5F1F

Crystal structure of CMY-10 adenylylated by acetyl-AMP

• PDB DOI: https://doi.org/10.2210/pdb5F1F/pdb

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


• Deposited: 2015-11-30 Released: 2016-12-07 
• Deposition Author(s): An, Y.J., Kim, M.K., Na, J.H., Cha, S.S.
• Funding Organization(s): National Research Foundation of Korea, KIOST in-house programs

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.197 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

Literature

Structural and mechanistic insights into the inhibition of class C beta-lactamases through the adenylylation of the nucleophilic serine.

Kim, M.K., An, Y.J., Na, J.H., Seol, J.H., Ryu, J.Y., Lee, J.W., Kang, L.W., Chung, K.M., Lee, J.H., Moon, J.H., Lee, J.S., Cha, S.S.

(2017) J Antimicrob Chemother 72: 735-743

• PubMed: 27999057 
• DOI: https://doi.org/10.1093/jac/dkw491
• Primary Citation of Related Structures:  
  5F1F, 5F1G, 5GZW


• PubMed Abstract: 
  

  : Investigation into the adenylylation of the nucleophilic serine in AmpC BER and CMY-10 extended-spectrum class C β-lactamases.

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Organizational Affiliation: 

Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Ansan, 15627, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.33 kDa 
• Atom Count: 3,055 
• Modelled Residue Count: 361 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	366	Klebsiella aerogenes	Mutation(s): 0  Gene Names: blaCMY-10 EC: 3.5.2.6
UniProt
Find proteins for Q99QC1 (Klebsiella aerogenes) Explore Q99QC1  Go to UniProtKB:  Q99QC1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	H [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
CD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.197 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.874	α = 90
b = 59.342	β = 90
c = 111.841	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): An, Y.J., Kim, M.K., Na, J.H., Cha, S.S.

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Funding Organization	Location	Grant Number
National Research Foundation of Korea	Korea, Republic Of	NRF-2015R 1A2A2A 01004168
National Research Foundation of Korea	Korea, Republic Of	NRF-2015M 1A5A 1037480
KIOST in-house programs	Korea, Republic Of	PE99314
KIOST in-house programs	Korea, Republic Of	PE99302

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description