8B08 | pdb_00008b08

TRYPTOPHAN SYNTHASE - Cryo-trapping by the spitrobot crystal plunger after 30 sec

• PDB DOI: https://doi.org/10.2210/pdb8B08/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-07 Released: 2023-05-03 
• Deposition Author(s): 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.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (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: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.47 kDa 
• Atom Count: 5,173 
• Modeled Residue Count: 663 
• Deposited Residue Count: 666 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A	269	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: trpA, STM1727 EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P00929  Go to UniProtKB:  P00929

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B	397	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: trpB, STM1726 EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2K1  Go to UniProtKB:  P0A2K1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLS (Subject of Investigation/LOI)	E [auth B]	[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE C11 H17 N2 O8 P ODVKKQWXKRZJLG-VIFPVBQESA-N
G3P (Subject of Investigation/LOI)	C [auth A]	SN-GLYCEROL-3-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-GSVOUGTGSA-N
CS	D [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N
CL	F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.482	α = 90
b = 60.093	β = 94.75
c = 67.341	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	664726

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 1.1: 2023-05-24
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Refinement description