Recombinant:Article Title: Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains.
Article Snippet: .. GAATTCCTCGAC-6-FAM palindromic DNA with 7nt 5’ overhang and 3’-6-FAM37 p_7nt_5oh_3FAM37 Recombinant DNA pSG1 plasmid Rotem Sorek pSG1 pUC19 plasmid Norrander et al.49 Addgene #50005 UC Berkeley Macrolab vector 2-CT Addgene Addgene #29706 UC Berkeley Macrolab vector 2-BT Addgene Addgene #29666 UC Berkeley Macrolab vector 8B Addgene Addgene #37502 Software and algorithms GraphPad Prism version 10 GraphPad Software Version 10 ASTRA version 8 Wyatt Technology Version 8 cryoSPARC version 3.2 Structura Biotechnology https://cryosparc.com ChimeraX version 1.8 UCSF RBVI https://www.cgl.ucsf.edu/chimerax/ PyMOL version 2.5.5 Schrödinger Inc. https://pymol.org/2/ EPU 2 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/electron-microscopy/products/ software-em-3d-vis/epu-software.html AlphaFold 2 (ColabFold version 1.5.3) Mirdita et al.50 https://github.com/sokrypton/ColabFold COOT Emsley et al.51 https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot Phenix.refine Afonine et al.52 N/A MolProbity Davis et al.53 http://molprobity.biochem.duke.edu/ EMRinger Barad et al.54 https://github.com/fraser-lab/EMRinger PSI-BLAST Altschul et al.55 https://blast.ncbi.nlm.nih.gov/Blast. cgi?PAGE_TYPE=BlastSearch& PROGRAM=blastp&BLAST_ PROGRAMS=psiBlast CD-HIT Fu et al.56 https://sites.google.com/view/cd-hit Entrez Direct Kans57 https://www.ncbi.nlm.nih.gov/ books/NBK179288/ CLANS Frickey and Lupas58 http://ftp.tuebingen.mpg.de/pub/ protevo/CLANS/ HMMSCAN Eddy59,60 http://hmmer.org/ BLASTCLUST Dondoshansky and Wolf61 https://ftp.ncbi.nih.gov/blast/ documents/blastclust.html PROMALS3D Pei et al.62 http://prodata.swmed.edu/promals3d/ promals3d.php DALI Holm37 http://ekhidna2.biocenter.helsinki.fi/ dali/README.v5.html Corrplot Wei et al., 2021 https://cran.r-project.org/web/packages/ corrplot/vignettes/corrplot-intro.html APBS Jurrus et al.63 PyMOL plugin .. For cloning and molecular biology, Escherichia coli strain NovaBlue (EMD Millipore) was used.
Plasmid Preparation:Article Title: Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains.
Article Snippet: .. GAATTCCTCGAC-6-FAM palindromic DNA with 7nt 5’ overhang and 3’-6-FAM37 p_7nt_5oh_3FAM37 Recombinant DNA pSG1 plasmid Rotem Sorek pSG1 pUC19 plasmid Norrander et al.49 Addgene #50005 UC Berkeley Macrolab vector 2-CT Addgene Addgene #29706 UC Berkeley Macrolab vector 2-BT Addgene Addgene #29666 UC Berkeley Macrolab vector 8B Addgene Addgene #37502 Software and algorithms GraphPad Prism version 10 GraphPad Software Version 10 ASTRA version 8 Wyatt Technology Version 8 cryoSPARC version 3.2 Structura Biotechnology https://cryosparc.com ChimeraX version 1.8 UCSF RBVI https://www.cgl.ucsf.edu/chimerax/ PyMOL version 2.5.5 Schrödinger Inc. https://pymol.org/2/ EPU 2 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/electron-microscopy/products/ software-em-3d-vis/epu-software.html AlphaFold 2 (ColabFold version 1.5.3) Mirdita et al.50 https://github.com/sokrypton/ColabFold COOT Emsley et al.51 https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot Phenix.refine Afonine et al.52 N/A MolProbity Davis et al.53 http://molprobity.biochem.duke.edu/ EMRinger Barad et al.54 https://github.com/fraser-lab/EMRinger PSI-BLAST Altschul et al.55 https://blast.ncbi.nlm.nih.gov/Blast. cgi?PAGE_TYPE=BlastSearch& PROGRAM=blastp&BLAST_ PROGRAMS=psiBlast CD-HIT Fu et al.56 https://sites.google.com/view/cd-hit Entrez Direct Kans57 https://www.ncbi.nlm.nih.gov/ books/NBK179288/ CLANS Frickey and Lupas58 http://ftp.tuebingen.mpg.de/pub/ protevo/CLANS/ HMMSCAN Eddy59,60 http://hmmer.org/ BLASTCLUST Dondoshansky and Wolf61 https://ftp.ncbi.nih.gov/blast/ documents/blastclust.html PROMALS3D Pei et al.62 http://prodata.swmed.edu/promals3d/ promals3d.php DALI Holm37 http://ekhidna2.biocenter.helsinki.fi/ dali/README.v5.html Corrplot Wei et al., 2021 https://cran.r-project.org/web/packages/ corrplot/vignettes/corrplot-intro.html APBS Jurrus et al.63 PyMOL plugin .. For cloning and molecular biology, Escherichia coli strain NovaBlue (EMD Millipore) was used.
