DOI: 10.5281/zenodo.5878429
title: Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase

description: <strong>Data type</strong>: spectroscopic measurements (UV-visible, ECD, EPR), DSC measurements, X-ray crystallography datasets, kinetic measurements, Molecular Dynamics simulations and data analysis. Files are in <strong>spc, par, DTA, DSC, dsx, csv, mtz </strong>formats Information on <strong>origin of the data</strong>: EPR spectroscopic measurements in <strong>spc</strong>,<strong> par</strong>,<strong> DTA </strong>and<strong> DSC</strong> formats EPR spectroscopic simulation and analyses in <strong>m </strong>and<strong> mat</strong> format UV-vis spectroscopic measurements in <strong>csv</strong> format ECD measurements in <strong>dsx</strong> format Enzyme activity data in <strong>csv</strong> format DSC measurements in <strong>csv </strong>format X-ray data in <strong>mtz</strong> format MD simulations data are in<strong> xlsx</strong> format The data are <strong>generated</strong> 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. Files in <strong>PARACAT_WP3_20211216_01_EPR </strong>folder includes EPR spectroscopic measurements and computer simulations/analyses, original data are in <strong>spc</strong>/<strong>par </strong>or<strong> DTA/DSC</strong> formats; files in <strong>m</strong> format were used to process the data. Files in <strong>PARACAT_WP3_20211216_02_UV-vis </strong>folder includes UV-Vis spectroscopic measurements of pH-titration in <strong>csv</strong> format. Files in <strong>PARACAT_WP3_20211216_03_ECD </strong>folder includes ECD measurements of the far UV (180–260 nm) and visible (260–500 nm) area, as well as unfolding curves in <strong>dsx</strong> format. Files in <strong>PARACAT_WP3_20211216_04_activity </strong>folder includes Clark electrode/activity measurements in<strong> csv</strong> format. Files in <strong>PARACAT_WP3_20211216_05_DSC </strong>folder includes DSC measurements in <strong>csv </strong>format. Files in <strong>PARACAT_WP3_20211216_06_Xray </strong>folder includes pre-processed (from the beamline pipeline) data sets in <strong>mtz</strong> format. Files in <strong>PARACAT_WP3_20211216_MD-Simulations </strong>folder includes pre-processed molecular dynamics data in<strong> xlsx</strong> format. NB. See the “READ ME” text file in each subfolder for more detailed information on files organization. <strong>Information on</strong>: Abbreviations:<strong> Cld</strong>, chlorite dismutase; <strong><em>C</em>Cld</strong>, chlorite dismutase from Cyanothece sp. PCC7425; <strong>CW</strong>, continuous wave; <strong><em>D</em></strong>, tetragonal zero-field splitting; <strong>DSC</strong>, differential circular calorimetry; <strong><em>E</em></strong>, rhombic zero-field splitting; <strong>ECD</strong>, electronic circular dichroism; <strong>EPR</strong>, electron paramagnetic resonance; <strong>HS</strong>, high-spin; <strong>LS</strong>, lowspin; <strong><em>Nd</em>Cld</strong>, chlorite dismutase from “Candidatus Nitrospira defluvii”; <strong>WT</strong>, wild type; <strong>ZFS</strong>, zero-field splitting. Units of measurement: Concentration: <strong>mM</strong> (millimolar), <strong>µM</strong> (micromolar), <strong>mg/mL</strong> (milligrams per milliliter), <strong>w/v %</strong> (weigth/volume) <strong>v/v %</strong> (volume/volume) Absorptivity: <strong>M<sup>-1</sup></strong> <strong>cm<sup>-1</sup></strong> Volume: <strong>mL</strong> (milliliters), <strong>µL </strong>(microliters), <strong>nL</strong> (nanoliters) Wavelength:<strong> nm</strong> (nanometers) Temperature:<strong> °C</strong> (Celsius degrees), <strong>K</strong> (Kelvin degrees) Time:<strong> min</strong> (minutes), <strong>h</strong> (hours), <strong>ns</strong> (nanoseconds) Ellipticity: millidegrees Frequency: <strong>GHz</strong> (gigahertz), <strong>kHz</strong> (kilohertz) Power: <strong>mW</strong> (milliwatt) Pressure: <strong>atm</strong> (atmosphere)
description:  EPR data: The spc, par, DTA and DSC files can be opened on proprietary EPR softwares from Bruker or MatLab (version R2020b, used by the authors) with EasySpin toolbox (version 6.0.0-dev.26, used by the authors). The simulation scripts of EPR measurements can be opened and run on MatLab (version R2021a, used by the authors) with EasySpin toolbox (version 6.0.0-dev.26, used by the authors). MatLab can be purchased/downloaded from: https://www.mathworks.com/products/matlab.html; EasySpin toolbox can be downloaded from: https://easyspin.org/  UV-vis data: The csv files can be opened with programs like Microsoft Excel/Open Office Calc.  ECD data: The dsx files can be opened with Pro-Data Viewer from Applied Photophysics.  Activity data: The csv files can be opened with programs like Microsoft Excel/Open Office Calc.  DSC data: The csv files can be opened with programs like Microsoft Excel/Open Office Calc.  X-ray data: The mtz files can be opened with software suites for the automated determination and refinement of macromolecular structures like PHENIX or CCP4i2.  MD-simulations data: The xlsx files can be opened with programs like Microsoft Excel/Open Office Calc.