7BH7

Room temperature, serial X-ray structure of the ertapenem-derived acylenzyme of CTX-M-15 (10 min soak) collected on fixed target chips at Diamond Light Source I24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography.

Butryn, A.Simon, P.S.Aller, P.Hinchliffe, P.Massad, R.N.Leen, G.Tooke, C.L.Bogacz, I.Kim, I.S.Bhowmick, A.Brewster, A.S.Devenish, N.E.Brem, J.Kamps, J.J.A.G.Lang, P.A.Rabe, P.Axford, D.Beale, J.H.Davy, B.Ebrahim, A.Orlans, J.Storm, S.L.S.Zhou, T.Owada, S.Tanaka, R.Tono, K.Evans, G.Owen, R.L.Houle, F.A.Sauter, N.K.Schofield, C.J.Spencer, J.Yachandra, V.K.Yano, J.Kern, J.F.Orville, A.M.

(2021) Nat Commun 12: 4461-4461

  • DOI: https://doi.org/10.1038/s41467-021-24757-7
  • Primary Citation of Related Structures:  
    7BH3, 7BH4, 7BH5, 7BH6, 7BH7, 7BHK, 7BHL, 7BHM, 7BHN

  • PubMed Abstract: 

    Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.


  • Organizational Affiliation

    Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase265Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaCTX-M-15
EC: 3.5.2.6
UniProt
Find proteins for G3G192 (Klebsiella pneumoniae)
Explore G3G192 
Go to UniProtKB:  G3G192
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3G192
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TVE (Subject of Investigation/LOI)
Query on TVE

Download Ideal Coordinates CCD File 
B [auth A](2~{S},3~{R},4~{R})-3-[5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl]sulfanyl-4-methyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid
C22 H27 N3 O7 S
IYAWOFDGKUIGMU-BLNVEPNZSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.258α = 90
b = 45.975β = 90
c = 119.032γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/J014400/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description