kurosaki, H.

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description