8B3M | pdb_00008b3m

Millisecond cryo-trapping by the spitrobot crystal plunger, CTXM-14 Avibactam complex, SSX, 1 sec

• PDB DOI: https://doi.org/10.2210/pdb8B3M/pdb

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


• Deposited: 2022-09-16 Released: 2023-05-24 
• Deposition Author(s): Mehrabi, P., Sung, S., von Stetten, D., Prester, A., Hatton, C.E., Kleine-Doepke, S., Berkes, A., Gore, G., Leimkohl, J.P., Schikora, H., Kollewe, M., Rohde, H., Wilmanns, M., Tellkamp, F., Schulz, E.C.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography.

Mehrabi, P., Sung, S., von Stetten, D., Prester, A., Hatton, C.E., Kleine-Dopke, S., Berkes, A., Gore, G., Leimkohl, J.P., Schikora, H., Kollewe, M., Rohde, H., Wilmanns, M., Tellkamp, F., Schulz, E.C.

(2023) Nat Commun 14: 2365-2365

• PubMed: 37185266 
• DOI: https://doi.org/10.1038/s41467-023-37834-w
• Primary Citation Related Structures: 
  8AW8, 8AW9, 8AWB, 8AWC, 8AWD, 8AWE, 8AWF, 8AWS, 8AWU, 8AWV, 8AWX, 8AWY, 8B03, 8B05, 8B06, 8B08, 8B2O, 8B2V, 8B2W, 8B3M


• PubMed Abstract: 
  

  We introduce the spitrobot, a protein crystal plunger, enabling reaction quenching via cryo-trapping with a time-resolution in the millisecond range. Protein crystals are mounted on canonical micromeshes on an electropneumatic piston, where the crystals are kept in a humidity and temperature-controlled environment, then reactions are initiated via the liquid application method (LAMA) and plunging into liquid nitrogen is initiated after an electronically set delay time to cryo-trap intermediate states. High-magnification images are automatically recorded before and after droplet deposition, prior to plunging. The SPINE-standard sample holder is directly plunged into a storage puck, enabling compatibility with high-throughput infrastructure. Here we demonstrate binding of glucose and 2,3-butanediol in microcrystals of xylose isomerase, and of avibactam and ampicillin in microcrystals of the extended spectrum beta-lactamase CTX-M-14. We also trap reaction intermediates and conformational changes in macroscopic crystals of tryptophan synthase to demonstrate that the spitrobot enables insight into catalytic events.

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Organizational Affiliation: 
• Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany. [e-mail].
Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany. [e-mail].
European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.
University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany.
Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany.
Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany. [e-mail].
Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany. [e-mail].
Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany. [e-mail].
University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. [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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.93 kDa 
• Atom Count: 2,225 
• Modeled Residue Count: 260 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	260	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: ctx-m-14 EC: 3.5.2.6
UniProt
Find proteins for A0A0H3H219 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3H219  Go to UniProtKB:  A0A0H3H219

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.85	α = 90
b = 41.85	β = 90
c = 232.85	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Mehrabi, P., Sung, S., von Stetten, D., Prester, A., Hatton, C.E., Kleine-Doepke, S., Berkes, A., Gore, G., Leimkohl, J.P., Schikora, H., Kollewe, M., Rohde, H., Wilmanns, M., Tellkamp, F., Schulz, E.C.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary