6B69

Beta-Lactamase, 500ms timepoint, mixed, shards crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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-lactamase
A, B, C, D
267Mycobacterium 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9F2
Query on 9F2

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
J [auth C],
K [auth D]
Ceftriaxone
C18 H18 N8 O7 S3
VAAUVRVFOQPIGI-TYHRLYECSA-N
CUG
Query on CUG

Download Ideal Coordinates CCD File 
H [auth B](2R)-2-[(S)-{[(2E)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}(carboxy)methyl]-5-(hydroxymethyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C14 H17 N5 O7 S2
FGHIYDLJRRPQPG-AMEUCZBGSA-N
FZS
Query on FZS

Download Ideal Coordinates CCD File 
L [auth D](2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C14 H17 N5 O5 S2
BPQMPOALEVUCBW-FFHDXYSJSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.86α = 90
b = 96.31β = 109.98
c = 113.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references