REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Bacterial strains | ||
XL10-Gold Ultracompetent Cells | Agilent Technologies | 200317 |
BL21(DE3) Competent Cells | Agilent Technologies | 200131 |
Chemicals, peptides, and recombinant proteins | ||
Ulp1 Sumo Protease | This work | Described above |
Ampicillin sodium salt | Sigma-Aldrich | A9518 |
Dithiothreitol (DTT) | Sigma-Aldrich | D9779 |
Isopropyl-β-D-thiogalactopyranoside (IPTG) | Sigma-Aldrich | I6758 |
Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) | Sigma-Aldrich | C4706 |
Super Optimal Broth with catabolite repression (SOC) medium | Sigma-Aldrich | S1797 |
LB broth powder (Miller) | Sigma-Aldrich | L3522 |
Super broth powder | Research Products International | S33050 |
Agar | Sigma-Aldrich | A1296 |
Dnase I | Sigma-Aldrich | DN25 |
Magnesium chloride (MgCl2) | Sigma-Aldrich | M8266 |
Sodium chloride (NaCl) | Sigma-Aldrich | S9888 |
Trizma base (Tris) | Sigma-Aldrich | T6066 |
Imidazole | Sigma-Aldrich | I2399 |
Ethylenediaminetetraacetic acid (EDTA) | Sigma-Aldrich | E9884 |
Iron(III) chloride hexahydrate (FeCl3 × 6H2O) | Sigma-Aldrich | 236489 |
Zinc sulfate heptahydrate (ZnSO4 × 7H2O) | Sigma-Aldrich | 221376 |
Cobalt(II) chloride hexahydrate (CoCl2 × 6H2O) | Sigma-Aldrich | 255599 |
Sodium molybdate dihydrate (Na2MoO4 × 2H2O) | Sigma-Aldrich | M1003 |
Copper(II) sulfate pentahydrate (CuSO4 × 5H2O) | Sigma-Aldrich | 209198 |
Boric acid (H3BO3) | Sigma-Aldrich | B0394 |
Manganese(II) sulfate (MnSO4) | Sigma-Aldrich | M7506 |
Hydrochloric acid (HCl) | Sigma-Aldrich | XX0628 |
Sodium phosphate monobasic (NaH2PO4) | Sigma-Aldrich | 74092 |
Potassium phosphate monobasic (KH2PO4) | J.T.Baker | 3246-05 |
Potassium phosphate dibasic (K2HPO4) | J.T.Baker | 3252-01 |
Sodium citrate dihydrate (NaC6H5O7 × 2H2O) | J.T.Baker | 3646-01 |
Magnesium sulfate heptahydrate (MgSO4 × 7H2O) | J.T.Baker | 2500-01 |
MEM Vitamin Solution (100×) | Sigma-Aldrich | M6895 |
15N-ammonium sulfate (15NH4)2SO4 | Sigma-Aldrich | 299286 |
12C D-Glucose | Sigma-Aldrich | G7520 |
D-Glucose (U-13C6,99 %; 1,2,3,4,5,6,6-D7, 97–98 %) | Cambridge Isotope | CLM-1396-5 |
Deuterium oxide (2H2O) | CortecNet | CD5251P1000 |
Nickel(II) sulfate (NiSO4) | Sigma-Aldrich | 656895 |
Critical commercial assays | ||
NucleoSpin Plasmid NoLid | Macherey-Nagel | 740499.50 |
Dabsyl-KTSAVLQ/SGFRKME-EDANS | GenScript Inc | Custom Synthesis |
5(2Aminoethylamino)1Napthalene sulfonic acid (EDANS) | MedChemExpress | ICN15474001 |
Recombinant DNA | ||
pGTM_CoV2_NSP5_004_SUMO | This work – available from Addgene | AddGene ID: 190062 |
pGTM_CoV2_NSP5_C145A_001_SUMO | This work – available from Addgene | AddGene ID: 192349 |
pGTM_YR375_SUMO_Protease_001 | This work – available from Addgene | AddGene ID: 190063 |
Other | ||
Sonicator 3000 | Misonix | S-3000/R2225 |
Amicon Ultra Centrifugal Filter Unit (MWCO 10000 Da) | Merck Millipore | UFC90110 |
5-mL HiTrap Chelating HP | Cytiva | 17040901 |
HiPrep 26/10 Desalting | Cytiva | 17508701 |
HiLoad® 16/60 Superdex® 75 | Cytiva | 28988946/17104401 |
Infinite M1000 PRO microplate reader | TECAN | 30063849/140100256 |
Jupiter C4 column | Phenomenex | 00F-4167-B0 |
ESI-Q-TOF spectrometer | Xevo, Waters | N/A |
Shigemi 5 mm Symmetrical NMR microtube | Shigemi, INC | BMS-005B |
Bruker INOVA 700 MHz NMR spectrometer | Bruker | N/A |
EasyXtal 15-well crystallization plate | NeXtal | 132006 132006 |
Protein Crystallization Cabinet | RUMED | PKS-E100 |
Magnetic Cryo Vials | Molecular Dimensions | MD7-402 |
SPINE Sample Changer Basket | Molecular Dimensions | MD7-510 |
Magnetic Mounted LithoLoops (0.20 mm) | Molecular Dimensions | MD7-136 |
Magnetic Cryo wand | Molecular Dimensions | MD7-411 |
Software and algorithms | ||
NMRPipe | Delaglio, F. et al. (1995)10 | https://www.ibbr.umd.edu/nmrpipe/ |
POKY | Lee, W. et al. (2021)11 | https://sites.google.com/view/pokynmr |
NMRFAM-SPARKY | Lee, W. et al. (2015)12 | https://nmrfam.wisc.edu/nmrfam-sparky-distribution/ |
MXCuBE | Gabaldinho, J. et al. (2010)13 Oscarsson, M. et al. (2019)14 |
https://mxcube.github.io/mxcube/ |
XDS | Kabsch, W. (2010)15 | https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xds |
CCP4 | Winn, M. D. et al. (2011)16 | https://www.ccp4.ac.uk/ |
AIMLESS | Evans, P. R. and Murshudov, G. N. (2013)17 | https://www.ccp4.ac.uk/html/aimless.html |
REFMAC | Murshudov, G. N. et al. (2011)18 | https://www.ccp4.ac.uk/html/refmac5/description.html |
COOT | Emsley P. and Cowtan K. (2004)19 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
Magellan™ v 7.2 | https://lifesciences.tecan.com/software-magellan | |
GraphPad Prism | https://www.graphpad.com | |
Microsoft Excel | https://www.microsoft.com/en-us/microsoft-365/excel |