8GCS | pdb_00008gcs

XFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals mixed with sulbactam for 3 ms

• PDB DOI: https://doi.org/10.2210/pdb8GCS/pdb

• Classification: HYDROLASE/Inhibitor
• Organism(s): Mycobacterium tuberculosis str. Beijing/W BT1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-03 Released: 2023-09-20 
• Deposition Author(s): Malla, T.N., Schmidt, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Heterogeneity in M. tuberculosis beta-lactamase inhibition by Sulbactam.

Malla, T.N., Zielinski, K., Aldama, L., Bajt, S., Feliz, D., Hayes, B., Hunter, M., Kupitz, C., Lisova, S., Knoska, J., Martin-Garcia, J.M., Mariani, V., Pandey, S., Poudyal, I., Sierra, R.G., Tolstikova, A., Yefanov, O., Yoon, C.H., Ourmazd, A., Fromme, P., Schwander, P., Barty, A., Chapman, H.N., Stojkovic, E.A., Batyuk, A., Boutet, S., Phillips Jr., G.N., Pollack, L., Schmidt, M.

(2023) Nat Commun 14: 5507-5507

• PubMed: 37679343 
• DOI: https://doi.org/10.1038/s41467-023-41246-1
• Primary Citation Related Structures: 
  8EBI, 8EBR, 8EC4, 8ECF, 8GCS, 8GCT, 8GCV, 8GCX


• PubMed Abstract: 
  

  For decades, researchers have elucidated essential enzymatic functions on the atomic length scale by tracing atomic positions in real-time. Our work builds on possibilities unleashed by mix-and-inject serial crystallography (MISC) at X-ray free electron laser facilities. In this approach, enzymatic reactions are triggered by mixing substrate or ligand solutions with enzyme microcrystals. Here, we report in atomic detail (between 2.2 and 2.7 Å resolution) by room-temperature, time-resolved crystallography with millisecond time-resolution (with timepoints between 3 ms and 700 ms) how the Mycobacterium tuberculosis enzyme BlaC is inhibited by sulbactam (SUB). Our results reveal ligand binding heterogeneity, ligand gating, cooperativity, induced fit, and conformational selection all from the same set of MISC data, detailing how SUB approaches the catalytic clefts and binds to the enzyme noncovalently before reacting to a trans-enamine. This was made possible in part by the application of singular value decomposition to the MISC data using a program that remains functional even if unit cell parameters change up to 3 Å during the reaction.

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Organizational Affiliation: 
• Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA.
Department of Biology, Northeastern Illinois University, Chicago, IL, USA.
The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany.
Center for Free-Electron Laser Science CFEL, Deutsches Elektronen Synchrotron, Hamburg, Germany.
Linac Coherent Light Source LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera, Spanish National Research Council (CSIC), Madrid, Spain.
Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, 20 Arizona State University, Tempe, AZ, USA.
Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
Department of Physics, Universität Hamburg, Hamburg, Germany.
Department of BioSciences, Rice University, Houston, TX, USA.
Department of Chemistry, Rice University, Houston, TX, USA.
Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 113.98 kDa 
• Atom Count: 8,124 
• Modeled Residue Count: 1,060 
• Deposited Residue Count: 1,068 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	267	Mycobacterium tuberculosis str. Beijing/W BT1	Mutation(s): 0  Gene Names: blaC, blaA, BQ2027_MB2094C EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKD3  Go to UniProtKB:  P9WKD3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth B], G [auth C], H [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.5	α = 90
b = 98.79	β = 108.48
c = 111.47	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Malla, T.N., Schmidt, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release