7A42 | pdb_00007a42

Fluoroacetate Dehalogenase measured by serial synchrotron crystallography

• PDB DOI: https://doi.org/10.2210/pdb7A42/pdb

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


• Deposited: 2020-08-19 Released: 2021-04-07 
• Deposition Author(s): Mehrabi, P., Schulz, E.C., Buecker, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison.

Mehrabi, P., Bucker, R., Bourenkov, G., Ginn, H.M., von Stetten, D., Muller-Werkmeister, H.M., Kuo, A., Morizumi, T., Eger, B.T., Ou, W.L., Oghbaey, S., Sarracini, A., Besaw, J.E., Pare-Labrosse, O., Meier, S., Schikora, H., Tellkamp, F., Marx, A., Sherrell, D.A., Axford, D., Owen, R.L., Ernst, O.P., Pai, E.F., Schulz, E.C., Miller, R.J.D.

(2021) Sci Adv 7

• PubMed: 33731353 
• DOI: https://doi.org/10.1126/sciadv.abf1380
• Primary Citation Related Structures: 
  7A42, 7A43, 7A44, 7A45


• PubMed Abstract: 
  

  For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.

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Organizational Affiliation: 
• Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. [e-mail] [e-mail].
Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany.
Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Notkestraße 85, 22607 Hamburg, Germany.
European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.
Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany.
Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.
Department of 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: 68.22 kDa 
• Atom Count: 5,093 
• Modeled Residue Count: 595 
• 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
CL (Subject of Investigation/LOI)	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.9	α = 90
b = 79.9	β = 103.4
c = 84.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Mehrabi, P., Schulz, E.C., Buecker, R.

Revision History  

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