2026-09-16 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-12-23 2026-09-16 2026-09-16 2026-09-16 Research Council of Lithuania S-MIP-22-13 Lithuania Focus map of chain C of the bacterial antiviral defense protein PD-T7-3 (H122A) in complex with single-stranded DNA Puteikiene R Sasnauskas G HEPN domain, nuclease, bacterial antiviral protein, PD-T7-3, ANTIVIRAL PROTEIN Puteikiene R Vassallo CN Songailiene I Juozapaitis J Silanskas A Laub MT Sasnauskas G Standalone anti-phage HEPN nuclease PD-T7-3 is activated by ssDNA for tRNA cleavage To Be Published 0353 EMDB EMD-56167 associated EM volume Bacterial antiviral defense protein PD-T7-3 (H122A) from Escherichia coli strain ECOR30 in complex with single-stranded DNA Bacterial antiviral defense protein PD-T7-3 (H122A) from Escherichia coli strain ECOR30 in complex with single-stranded DNA 0 1 2 Escherichia coli ECOR30 Bacterial antiviral defense protein PD-T7-3 from Escherichia coli strain ECOR30, HEPN active site mutant H122A Escherichia coli ECOR30 Escherichia coli BL21(DE3) LEVO MDVRIFSLESQKSKIYDRRTRKYFEEVYKSYANGCYRSATVMLWSVVVCDIIFKLQELRDVHNDAVAEKILLEIEALQNDDPYSPKWEKELIKRVFERTQLLDTASNHKVLLIQKHRHLSAAPVISDEDTLFEPTQEMIRSDIRNSIEVILSKPPFMSQKILSTFVADLEKVKDLFPSDNALKKYLDVKYFKSLNKEVLVKIFKGLWKFSFRSEEAKPLENREINIRAMKLIFEKDRQAMVDSVKAETAYYSNISNNHDAIKALIEFISMEKEIYNALDDSVKELIKPIIKDNISYFGIAFFISESPEEHINRVTKRISEKYYKKYGDNGNFLNQQHLAIFKNVCSELGLESEYRDFGIACFINSADFERADIYFDRFIDKDLANYSSEQMLTLLEGANKNNQCYWRNRSRNGNDSIRILKAAKNKLPDGFDFSKYDNLPVDKIDHVLEEDVGERFESGHHHHHH single-stranded DNA synthetic construct (DA)(DC)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DA)(DA)(DT)(DT)(DA)(DT)(DA)(DG)(DT)(DT)(DC)(DC)(DT)(DA)(DT)(DT)(DA)(DA)(DA)(DT)(DT)(DC)(DT)(DC)(DG) DNA singleParticle particle 7.5 Quantifoil R1.2/1.3 COPPER 300 ETHANE TFS GLACIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 1.0 2.0 92000.0 NITROGEN FEI FALCON III (4k x 4k) COUNTING 1 3114 29.0 1 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION cryoSPARC ab-initio model 2.93 FSC 0.143 CUT-OFF cryoSPARC 4.7.1
Number of particles after D2 symmetry expansion.
452827 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD emd_56167.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 440.0 440.0 440.0 90.0 90.0 90.0 X Y Z -0.3826472 1.1531667 -0.0027919034 0.010450113 1.1 1.1 1.1 0.07 AUTHOR focus map (cryoSPARC local refinement of chain C) AlphaFold in silico model emd_56167_msk_1.map emd_56167_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 440.0 440.0 440.0 90.0 90.0 90.0 X Y Z -0.75824666 1.2992332 -0.0007941594 0.014967316 1.1 1.1 1.1 AUTHOR half map 2 emd_56167_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 440.0 440.0 440.0 90.0 90.0 90.0 X Y Z -0.7014104 1.871618 -0.0007986209 0.014950139 1.1 1.1 1.1 AUTHOR half map 1