Time resolved structural analysis of the full turnover of an enzyme - 100 ms

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Time-resolved crystallography reveals allosteric communication aligned with molecular breathing.

Mehrabi, P.Schulz, E.C.Dsouza, R.Muller-Werkmeister, H.M.Tellkamp, F.Miller, R.J.D.Pai, E.F.

(2019) Science 365: 1167-1170

  • DOI: https://doi.org/10.1126/science.aaw9904
  • Primary Citation of Related Structures:  
    6QHP, 6QHQ, 6QHS, 6QHT, 6QHU, 6QHV, 6QHW, 6QHX, 6QHY, 6QHZ, 6QI0, 6QI1, 6QI2, 6QI3

  • PubMed Abstract: 

    A comprehensive understanding of protein function demands correlating structure and dynamic changes. Using time-resolved serial synchrotron crystallography, we visualized half-of-the-sites reactivity and correlated molecular-breathing motions in the enzyme fluoroacetate dehalogenase. Eighteen time points from 30 milliseconds to 30 seconds cover four turnover cycles of the irreversible reaction. They reveal sequential substrate binding, covalent-intermediate formation, setup of a hydrolytic water molecule, and product release. Small structural changes of the protein mold and variations in the number and placement of water molecules accompany the various chemical steps of catalysis. Triggered by enzyme-ligand interactions, these repetitive changes in the protein framework's dynamics and entropy constitute crucial components of the catalytic machinery.

  • Organizational Affiliation

    Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fluoroacetate dehalogenase
A, B
306Rhodopseudomonas palustrisMutation(s): 0 
Gene Names: RPA1163
Find proteins for Q6NAM1 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore Q6NAM1 
Go to UniProtKB:  Q6NAM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NAM1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAH (Subject of Investigation/LOI)
Query on FAH

Download Ideal Coordinates CCD File 
C [auth A]fluoroacetic acid
C2 H3 F O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.73α = 90
b = 79.39β = 102.95
c = 84.44γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Advisory, Data collection, Database references, Refinement description