6QI1 | pdb_00006qi1

Time resolved structural analysis of the full turnover of an enzyme - 12312 ms

• PDB DOI: https://doi.org/10.2210/pdb6QI1/pdb

• Classification: HYDROLASE
• Organism(s): Rhodopseudomonas palustris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-17 Released: 2019-09-25 
• Deposition Author(s): Schulz, E.C., Mehrabi, P., Pai, E.F., Miller, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

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

• PubMed: 31515393 
• DOI: https://doi.org/10.1126/science.aaw9904
• Primary Citation 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.

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Organizational Affiliation: 
• Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
The Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
Department of Physics, University of Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany.
Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. [e-mail] [e-mail].
Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.
Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada. [e-mail] [e-mail].
Departments of Biochemistry and Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 68.23 kDa 
• Atom Count: 5,179 
• Modeled Residue Count: 591 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluoroacetate dehalogenase	A, B	306	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: RPA1163 EC: 3.8.1.3
UniProt
Find proteins for Q6NAM1 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NAM1  Go to UniProtKB:  Q6NAM1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAH	C [auth A]	fluoroacetic acid C2 H3 F O2 QEWYKACRFQMRMB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.76	α = 90
b = 79.61	β = 102.86
c = 84.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Schulz, E.C., Mehrabi, P., Pai, E.F., Miller, D.

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Advisory, Data collection, Database references