8PCM

Structure of serine-beta-lactamase CTX-M-14 following the time-resolved active site binding of boric acid and subsequent glycerol-boric acid-ester formation, 80 ms

• PDB DOI: https://doi.org/10.2210/pdb8PCM/pdb

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


• Deposited: 2023-06-11 Released: 2024-06-26 
• Deposition Author(s): Prester, A., Perbandt, M., Galchenkova, M., Oberthuer, D., Yefanov, O., Hinrichs, W., Rohde, H., Betzel, C.
• Funding Organization(s): Joachim Herz Stiftung, German Federal Ministry for Education and Research, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.210 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

Time resolved crystallography of boric acid binding to the active site serine of the beta-lactamase CTX-M-14 and subsequent 1,2-diol esterification

Prester, A., Perbandt, M., Galchenkova, M., Oberthuer, D., Werner, N., Henkel, A., Maracke, J., Yefanov, O., Hakanpaeae, J., Pompidor, G., Meyer, J., Chapman, H., Aepfelbacher, M., Hinrichs, W., Rohde, H., Betzel, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 28.29 kDa 
• Atom Count: 2,258 
• Modelled Residue Count: 261 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	263	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: ctx-m-14 EC: 3.5.2.6
UniProt
Find proteins for D2D9A0 (Klebsiella pneumoniae) Explore D2D9A0  Go to UniProtKB:  D2D9A0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YCH (Subject of Investigation/LOI)	B [auth A]	[(4~{S})-2-oxidanyl-1,3,2-dioxaborolan-4-yl]methanol C3 H7 B O4 HXGHIZVNPXUHFK-VKHMYHEASA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BO4 (Subject of Investigation/LOI)	C [auth A]	BORATE ION B H4 O4 KCFLOKKYWBPKFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.210 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.84	α = 90
b = 41.84	β = 90
c = 233.28	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Prester, A., Perbandt, M., Galchenkova, M., Oberthuer, D., Yefanov, O., Hinrichs, W., Rohde, H., Betzel, C.

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Funding Organization	Location	Grant Number
Joachim Herz Stiftung	Germany	--
German Federal Ministry for Education and Research	Germany	--
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release