Appendix 1—key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Escherichia coli) | BL21-AI | Invitrogen | Recombinant protein expression | |
| Strain, strain background (Escherichia coli) | AG1/pCA24N (gfp-)::speD | ASKA library doi:10.1093/dnares/dsi012 | JW0116-AP | |
| Strain, strain background (Escherichia coli K-12 MG1655) | KEIO:1693 or DA41453 | KEIO collection doi:10.1038/msb4100050 | ||
| Strain, strain background (constructed strain E. coli K-12 MG1655) |
DA67469 | This paper | The native T3 SAM hydrolase was inserted on the chromosome replacing the araBAD coding region and is under the control of ParaBAD | |
| Strain, strain background (constructed strain E. coli K-12 MG1655) |
DA67467 | This paper | The T3 SAM hydrolase variant E67Q was inserted on the chromosome replacing the araBAD coding region and is under the control of ParaBAD | |
| Strain, strain background (constructed strain E. coli K-12 MG1655) |
DA67468 | This paper | The T3 SAM hydrolase variant E68Q was inserted on the chromosome replacing the araBAD coding region and is under the control of ParaBAD | |
| Gene (environmental phage DNA cloned on plasmid pCA24N) |
DA48932 | doi:10.1038/s41559-018-0568-5 | KY556690.1 | Resynthesized Svi3-3 gene consisting of E. coli optimized codons (Eurofins) was cloned into pCA24N |
| Gene (environmental phage DNA cloned on plasmid pCA24N) |
DA57022 | This paper | A variant of the resynthesized Svi3-3 (E69Q) was cloned into pCA24N | |
| Gene (environmental phage DNA cloned on plasmid pCA24N) |
DA57021 | This paper | A variant of the resynthesized Svi3-3 (E69A) was cloned into pCA24N | |
| Gene (environmental phage DNA cloned on plasmid pCA24N) |
DA51653 | This paper | Similar to DA50765 from Jerlström Hultqvist et al., 2018 | |
| Gene (environmental phage DNA cloned on plasmid pCA24N) |
DA67997 | This paper | A variant of the Orf1(E50Q) was cloned into pCA24N | |
| Gene (environmental phage DNA cloned on plasmid pCA24N) |
DA67998 | This paper | A variant of the Orf1(D51N) was cloned into pCA24N | |
| Gene (environmental phage DNA cloned on plasmid pRD2) | DA57899 | doi:10.1038/s41559-018-0568-5 | T3 SAM hydrolase was cloned into pCA24N | |
| Gene (environmental phage DNA cloned on plasmid pRD2) | DA58126 | This paper | A variant of the T3 SAM hydrolase (E67Q) was cloned into pCA24N | |
| Gene (environmental phage DNA cloned on plasmid pRD2) | DA58127 | This paper | A variant of the T3 SAM hydrolase (E68Q) was cloned into pCA24N | |
| Recombinant DNA reagent | pCA24N | other | AB052891 | Plasmid used as backbone in ASKA library |
| Recombinant DNA reagent | pRD2 | other | MH298521.1 | |
| Recombinant DNA reagent | pSIM5-Tet plasmid | doi:10.1111/j.1365-2958.2011.07657.x | λ-red recombineering plasmid | |
| Recombinant DNA reagent | pEXP5-NT/TOPO | Invitrogen | V96005 | |
| Recombinant DNA reagent | pEXP5-NT-Svi3-3_d19 | This paper | Truncated variant of Svi3-3 cloned in pEXP5-NT | |
| Recombinant DNA reagent | pEXP5-NT-Svi3-3_d19_Y58F | This paper | Mutated variant of the truncated Svi3-3 cloned in pEXP5-NT | |
