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. 2021 Oct 21;81(20):4176–4190.e6. doi: 10.1016/j.molcel.2021.08.024
REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial strains
E.coli BL21-CodonPlus (DE3)-RIL Agilent Cat# 230245
Chemicals, peptides, and recombinant proteins
Propargylamine Sigma Aldrich Cat# P50900-5G
Ampicillin sodium Formedium Cat# AMP100
Gluthahione Sepharose 4B Abcam Cat# ab193267
Protease inhibitor cocktail tablets Thermo Scientific Cat# A32965
AEBSF Melford Laboratories Ltd Cat# A20010
IRDye 800CW Maleimide Li-Cor Cat# 929-80020
Precision Plus Protein™ standards Bio-Rad Cat:# 1610373
Pierce™ silver stain kit Thermo Scientific Cat# 24612
InstantBlue protein stain Abcam Cat# 119211
Ubiquitin This study N/A
MINDY1 and mutants This study N/A
MINDY2 and mutants This study N/A
E1, E2 enzymes This study N/A
Recombinant DNA
This study Table S3 (https://mrcppureagents.dundee.ac.uk/)
Deposited data
Structure factor and coordinates files RCSB-PDB MINDY1C137A:K48-Ub2: 6TUV, MINDY2C266A:K48-Ub2: 6Z7V, MINDY1P138A C137A:K48-Ub2: 6TXB, MINDY1Y114F: 6YJG, MINDY1T335D: 6Y6R, MINDY1P138A: 6Z90, MINDY2apo: 6Z49, MINDY2C266A:K48-Ub5: 7NPI.
SAXS data SASBDB MINDY2apo: SASDJ93, MINDY2-UbPrg: SASDJA3, MINDY2C266A:K48-Ub2: SASDJB3, MINDY2C266A:K48-Ub3: SASDJC3, MINDY2C266A:K48-Ub4: SASDJD3, MINDY2C266A:K48-Ub5: SASDJE3.
Original gel Scans Mendeley Data https://doi.org/10.17632/f6zfttw8zg
Software and algorithms
Prism Graphpad https://www.graphpad.com/scientific-software/prism/
Image Studio Lite LI-COR https://www.licor.com/bio/image-studio-lite/
XDS Kabsch, 2010 http://xds.mpimf-heidelberg.mpg.de/https://xds.mr.mpg.de
AIMLESS Evans and Murshudov, 2013 https://www.ccp4.ac.uk/html/aimless.html
CCP4 interface version 7.0.04 Winn et al., 2011 https://www.ccp4.ac.uk/
Phenix Liebschner et al., 2019 https://phenix-online.org/
COOT Emsley et al., 2010 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
REFMAC5 Murshudov et al., 2011 https://www.ccp4.ac.uk/html/refmac5/description.html
PDB-REDO Joosten et al., 2014 https://pdb-redo.eu
PyMOL Schrödinger https://pymol.org/2/
Adobe Illustrator Adobe https://www.adobe.com/uk/products/illustrator.html
MicroCal PEAQ-ITC Malvern Panalytical https://www.malvernpanalytical.com/en
Other
HisTrap FF 5ml Cytiva Cat# 17525501
HiPrep 26/10 desalting Cytiva Cat# 17508701
Resource Q 6ml Cytiva Cat # 17117901
HiLoad 16/60 Superdex 200 pg GE Healthcare Cat# 28989335
HiLoad 16/60 Superdex 75 pg Cytiva Cat# 28989333
Odyssey CLx fluorescence imager LI-COR RRID: SCR_014579
NuPAGE™ 4 – 12% Bis-Tris SDS-PAGE gels Thermo Scientific Cat# NP0321; Cat# WG1402; Cat# WG1403A