8GCV

XFEL structure of Mycobacterium tuberculosis beta lactamase microcrystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-023-41246-1
  • Primary Citation of 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.


  • Organizational Affiliation

    Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B, C, D
267Mycobacterium tuberculosisMutation(s): 0 
Gene Names: blaCERS027646_02769
EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKD3 
Go to UniProtKB:  P9WKD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKD3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.64α = 90
b = 98.09β = 108.45
c = 110.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

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