| Recombinant DNA reagent | pEXP5-NT-Svi3-3_d19_E69Q | This paper | Mutated variant of the truncated Svi3-3 cloned in pEXP5-NT | |
| Recombinant DNA reagent | pEXP5-NT-Svi3-3_d19_E69A | This paper | Mutated variant of the truncated Svi3-3 cloned in pEXP5-NT | |
| Recombinant DNA reagent | pEXP5-NT-Svi3-3_d19_E105Q | This paper | Mutated variant of the truncated Svi3-3 cloned in pEXP5-NT | |
| Recombinant DNA reagent | pEXP5-NT-Orf1 | doi: 10.1038/s41559-018-0568-5 | ||
| Recombinant protein | Pfu DNA polymerase | Thermo scientific | #EP0501 | |
| Recombinant protein | TEVSH protease | doi: 10.1016/j.jbiotec.2005.08.006 | RRID:Addgene_125194 | |
| Chemical compound | S-(5’-Adenosyl)-L-methionine p-toluenesulfonate salt | Sigma-Aldrich | A2408 | |
| Chemical compound | S-(5’-Adenosyl)-L-homocysteine | Sigma-Aldrich | A9384 | |
| Chemical compound | 5’-Deoxy-5’-(methylthio)adenosine | Sigma-Aldrich | D5011 | |
| Chemical compound | L-Homoserine lactone hydrochloride | Sigma-Aldrich | H7890 | |
| Chemical compound | cOmplete EDTA-free protease inhibitor | Roche | Sigma-Aldrich 11873580001 | |
| Chemical compound | SYPRO Orange | Invitrogen | S6651 | |
| Chemical compound | Ninhydrin | Sigma-Aldrich | 151173 | |
| Software, algorithm | XDS | doi:10.1107/S0907444909047337 | RRID: SCR_015652 | |
| Software, algorithm | Arcimboldo_lite | doi:10.1038/nmeth.1365 | ||
| Software, algorithm | Phaser | doi:10.1107/S0021889807021206 | RRID:SCR_014219 | |
| Software, algorithm | Coot | doi:10.1107/S0907444910007493 | RRID:SCR_014222 | |
| Software, algorithm | phenix.refine | doi:10.1107/S0907444912001308 | RRID:SCR_016736 | |
| Software, algorithm | PyMol | Schrödinger LLC | Version 2.2; RRID:SCR_000305 | |
| Software, algorithm | ScÅtter | doi:10.1107/S0021889810008289 | RRID:SCR_017271 | |
| Software, algorithm | Primus | doi:10.1107/S0021889803012779 | RRID:SCR_015648 | |
| Software, algorithm | SAXSMoW | doi:10.1002/pro.3528 | RRID:SCR_018137 | |
| Software, algorithm | PROMALS3D | doi:10.1093/nar/gkn072 | RRID:SCR_018161 | |
| Software, algorithm | ESPript | doi:10.1093/nar/gkg556 | RRID:SCR_006587 | |
| Software, algorithm | Desmond | D E Shaw Research ISBN: 978-0-7695-2700-0 |
RRID:SCR_014575 | |
| Software, algorithm | Maestro | Schrodinger, LLC, New York | ||
| Software, algorithm | Protein Preparation wizard | https://doi.org/10.1007/s10822-013-9644-8 | RRID:SCR_016749 | |
| Software, algorithm | Glide | https://doi.org/10.1021/jm051256o | RRID:SCR_000187 | |
| Software, algorithm | Gaussian09 | Gaussian 09, Revision E.01 | RRID:SCR_014897 | |
| Software, algorithm | OPLS3 | https://doi.org/10.1021/acs.jctc.5b00864 | ||
| Software, algorithm | Topspin | Bruker Corp. | Version 4.0.6 RRID:SCR_014227 |
|
| Software, algorithm | MestReNova | Mestrelab Research S. L. | Version 14.1.2–25024 | |
| Other | Ni Sepharose6 Fast Flow | GE Healthcare | GE17-5318-02 | |
| Other | HiLoad 16/60 Superdex 75 pg | GE Healthcare | GE28-9893-33 | |
| Other | TLC Silica gel 60 F254 | Merck / Supelco | 1.05554.0001 |