9ORH | pdb_00009orh

MicroED structure of the CTX-M-14 beta-lactamase-avibactam complex from inhibitor cocktail-soaked crystals

• PDB DOI: https://doi.org/10.2210/pdb9ORH/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-22 Released: 2025-06-18 
• Deposition Author(s): Vlahakis, N., Rodriguez, J.A., Jacobs, L.M.C., Chen, Y.
• Funding Organization(s): National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.00 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Combining MicroED and native mass spectrometry for structural discovery of enzyme-small molecules complexes

Vlahakis, N.W., Flowers, C.W., Liu, M., Agdanowski, M., Johnson, S., Summers, J.A., Jacobs, L.M.C., Keyser, C., Russell, P., Rose, S., Orlans, J., Adhami, N., Chen, Y., Sawaya, M.R., Basu, S., De Sanctis, D., Chen, Y., Wakatsuki, S., Nelson, H.M., Loo, J.A., Tang, Y., Rodriguez, J.A.

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)

Macromolecule Content 

• Total Structure Weight: 56.28 kDa 
• Atom Count: 4,022 
• Modeled Residue Count: 524 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	262	Escherichia coli	Mutation(s): 0  Gene Names:  blaCTX-M-14, beta-lactamase CTX-M-14, bla, bla CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, BKL28_004840, BKL28_005521, BXT93_06855, CR538_26855, E4K51_21070, EIA08_25160, ETN48_p0088, HL563_21800, HL563_23665, HLZ39_20540, HLZ39_26710, NY836_21775, pCT_085, pHK01_011, RCS101_P0028, RCS103_P0010, RCS30_P0082, RCS56_P0085, RCS60_P0031, RCS63_P0006, RCS65_P0008, RCS66_P0053, RCS68_P0054, SAMEA4362930_00013, SAMEA4363083_00099, SAMEA4370290_00046 EC: 3.5.2.6
UniProt
Find proteins for Q9L5C7 (Escherichia coli) Explore Q9L5C7  Go to UniProtKB:  Q9L5C7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NXL	C [auth A], D [auth B]	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C7 H13 N3 O6 S WJDGWXPPFHLLNL-RITPCOANSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.00 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.9	α = 90
b = 106.42	β = 100.69
c = 47.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Vlahakis, N., Rodriguez, J.A., Jacobs, L.M.C., Chen, Y.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DMR-1548924
Howard Hughes Medical Institute (HHMI)	United States	HHMI-EPI
Department of Energy (DOE, United States)	United States	DE-FC02-02ER63421

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release