Bacterial and Virus Strains |
E. coli BL21 (DE3) cells |
Invitrogen |
Cat. # C600003 |
Chemicals, Peptides, and Recombinant Proteins |
Ampicillin |
Fisher Scientific |
Cat. # BP1760–5 |
Isopropyl β-D-Thiogalactoside (IPTG) |
Sigma-Aldrich |
Cat. # I6758 |
Thrombin from bovine plasma |
Millipore |
Cat. # T7201 |
SYPRO-Orange |
Invitrogen |
Cat. # S6651 |
Amylose resin |
New England Biolabs |
Cat. # E8021L |
Ni-NTA resin |
QIAGEN |
Cat. # 30210 |
Superdex 75 Increase 10/300 GL |
GE Healthcare |
Cat. # 29148721 |
N-succinyl-Leu-Tyr-7-amido-4-methylcoumarin (sLY-AMC) |
Cayman Chemical |
Cat. # 10008120 |
Ac-Leu-Leu-Tyr-7-amino-4-trifluoromethylcoumarin (Ac-LLY-AFC) |
Fisher Scientific |
Cat. # MP3AFC11610 |
Trans-epoxysuccinyl-L-leucylamido-(4-guanidino)-butane (E64) |
Sigma-Aldrich |
Cat. # E3132 |
Human calpastatin B27 domain |
Calbiochem |
Cat. # 208902 |
ProPlex HT-96 Screen |
Molecular Dimensions |
Cat. # MD1–42 |
H-E(EDANS)-KIEIVRKKPIFKKATV-K(DABCYL)-OH |
Biopeptek |
Order #. BPT18360101–3 |
Deposited Data |
hCAPN5-PC |
This work |
PDB: 6P3Q |
rCAPN1-PC complexed with ZLAK-3001 |
Qian et al., 2008 |
PDB: 2R9C |
rCAPN1-PC complexed with ZLAK-3002 |
Qian et al., 2008 |
PDB: 2R9F |
rCAPN1-PC complexed with SNJ-1945 |
Cuerrier et al., 2006 |
PDB: 2G8J |
rCAPN1-PC complexed with leupeptin |
Moldoveanu et al., 2004a |
PDB: 1TL9 |
rCAPN1-PC complexed with E64 |
Moldoveanu et al., 2004a |
PDB: 1TLO |
rCAPN1-PC complexed with SNJ-1715 |
Cuerrier et al., 2006 |
PDB: 2G8E |
hCAPN1-PC |
Davis et al., 2007 |
PDB: 2ARY |
hCAPN1-PC complexed with ZLLYCH2F |
Li et al., 2006 |
PDB: 1ZCM |
hCAPN9-PC complexed with leupeptin |
Davis et al., 2007 |
PDB: 2P0R |
hCAPN9-PC |
Davis et al., 2007 |
PDB: 1ZIV |
rCAPN2-PC |
Moldoveanu et al., 2004a |
PDB: 1MDW |
rCAPN2 complexed with calpastatin |
Hanna et al., 2008 |
PDB: 3BOW |
rCAPN2-PC complexed with calpastatin |
Moldoveanu et al., 2004a |
PDB: 3DF0 |
hCAPN3-PC complexed with leupeptin |
Yeetal., 2018 |
PDB: 6BKJ |
hCAPN3-PC complexed with E64 |
Yeetal., 2018 |
PDB: 6BJD |
hCAPN3-PC C129S mutant |
Yeetal., 2018 |
PDB: 6BDT |
hCAPN3-PC C129A mutant |
Yeetal., 2018 |
PDB: 6BGP |
hCAPN8-PC |
Davis et al., 2006 |
PDB: 2NQA |
Recombinant DNA |
pMAL-C5X-hCAPN5-PC |
This work |
N/A |
pMAL-C5X-hCAPN5-PC mutants |
This work |
N/A |
pMAL-C5X-rCAPN1/5-PCDC2-loop |
This work |
N/A |
pMAL-C5X-rCAPN1/5-PCDC2-loop mutants |
This work |
N/A |
Software and Algorithms |
XDS |
Kabsch, 2010 |
http://xds.mpimf-heidelberg.mpg.de/ |
PHASER |
McCoy et al., 2007 |
http://www.ccp4.ac.uk/html/phaser.html |
PHENIX |
Adams et al., 2011 |
http://www.phenix-online.org/ |
REFMAC |
Murshudov et al., 2011 |
http://www.ccp4.ac.uk/html/refmac5.html |
COOT |
Emsley and Cowtan, 2004 |
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/ |
SasTool |
4–2 Beamline, SSRL |
https://www-ssrl.slac.stanford.edu/smb-saxs/content/documentation/sastool |
ATSAS |
Konarev et al., 2006 |
https://www.embl-hamburg.de/biosaxs/software.html |
ScAtter |
SIBLYS Beamline, ALS |
https://bl1231.als.lbl.gov/scatter/ |
CRYSOL |
Svergun et al., 1995 |
https://www.embl-hamburg.de/biosaxs/crysol.html |
DMAN |
Wang et al., 2012 |
http://www.structuralchemistry.org/pcsb/dman.php |
MODELLER |
Webb and Sali, 2017 |
https://salilab.org/modeller/ |
PDB-REDO |
Gore et al., 2017; Joosten et al., 2009
|
https://pdb-redo.eu/ |
PyMOL |
Schrödinger, LLC |
https://pymol.org/2/ |
HMMER 3.1 |
Finn et al., 2011 |
http://hmmer.org/ |
MAFFT v7 |
Katoh and Standley, 2013 |
https://mafft.cbrc.jp/alignment/software/ |
CD-HIT |
Li and Godzik, 2006 |
http://weizhongli-lab.org/cd-hit/ |
MaxAlign 1.1 |
Gouveia-Oliveira et al., 2007 |
http://www.cbs.dtu.dk/services/MaxAlign/ |
FastTree 2 |
Price et al., 2010 |
http://www.microbesonline.org/fasttree/ |
Geneious Tree Builder |
Geneious, LLC |
https://www.geneious.com/ |
ConSurf |
Armon et al., 2001; Ashkenazy et al., 2016
|
https://consurf.tau.ac.il/ |
MEGA7 |
Kumar et al., 2016 |
https://www.megasoftware.net/ |
EsPript |
Patrice Gouet and Xavier Robert |
http://espript.ibcp.fr/ |
GraphPad Prism |
GraphPad Software, Inc. |
https://www.graphpad.com/ |