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7 protocols using ni nta superflow columns

1

Genetic Analysis of Streptomyces sp. RM-5-8

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The genetic DNA of Streptomyces sp. RM-5–8 was previously isolated and sequenced.20 (link) All primers were purchased from Integrated DNA Technologies, and E. coli 5α and BL21(DE3) competent cells were purchased from New England Biolabs. All DNA sequencing was conducted with the primers T7 promoter and T7 terminator (Table S3). Crystallization screens Index HT, PEGRx HT, Crystal Screen HT, and SaltRx HT were obtained from Hampton Research. Rigaku Wizard Classic screens were purchased from Molecular Dimensions. N-(2-hydroxyethyl)-piperazine-N′-ethanesulfonic acid (HEPES) buffer was purchased from Gold Biotechnology in a sodium salt form. All other reagents and chemicals were purchased from Sigma-Aldrich or Fisher Scientific and were used without further purification unless otherwise stated. PD-10 columns and Ni-NTA superflow columns were purchased from GE Healthcare. All solvents used were of ACS grade and purchased from Fisher Scientific or Pharmco-AAPER.
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2

Isolation and Characterization of Streptomyces sp. RM-5-8

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Streptomyces sp. RM-5-8 was isolated from the Ruth Mullins underground coal mine fire site and was provided by the University of Kentucky CPRI Natural Products Repository. All primers were purchased from Integrated DNA Technology, E. coli 5α and BL21(DE3) competent cells were purchased from New England Biolabs. Dimethylallyl S-thiolodiphosphate (DMSPP) was purchased from Echelon Biosciences. Polyethylene glycol 3350 (PEG 3350) and PEG 4000 both in the form of a 50% w/v solution, as well as crystallization screens Index HT, PEGRx HT, Crystal Screen HT and SaltRx HT were obtained from Hampton Research. Crystallization screens JCSG-plus HT-96, Morpheus and MIDAS were from Molecular Dimensions. All other reagents and chemicals were purchased from Sigma-Aldrich or Fisher Scientific and were used without further purification unless otherwise stated. PD-10 columns and Ni-NTA superflow columns were purchased from GE Healthcare. All non-native synthetic prenyl donors were synthesized as previously reported26 (link),27 (link). All solvents used were of ACS grade and purchased from Pharmco-AAPER. All DNA sequencing was conducted with the primers T7 promoter (5′-TAATACGACTCACTATAGGG-3′) and T7 terminator (5′-GCTAGTTATTGCTCAGCGG-3′). Daptomycin (DAP, Cubicin®) was generously provided by Merck.
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3

Farnesyl Monophosphate Purification

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Unless otherwise stated, all chemicals and reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA), Acros Organics (Fair Lawn, NJ, USA), Alfa-Aesar (Ward Hill, MA, USA), TCI (Portland, OR, USA), Ambeed (Arlington Heights, IL, USA), or AK Scientific (Union City, CA, USA) and were reagent grade or better. PD-10 and Ni-NTA super-flow columns were purchased from GE Healthcare (Piscat-away, NJ). Farnesyl monophosphate (44) was obtained from Isoprenoids LC (Tampa, FL, USA).
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4

Purification and Synthesis of Isoprenoid Compounds

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Dap was purchased from TCI (Portland, OR, USA), while all other reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA), Acros (New Jersey, USA), Alfa-Aesar (Ward Hill, MA, USA), or TCI (Portland, OR, USA) and were of reagent grade or better. PD-10 and Ni-NTA superflow columns were purchased from GE Healthcare (Piscataway, NJ). All alkyl-PPs were synthesized as previously reported (Bandari et al. 2019 (link); Bandari et al. 2017 (link); Johnson et al. 2020 (link)). The CdpNPT plasmid was generously provided by Prof. Jon S. Thorson (UK, Lexington, KY). All bacterial strains were obtained from the American Type Culture Collection (ATCC) or the Biodefense and Emerging Infections Research Resources Repository (BEI Resources).
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5

Purification of Farnesyl Monophosphate

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Unless otherwise stated, all chemicals and reagents were purchased from Sigma‐Aldrich (St. Louis, MO, USA), Acros Organics (Fair Lawn, NJ, USA), Alfa‐Aesar (Ward Hill, MA, USA), TCI (Portland, OR, USA), Ambeed (Arlington Heights, IL, USA), or AK Scientific (Union City, CA, USA) and were reagent grade or better. PD‐10 and Ni‐NTA super‐flow columns were purchased from GE Healthcare (Piscataway, NJ). Farnesyl monophosphate (44) was obtained from Isoprenoids LC (Tampa, FL, USA).
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6

Isolation and Characterization of Streptomyces sp. RM-5-8

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Streptomyces sp. RM-5-8 was isolated from the Ruth Mullins underground coal mine fire site and was provided by the University of Kentucky CPRI Natural Products Repository. All primers were purchased from Integrated DNA Technology, E. coli 5α and BL21(DE3) competent cells were purchased from New England Biolabs. Dimethylallyl S-thiolodiphosphate (DMSPP) was purchased from Echelon Biosciences. Polyethylene glycol 3350 (PEG 3350) and PEG 4000 both in the form of a 50% w/v solution, as well as crystallization screens Index HT, PEGRx HT, Crystal Screen HT and SaltRx HT were obtained from Hampton Research. Crystallization screens JCSG-plus HT-96, Morpheus and MIDAS were from Molecular Dimensions. All other reagents and chemicals were purchased from Sigma-Aldrich or Fisher Scientific and were used without further purification unless otherwise stated. PD-10 columns and Ni-NTA superflow columns were purchased from GE Healthcare. All non-native synthetic prenyl donors were synthesized as previously reported26 (link),27 (link). All solvents used were of ACS grade and purchased from Pharmco-AAPER. All DNA sequencing was conducted with the primers T7 promoter (5′-TAATACGACTCACTATAGGG-3′) and T7 terminator (5′-GCTAGTTATTGCTCAGCGG-3′). Daptomycin (DAP, Cubicin®) was generously provided by Merck.
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7

Purification and Characterization of Proteins

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Unless otherwise stated, all chemicals and reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA), Acros (New Jersey, USA), Alfa-Aesar (Ward Hill, MA, USA) or TCI (Portland, OR, USA) and were of reagent grade or better. The PD-10 column and Ni-NTA superflow columns were purchased from GE Healthcare (Piscataway, NJ). The HCT-116 cell line was purchased from ATTC (ATCC® CCL-247™).
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