4R4S

Crystal structure of chimeric beta-lactamase cTEM-19m at 1.1 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.105 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structural Dynamics of Engineered beta-Lactamases Vary Broadly on Three Timescales yet Sustain Native Function.

Gobeil, S.M.C.Ebert, M.C.C.J.C.Park, J.Gagne, D.Doucet, N.Berghuis, A.M.Pleiss, J.Pelletier, J.N.

(2019) Sci Rep 9: 6656-6656

  • DOI: 10.1038/s41598-019-42866-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Understanding the principles of protein dynamics will help guide engineering of protein function: altering protein motions may be a barrier to success or may be an enabling tool for protein engineering. The impact of dynamics on protein function is t ...

    Understanding the principles of protein dynamics will help guide engineering of protein function: altering protein motions may be a barrier to success or may be an enabling tool for protein engineering. The impact of dynamics on protein function is typically reported over a fraction of the full scope of motional timescales. If motional patterns vary significantly at different timescales, then only by monitoring motions broadly will we understand the impact of protein dynamics on engineering functional proteins. Using an integrative approach combining experimental and in silico methodologies, we elucidate protein dynamics over the entire span of fast to slow timescales (ps to ms) for a laboratory-engineered system composed of five interrelated β-lactamases: two natural homologs and three laboratory-recombined variants. Fast (ps-ns) and intermediate (ns-µs) dynamics were mostly conserved. However, slow motions (µs-ms) were few and conserved in the natural homologs yet were numerous and widely dispersed in their recombinants. Nonetheless, modified slow dynamics were functionally tolerated. Crystallographic B-factors from high-resolution X-ray structures were partly predictive of the conserved motions but not of the new slow motions captured in our solution studies. Our inspection of protein dynamics over a continuous range of timescales vividly illustrates the complexity of dynamic impacts of protein engineering as well as the functional tolerance of an engineered enzyme system to new slow motions.


    Organizational Affiliation

    Département de chimie, Université de Montréal, Montréal, QC, H3T 1J4, Canada. joelle.pelletier@umontreal.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase TEM,Beta-lactamase PSE-4
A
263Escherichia coliPseudomonas aeruginosaMutation(s): 0 
Gene Names: blablaT-3blaT-4blaT-5blaT-6pse4carB1
EC: 3.5.2.6
Find proteins for P62593 (Escherichia coli)
Go to UniProtKB:  P62593
Find proteins for P16897 (Pseudomonas aeruginosa)
Go to UniProtKB:  P16897
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.105 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.71α = 90
b = 58.71β = 90
c = 109.77γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.2: 2020-04-22
    Changes: Database references