Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase

• Data type: spectroscopic measurements (UV-visible, ECD, EPR), DSC measurements, X-ray crystallography datasets, kinetic measurements, Molecular Dynamics simulations and data analysis.
• Files are in spc, par, DTA, DSC, dsx, csv, mtz formats
• Information on origin of the data:
  • EPR spectroscopic measurements in spc, par, DTA and DSC formats
  • EPR spectroscopic simulation and analyses in m and mat format
  • UV-vis spectroscopic measurements in csv format
  • ECD measurements in dsx format
  • Enzyme activity data in csv format
  • DSC measurements in csv format
  • X-ray data in mtz format
  • MD simulations data are in xlsx format
• The data are generated by:
  • UV−vis spectra were recorded using a Cary 60 UV−vis spectrophotometer (Agilent).
  • Electronic circular dichroism spectroscopy was performed using Chirascan (Applied Photophysics, Leatherhead, U.K.).
  • X-Band CW-EPR experiments were performed on A) a Bruker ESP300E spectrometer equipped with a liquid helium cryostat (Oxford Inc.); B) a Bruker ELEXSYS E580 X-band spectrometer equipped with an Oxford ESR 900 continuous-flow helium cryostat and a Bruker ER 4122 SHQ resonator.
  • Enzyme activity was measured polarographically following the release of O2 by using a Clark-type oxygen electrode (Oxygraph Plus; Hansatech Instruments, Norfolk, U.K.).
  • Differential scanning calorimetry experiments were performed on a Micro-Cal PEAQ-DSC Automated instrument (Malvern Panalytical Ltd., Malvern, U.K.) equipped with an autosampler for 96-well plates and controlled by the MicroCal PEAQ-DSC software.
  • Crystallization experiments were performed using the sitting drop vapor diffusion method in SWISSCI MRC three-well crystallization plates (Molecular Dimensions, Newmarket, U.K.). Crystallization drops were set up using a mosquito crystallization robot (TTP Labtech). Commercially available crystallization screens were used for further screening. Crystallization plates were stored in a Formulatrix RI-1000 imaging device at 22 °C. Data were collected at 100 K using an Eiger2 XE 16 M detector at the beamline i04 at the Diamond Light Source (DLS, Didcot, United Kingdom). Further data was collected at 100 K at beamline ID30A-3 using a Eiger X 4 M detector, at beamline ID-23-1 using a Pilatus 6 M detector and at beamline ID23-2 using a PILATUS3 X 2 M detector at the of European Synchrotron Radiation Facility (ESRF, Grenoble, France). Data sets were processed with XDS, and symmetry equivalent reflections merged with XDSCONV.
  • Molecular dynamics simulations were performed using the GROMOS11 molecular simulation package and GROMOS force field 54A8. Analyses of the coordinate trajectories was done with Gromos++ programs hbond, rdf and mdf. Coordinates at specific time point were generated using Gromos++ program frameout and analysed using PyMOL Molecular Graphics System.
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    • Files in PARACAT_WP3_20211216_01_EPR folder includes EPR spectroscopic measurements and computer simulations/analyses, original data are in spc/par or DTA/DSC formats; files in m format were used to process the data.
    • Files in PARACAT_WP3_20211216_02_UV-vis folder includes UV-Vis spectroscopic measurements of pH-titration in csv format.
    • Files in PARACAT_WP3_20211216_03_ECD folder includes ECD measurements of the far UV (180–260 nm) and visible (260–500 nm) area, as well as unfolding curves in dsx format.
    • Files in PARACAT_WP3_20211216_04_activity folder includes Clark electrode/activity measurements in csv format.
    • Files in PARACAT_WP3_20211216_05_DSC folder includes DSC measurements in csv format.
    • Files in PARACAT_WP3_20211216_06_Xray folder includes pre-processed (from the beamline pipeline) data sets in mtz format.
    • Files in PARACAT_WP3_20211216_MD-Simulations folder includes pre-processed molecular dynamics data in xlsx format.

NB. See the “READ ME” text file in each subfolder for more detailed information on files organization.

• Information on:
  • Abbreviations: Cld, chlorite dismutase; CCld, chlorite dismutase from Cyanothece sp. PCC7425; CW, continuous wave; D, tetragonal zero-field splitting; DSC, differential circular calorimetry; E, rhombic zero-field splitting; ECD, electronic circular dichroism; EPR, electron paramagnetic resonance; HS, high-spin; LS, lowspin; NdCld, chlorite dismutase from “Candidatus Nitrospira defluvii”; WT, wild type; ZFS, zero-field splitting.

• Units of measurement:
  • Concentration: mM (millimolar), µM (micromolar), mg/mL (milligrams per milliliter), w/v % (weigth/volume) v/v % (volume/volume)
  • Absorptivity: M^-1 cm^-1
  • Volume: mL (milliliters), µL (microliters), nL (nanoliters)
  • Wavelength: nm (nanometers)
  • Temperature: °C (Celsius degrees), K (Kelvin degrees)
  • Time: min (minutes), h (hours), ns (nanoseconds)
  • Ellipticity: millidegrees
  • Frequency: GHz (gigahertz), kHz (kilohertz)
  • Power: mW (milliwatt)
  • Pressure: atm (atmosphere)