Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Escherichia coli) | kdpFABC | Uniprot IDs: kdpF: P36937; kdpA: P03959; kdpB: P03960; kdpC: P03961 | ||
| Genetic reagent | pBXC3H | doi:10.1007/978-1-62703-764-8_11 | Addgene catalog #47068 | Plasmid backbone |
| Strain, strain background (Escherichia coli) | LB2003 (F−thi metE rpsL gaI rha kup1 ∆kdpFABC5 ∆trkA) | doi:10.1007/s002030050425 | ||
| Sequence-based reagent | kdpB_S162A_for | Eurofins Genomics (Luxembourg) | 5′-GCGCCATCACCGGGGAAGCGGCACC-3′ | |
| Sequence-based reagent | kdpB_S162A_for | Eurofins Genomics (Luxembourg) | 5′-ACCGGTGCCGCTTCCCCGGTGATGG-3′ | |
| Sequence-based reagent | kdpB_D307N_for | Eurofins Genomics (Luxembourg) | 5′-GCTACTGAATAAAACCGGCACCATCAC-3′ | |
| Sequence-based reagent | kdpB_D307N_rev | Eurofins Genomics (Luxembourg) | 5′-GGTGCCGGTTTTATTCAGTAGCAGAACG-3′ | |
| Sequence-based reagent | kdpB_A407C_for | Eurofins Genomics (Luxembourg) | 5′-CATTCGTCGCCATGTTGAGTGTAACGG-3′ | |
| Sequence-based reagent | kdpB_A407C_rev | Eurofins Genomics (Luxembourg) | 5′-CGTTACACTCAACATGGCGACGAATGG-3′ | |
| Sequence-based reagent | kdpB_A494C_for | Eurofins Genomics (Luxembourg) | 5′-GATTTTCTCGCCGAATGTACACCGGAGGCC-3′ | |
| Sequence-based reagent | kdpB_A494C_rev | Eurofins Genomics (Luxembourg) | 5′-GGCCTCCGGTGTACATTCGGCGAGAAAATC-3′ | |
| Chemical compound, drug | MTSSL | Toronto Research Chemicals Inc, North York, Canada | EPR spin label | |
| Chemical compound, drug | Orthovanadate | Merck KGaA, Darmstadt, Germany | ||
| Chemical compound, drug | Adenosine 5′-triphosphate | Merck KGaA, Darmstadt, Germany | ||
| Software, algorithm | DeerAnalysis | doi:10.1007/BF03166213 | ||
| Other | 200 and 300 mesh Au R1.2/1.3 cryo-EM grids | Quantifoil, Großlöbichau, Germany | Cryo-EM Grids | |
| Software, algorithm | EPU v 2.3 | Thermo Fisher (Eindhoven, Netherlands) https://www.thermofisher.com/nl/en/home/electron-microscopy/products/software-em-3d-vis/epu-software.html |
||
| Software, algorithm | Sample thickness measurement script | https://doi.org/10.1101/2020.12.01.392100 | ||
| Software, algorithm | Focus | https://doi.org/10.1016/j.jsb.2017.03.007 https://focus.c-cina.unibas.ch/about.php | ||
| Software, algorithm | SBGrid | https://doi.org/10.7554/eLife.01456 https://sbgrid.org/software/ | ||
| Software, algorithm | MotionCor2 | https://doi.org/10.1038/nmeth.4193 http://msg.ucsf.edu/em/software/motioncor2.html | ||
| Software, algorithm | Ctffind 4.1.13 | https://doi.org/10.1016/j.jsb.2015.08.008 http://grigoriefflab.janelia.org/ctf | ||
| Software, algorithm | Ctffind 4.1.14 |
https://doi.org/10.1016/j.jsb.2015.08.008
http://grigoriefflab.janelia.org/ctf |
||
| Software, algorithm | crYOLO 1.3.1 | https://doi.org/10.1038/s42003-019-0437-z https://cryolo.readthedocs.io/en/stable/ | ||
| Software, algorithm | crYOLO 1.7.6 | https://doi.org/10.1038/s42003-019-0437-z https://cryolo.readthedocs.io/en/stable/ | ||
| Software, algorithm | cryoSPARC 3.2.0 |
https://doi.org/10.1038/nmeth.4169
https://cryosparc.com |
||
| Software, algorithm | RELION 3.0.8 |
https://doi.org/10.7554/eLife.42166
https://www2.mrc-lmb.cam.ac.uk/relion/ |
||
| Software, algorithm | RELION 3.1.1 |
https://doi.org/10.7554/eLife.42166
https://www2.mrc-lmb.cam.ac.uk/relion/ |
||
| Software, algorithm | Coot 0.9 |
https://doi.org/10.1107/S0907444904019158
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
||
| Software, algorithm | Phenix 1.19.2 |
https://doi.org/10.1107/S2059798318006551
http://phenix-online.org/ |
||
| Software, algorithm | Molprobity 4.5.1 |
https://doi.org/10.1002/pro.3330
http://molprobity.biochem.duke.edu |
||
| Software, algorithm | UCSF Chimera 1.15 |
https://doi.org/10.1002/jcc.20084
https://www.cgl.ucsf.edu/chimera/ |
||
| Software, algorithm | UCSF Chimerax 1.1.1 | https://doi.org/10.1002/pro.3943 https://www.rbvi.ucsf.edu/chimerax/ | ||
| Software, algorithm | Origin Pro 2016 | OriginLab https://www.originlab.com/2016 | ||
| Software, algorithm | Gromacs 2019.4 | https://doi.org/10.1016/0010-4655(95)00042-E https://www.gromacs.org/ | ||
| Software, algorithm | VMD 1.9.4a12 |
https://doi.org/10.1016/0263-7855(96)00018-5
http://www.ks.uiuc.edu/Research/vmd/ |
||
| Software, algorithm | charmm-gui |
https://doi.org/10.1021/acs.jctc.5b00935
http://www.charmm-gui.org/ |
||
| Software, algorithm | MDAnalysis 1.0.1 |
https://doi.org/10.1002/jcc.21787
https://www.mdanalysis.org/ |
||
| Software, algorithm | NumPy 1.20.0 |
https://doi.org/10.1038/s41586-020-2649-2
https://numpy.org/ |
||
| Software, algorithm | matplotlib 3.3.4 |
https://doi.org/10.1109/MCSE.2007.55
https://matplotlib.org/ |
||
| Software, algorithm | GraphPad Prism 8 and 9 | https://www.graphpad.com/scientific-software/prism/ | ||
| Software, algorithm | HOLE 2.2.004 | https://doi.org/10.1016/S0263-7855(97)00,009X | ||
| Software, algorithm | HOLLOW 1.3 | https://doi.org/10.1186/1472-6807-8-49 |