Software:Article Title: Bacterial Shedu immune nucleases share a common enzymatic core regulated by diverse sensor domains.
Article Snippet: .. GAATTCCTCGAC-6-FAM palindromic DNA with 7nt 5’ overhang and 3’-6-FAM37 p_7nt_5oh_3FAM37 Recombinant DNA pSG1 plasmid Rotem Sorek pSG1 pUC19 plasmid Norrander et al.49 Addgene #50005 UC Berkeley Macrolab vector 2-CT Addgene Addgene #29706 UC Berkeley Macrolab vector 2-BT Addgene Addgene #29666 UC Berkeley Macrolab vector 8B Addgene Addgene #37502 Software and algorithms GraphPad Prism version 10 GraphPad Software Version 10 ASTRA version 8 Wyatt Technology Version 8 cryoSPARC version 3.2 Structura Biotechnology https://cryosparc.com ChimeraX version 1.8 UCSF RBVI https://www.cgl.ucsf.edu/chimerax/ PyMOL version 2.5.5 Schrödinger Inc. https://pymol.org/2/ EPU 2 Thermo Fisher Scientific https://www.thermofisher.com/us/en/ home/electron-microscopy/products/ software-em-3d-vis/epu-software.html AlphaFold 2 (ColabFold version 1.5.3) Mirdita et al.50 https://github.com/sokrypton/ColabFold COOT Emsley et al.51 https://www2.mrc-lmb.cam.ac.uk/ personal/pemsley/coot Phenix.refine Afonine et al.52 N/A MolProbity Davis et al.53 http://molprobity.biochem.duke.edu/ EMRinger Barad et al.54 https://github.com/fraser-lab/EMRinger PSI-BLAST Altschul et al.55 https://blast.ncbi.nlm.nih.gov/Blast. cgi?PAGE_TYPE=BlastSearch& PROGRAM=blastp&BLAST_ PROGRAMS=psiBlast CD-HIT Fu et al.56 https://sites.google.com/view/cd-hit Entrez Direct Kans57 https://www.ncbi.nlm.nih.gov/ books/NBK179288/ CLANS Frickey and Lupas58 http://ftp.tuebingen.mpg.de/pub/ protevo/CLANS/ HMMSCAN Eddy59,60 http://hmmer.org/ BLASTCLUST Dondoshansky and Wolf61 https://ftp.ncbi.nih.gov/blast/ documents/blastclust.html PROMALS3D Pei et al.62 http://prodata.swmed.edu/promals3d/ promals3d.php DALI Holm37 http://ekhidna2.biocenter.helsinki.fi/ dali/README.v5.html Corrplot Wei et al., 2021 https://cran.r-project.org/web/packages/ corrplot/vignettes/corrplot-intro.html APBS Jurrus et al.63 PyMOL plugin .. For cloning and molecular biology, Escherichia coli strain NovaBlue (EMD Millipore) was used.
|
Addgene inc is a verified supplier 