2025-05-21 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2024-02-13 2024-10-30 2024-10-30 2025-05-21 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM105691 United States BsaXI -- Type IIB R-M system Shen BW Stoddard BL R-M system, restriction nucleases, Type IIB, protein-DNA complex, BsaXI., ANTIMICROBIAL PROTEIN Shen BW Stoddard BL Atomic insights into the mechanism of DNA recognition and methylation by type IIB restriction-modification system: CryoEM structures of DNA free and cognate DNA bound BsaXI. To Be Published 0353 8w0p FULLOVERLAP heterotrimers of RM fusion and S subunit heterotrimers of RM fusion and S subunit 0 1 2
reconstituted RM and S subunits of type IIB R-M systems.
Geobacillus stearothermophilus Cpw230 0.59 RM.BsaXI Geobacillus stearothermophilus Cpw230 0.10719523399999999
RM fusion protein
2 Escherichia coli LEVO MKNWQRIVEAKLEQQKHKVAEISLENGTVNYSKKIKHNRNLKALTGDEEIVRAFLIDRLVNELDYKPEYLETEKEYTIKG GHSKINPRVDVLVKDDKGNPFFFIEVKAPNKFEEDKDEIEGQLFALAQAEERDFKTKVKYLVYYTVELIDDEIVDRAIII DFEKYPTYTDWSNGGFISTGTELTAGYGEPKKQPLIKGHEKYDLRVRIDREEIEGLGRNLHNVLWGGGGTNDSEIFYSLV NIILAKIQDEYEKEDGQEYDFQVYQYGDNVESPQKLFDRINALYKRALREQLNVTDEQKIAEDNVINRNKFPLNKLVYTV QALESLSFLEGRNSLDGKDILGDFFESIIRDGFKQTKGQFFTPTPIVKFILYALQLDKLAIDRLNNDRELPLIIDPSAGS GTFLIEAMKLITKEVKYKQNHKVKSSRQITKRFEELFMPDHNENKWAREYLYGCEINFDLGTASKVNMILHGDGSANIFV QDGLLPFRFYVKETSPNYLETASPDALYGDKEVNGKFDVVVSNPPFSVDLDTQTQREVRNAFLFGDKKNSENLFIERYYQ LLKEGGRLGVVLPESVFDTTENKYIRLFIFKYFKVKAVVSLPQVTFEPFTSTKTSLLFAQKKTKEEVEQWNELWDKYGKE WSLLKTRINDYFSYFVKGRPLNKKWAPDVVKDIQEGNEDNIRKNIFRFLKDHIKEEDKNLEIKDLLIKYAEEISSISKHE KETDVFGFYNAWWVFGEVAKELDYPIFMAEAENVGYKRTKKGEKPMPNDLYDLEYAPSTLDCEKVLSSFDIEINALEASK TKLSVEKGLLEEKLKDKEDKENEKIQKRLNKISELLETIENQLDSIRSKKLEVEGILEKYYENNKLKEEYSERDDEELIN HFKHGVLYQYRSEDILLRNKTVHKILDEIRQGVIWD A0A4D7QEP1 2.1.1.72 S.BsaXI Geobacillus stearothermophilus Cpw230 0.055038824 1 Escherichia coli LEVO MGLIQRRNFSTFASEPSVRFDFNYMKSVTPTTEEYYTYKSLFEVVPSTVPTLDESEPFKYAEIGHVSKNGEVFPVTLSFE DRDELNEDLFKKIEKGDIFLPERGNILISAIRPYLNKIVLIKEDDKTDIYFTKAFIQIKPLINSRILYYALRTIFSEKIN AVSRQGKGYPTLKEDDLKTIQFSKKVIDNLLAKEEELISNIDALEKDIKELKSIQRSKKEIVDEVFSSHFNINMVELMAL DSQRRVDVGLSSISSLNSTIRYSYRWNKMKLIQKYLYRDIDCIEPLGKYILSSNNGWSPESVVGGEGIPILGQEHLEFDG VLNVSPTKATTKTKNNMENFFIQEGDLFISRGNTVDLVGLACVVETEVTEDIIYPDLYIRLKIDEKVIHKKYLALLFNSF FGRLYFKYVSKGKNQTMVKISSNELLNYYLPIPPMEEQLEIVGKIEEQIGAQNEIEKQIEEKRNQIRVIIEETARS A0A226QBA7 S-ADENOSYLMETHIONINE 0.000398437 2 SAM singleParticle particle 0.35 8.0
20 mM TrisHCl, ph 8.0, 2 mM CaCl2, 150 mM NaCl
 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 95 298 FEI VITROBOT MARK IV
Monodisperse
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.2 5.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 2-50 1 6227 2.0 40.0 1 2487316 cryoSPARC 3.32 PHASE FLIPPING AND AMPLITUDE CORRECTION The alpha carbon trace of a phyr2 structure prediction for the methyl transferase domain was ducked into the refined map and was used as reference for manual building of the RM model, including the alpha carbon of the Knocker and Paddle domains. C1 FOURIER SPACE 3.26 FSC 0.143 CUT-OFF cryoSPARC 3.32 194038 ANGULAR RECONSTITUTION cryoSPARC 3.32 ANGULAR RECONSTITUTION cryoSPARC 3.32 2 cryoSPARC 3.32 emd_43711.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 414.336 414.336 414.336 90.0 90.0 90.0 X Y Z -0.36282444 0.9502708 0.00029064124 0.017084736 1.079 1.079 1.079 0.15 AUTHOR cryosparc2_P35_J607, app BsaXI emd_43711_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 414.336 414.336 414.336 90.0 90.0 90.0 X Y Z -0.62618816 1.1922152 0.00041282797 0.06762123 1.079 1.079 1.079 AUTHOR apoBsaXI, half_map_A CS_P35_607_A emd_43711_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 414.336 414.336 414.336 90.0 90.0 90.0 X Y Z -0.522725 1.1858647 0.00041356328 0.06778512 1.079 1.079 1.079 AUTHOR apoBsaXI; half_map_B CS_P35_J607_B