6B6B

Beta-Lactamase, unmixed needles crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.

Olmos, J.L.Pandey, S.Martin-Garcia, J.M.Calvey, G.Katz, A.Knoska, J.Kupitz, C.Hunter, M.S.Liang, M.Oberthuer, D.Yefanov, O.Wiedorn, M.Heyman, M.Holl, M.Pande, K.Barty, A.Miller, M.D.Stern, S.Roy-Chowdhury, S.Coe, J.Nagaratnam, N.Zook, J.Verburgt, J.Norwood, T.Poudyal, I.Xu, D.Koglin, J.Seaberg, M.H.Zhao, Y.Bajt, S.Grant, T.Mariani, V.Nelson, G.Subramanian, G.Bae, E.Fromme, R.Fung, R.Schwander, P.Frank, M.White, T.A.Weierstall, U.Zatsepin, N.Spence, J.Fromme, P.Chapman, H.N.Pollack, L.Tremblay, L.Ourmazd, A.Phillips, G.N.Schmidt, M.

(2018) BMC Biol 16: 59-59

  • DOI: https://doi.org/10.1186/s12915-018-0524-5
  • Primary Citation of Related Structures:  
    6B5X, 6B5Y, 6B68, 6B69, 6B6A, 6B6B, 6B6C, 6B6D, 6B6E, 6B6F

  • PubMed Abstract: 

    Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Here, we demonstrate a general method for capturing enzyme catalysis "in action" by mix-and-inject serial crystallography (MISC). Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis β-lactamase with the third-generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation from 30 ms to 2 s. MISC is a versatile and generally applicable method to investigate reactions of biological macromolecules, some of which are of immense biological significance and might be, in addition, important targets for structure-based drug design. With megahertz X-ray pulse rates expected at the Linac Coherent Light Source II and the European X-ray free-electron laser, multiple, finely spaced time delays can be collected rapidly, allowing a comprehensive description of biomolecular reactions in terms of structure and kinetics from the same set of X-ray data.


  • Organizational Affiliation

    Department of BioSciences, Rice University, 6100 Main Street, Houston, TX, 77005, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase267Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: blaCblaARv2068cMTCY49.07c
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: 1.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.6α = 90
b = 41.6β = 104.82
c = 69.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references