2025-03-05 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2023-07-10 2025-02-12 2025-02-12 2025-03-05 Knut and Alice Wallenberg Foundation Sweden Sak Single Strand Annealing Protein from Staphylococcal Bacteriophage 80a - dCTD Debiasi-Anders G Mir-Sanchis I Annealase, SSAP, Single Strand Annealing, Single Strand Binding, Recombineering, Recombination, SaPI, Bacteriophage, Staphylococcal, Complex, SaPI induction, SaPI2, Mobile Genetic Element, MGE, PICI, Phage-Inducible Chromosomal Island, C18, Ring Debiasi-Anders G Qiao C Salim A Li N Mir-Sanchis I Phage parasites targeting phage homologous recombinases provide antiviral immunity. Nat Commun UK 16 1889 1889 2025 39987160 doi:10.1038/s41467-025-57156-3 2041-1723 8pq8 FULLOVERLAP 18-mer ring cryoEM structure of the 80a-Sak NTD in apo state 18-mer ring cryoEM structure of the 80a-Sak NTD in apo state 0 1 Staphylococcus phage 80alpha NA NA NA NA 0.46 Topoisomerase Staphylococcus phage 80alpha 0.019417621 1 Escherichia coli BL21(DE3) LEVO MKHHHHHHPMSDYDIPTTENLYFQGAMGMTEQTLFEQLNSKNVNDHTEQKNGLTYLAWSYAHQELKKIDPNYTVKVHEFP HPDINTENYFVPYLATPEGYFVQVSVTVKDSTETEWLPVLDFRNKSLAKGSATTFDINKAQKRCFVKASALHGLGLYIYN GEELPSASD C8CGY8 water 1.8015e-05 9 HOH singleParticle particle 1 8.1 20.0 Tris-HCl Tris-HCl pH 7.6 100.0 NaCl Sodium Chloride 1.0 DTT Dithiothreitol
20mM Tris-HCl pH 7.6, 100mM NaCl, 1mM DTT
 Quantifoil R2/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK IV
Monodisperse sample
 TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.6 2.9 190000.0 NITROGEN TFS FALCON 4i (4k x 4k) 1 4344 2.99 50.0 1 C18 3.21 FSC 0.143 CUT-OFF cryoSPARC 4.2.1 Local refinement job after symmetry expansion
Symmetry expanded to C18, multiplying the stack by 18, from 75703 to 1365300 particles.
75703 MAXIMUM LIKELIHOOD cryoSPARC 4.2.1 MAXIMUM LIKELIHOOD cryoSPARC 4.2.1 emd_17821.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 298.4 298.4 298.4 90.0 90.0 90.0 X Y Z -0.43517983 0.83766866 0.00014438934 0.019485127 0.746 0.746 0.746 0.085 AUTHOR A 1-141 AlphaFold in silico model
AlphaFold prediction was done locally. CTD residues of the full-length AlphaFold prediction were deleted before fiting with ChimeraX.
 RIGID BODY FIT
Fitting of the truncated AlphaFold prediction was done with ChimeraX and then subjected to real space refinement in PHENIX. The output was then repeatedly adjusted with Coot and verified in PHENIX.
REAL emd_17821_msk_1.map emd_17821_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 298.4 298.4 298.4 90.0 90.0 90.0 X Y Z -0.3355289 0.31145754 0.00015502294 0.021964349 0.746 0.746 0.746 AUTHOR emd_17821_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 298.4 298.4 298.4 90.0 90.0 90.0 X Y Z -0.24551272 0.29767433 0.00016217049 0.021901343 0.746 0.746 0.746 AUTHOR