HEADER RECOMBINATION 10-JUL-23 8PQ8 TITLE SAK SINGLE STRAND ANNEALING PROTEIN FROM STAPHYLOCOCCAL BACTERIOPHAGE TITLE 2 80A - DCTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOPOISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SAK SINGLE-STRAND ANNEALING PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS PHAGE 80ALPHA; SOURCE 3 ORGANISM_TAXID: 2911440; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_ORGAN: NA; SOURCE 8 EXPRESSION_SYSTEM_TISSUE: NA; SOURCE 9 EXPRESSION_SYSTEM_CELL: NA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ANNEALASE, SSAP, SINGLE STRAND ANNEALING, SINGLE STRAND BINDING, KEYWDS 2 RECOMBINEERING, RECOMBINATION, SAPI, BACTERIOPHAGE, STAPHYLOCOCCAL, KEYWDS 3 COMPLEX, SAPI INDUCTION, SAPI2, MOBILE GENETIC ELEMENT, MGE, PICI, KEYWDS 4 PHAGE-INDUCIBLE CHROMOSOMAL ISLAND, C18, RING EXPDTA ELECTRON MICROSCOPY AUTHOR G.DEBIASI-ANDERS,I.MIR-SANCHIS REVDAT 2 05-MAR-25 8PQ8 1 JRNL REVDAT 1 12-FEB-25 8PQ8 0 JRNL AUTH G.DEBIASI-ANDERS,C.QIAO,A.SALIM,N.LI,I.MIR-SANCHIS JRNL TITL PHAGE PARASITES TARGETING PHAGE HOMOLOGOUS RECOMBINASES JRNL TITL 2 PROVIDE ANTIVIRAL IMMUNITY. JRNL REF NAT COMMUN V. 16 1889 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 39987160 JRNL DOI 10.1038/S41467-025-57156-3 REMARK 2 REMARK 2 RESOLUTION. 3.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, UCSF REMARK 3 CHIMERAX, PHENIX, COOT, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : FITTING OF THE TRUNCATED ALPHAFOLD PREDICTION REMARK 3 WAS DONE WITH CHIMERAX AND THEN SUBJECTED TO REAL SPACE REMARK 3 REFINEMENT IN PHENIX. THE OUTPUT WAS THEN REPEATEDLY ADJUSTED REMARK 3 WITH COOT AND VERIFIED IN PHENIX. REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.210 REMARK 3 NUMBER OF PARTICLES : 75703 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: SYMMETRY EXPANDED TO C18, MULTIPLYING THE STACK BY REMARK 3 18, FROM 75703 TO 1365300 PARTICLES. REMARK 4 REMARK 4 8PQ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131753. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : 18-MER RING CRYOEM STRUCTURE OF REMARK 245 THE 80A-SAK NTD IN APO STATE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.10 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4344 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2900.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 190000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 18-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 18-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.939700 -0.341999 0.000000 60.02604 REMARK 350 BIOMT2 2 0.341999 0.939700 0.000001 -42.03273 REMARK 350 BIOMT3 2 0.000000 -0.000001 1.000000 0.00015 REMARK 350 BIOMT1 3 0.766019 -0.642817 -0.000005 130.81855 REMARK 350 BIOMT2 3 0.642817 0.766019 -0.000001 -60.98850 REMARK 350 BIOMT3 3 0.000004 -0.000003 1.000000 -0.00051 REMARK 350 BIOMT1 4 0.500011 -0.866019 -0.000004 203.81498 REMARK 350 BIOMT2 4 0.866019 0.500011 -0.000002 -54.60921 REMARK 350 BIOMT3 4 0.000004 -0.000002 1.000000 -0.00047 REMARK 350 BIOMT1 5 0.173603 -0.984816 -0.000002 270.22907 REMARK 350 BIOMT2 5 0.984816 0.173603 -0.000002 -23.62560 REMARK 350 BIOMT3 5 0.000002 -0.000001 1.000000 -0.00030 REMARK 350 BIOMT1 6 -0.173604 -0.984816 -0.000001 322.04565 REMARK 350 BIOMT2 6 0.984816 -0.173604 -0.000003 28.16424 REMARK 350 BIOMT3 6 0.000003 -0.000001 1.000000 -0.00038 REMARK 350 BIOMT1 7 -0.500011 -0.866019 -0.000001 353.01287 REMARK 350 BIOMT2 7 0.866019 -0.500011 -0.000004 94.59890 REMARK 350 BIOMT3 7 0.000003 -0.000002 1.000000 -0.00029 REMARK 350 BIOMT1 8 -0.766019 -0.642818 0.000002 359.40680 REMARK 350 BIOMT2 8 0.642818 -0.766019 -0.000004 167.58221 REMARK 350 BIOMT3 8 0.000005 -0.000002 1.000000 -0.00068 REMARK 350 BIOMT1 9 -0.939700 -0.342001 0.000000 340.42608 REMARK 350 BIOMT2 9 0.342001 -0.939700 0.000000 238.38017 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -0.00003 REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 298.40000 REMARK 350 BIOMT2 10 0.000000 -1.000000 0.000000 298.40000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 -0.939700 0.342000 0.000000 238.37964 REMARK 350 BIOMT2 11 -0.342000 -0.939700 -0.000001 340.42697 REMARK 350 BIOMT3 11 0.000000 -0.000001 1.000000 0.00013 REMARK 350 BIOMT1 12 -0.766020 0.642816 0.000005 167.57760 REMARK 350 BIOMT2 12 -0.642816 -0.766020 0.000000 359.40819 REMARK 350 BIOMT3 12 0.000004 -0.000003 1.000000 -0.00035 REMARK 350 BIOMT1 13 -0.500011 0.866019 0.000003 94.59464 REMARK 350 BIOMT2 13 -0.866019 -0.500011 0.000002 353.01258 REMARK 350 BIOMT3 13 0.000004 -0.000002 1.000000 -0.00055 REMARK 350 BIOMT1 14 -0.173700 0.984799 -0.000001 28.19118 REMARK 350 BIOMT2 14 -0.984799 -0.173700 0.000000 322.04061 REMARK 350 BIOMT3 14 0.000000 0.000001 1.000000 -0.00003 REMARK 350 BIOMT1 15 0.173602 0.984816 0.000001 -23.62781 REMARK 350 BIOMT2 15 -0.984816 0.173602 0.000003 270.22776 REMARK 350 BIOMT3 15 0.000003 -0.000002 1.000000 -0.00039 REMARK 350 BIOMT1 16 0.500010 0.866019 0.000000 -54.61099 REMARK 350 BIOMT2 16 -0.866019 0.500010 0.000003 203.81260 REMARK 350 BIOMT3 16 0.000003 -0.000002 1.000000 -0.00029 REMARK 350 BIOMT1 17 0.766020 0.642816 -0.000002 -60.98886 REMARK 350 BIOMT2 17 -0.642816 0.766020 0.000004 130.81479 REMARK 350 BIOMT3 17 0.000004 -0.000002 1.000000 -0.00051 REMARK 350 BIOMT1 18 0.939700 0.341999 0.000000 -42.03351 REMARK 350 BIOMT2 18 -0.341999 0.939700 0.000000 60.02679 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 0.00001 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -27 REMARK 465 LYS A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 HIS A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 PRO A -19 REMARK 465 MET A -18 REMARK 465 SER A -17 REMARK 465 ASP A -16 REMARK 465 TYR A -15 REMARK 465 ASP A -14 REMARK 465 ILE A -13 REMARK 465 PRO A -12 REMARK 465 THR A -11 REMARK 465 THR A -10 REMARK 465 GLU A -9 REMARK 465 ASN A -8 REMARK 465 LEU A -7 REMARK 465 TYR A -6 REMARK 465 PHE A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLU A 3 REMARK 465 ASN A 132 REMARK 465 GLY A 133 REMARK 465 GLU A 134 REMARK 465 GLU A 135 REMARK 465 LEU A 136 REMARK 465 PRO A 137 REMARK 465 SER A 138 REMARK 465 ALA A 139 REMARK 465 SER A 140 REMARK 465 ASP A 141 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17821 RELATED DB: EMDB REMARK 900 SAK SINGLE STRAND ANNEALING PROTEIN FROM STAPHYLOCOCCAL REMARK 900 BACTERIOPHAGE 80A - DCTD DBREF 8PQ8 A 1 141 UNP C8CGY8 C8CGY8_9CAUD 1 141 SEQADV 8PQ8 MET A -27 UNP C8CGY8 INITIATING METHIONINE SEQADV 8PQ8 LYS A -26 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 HIS A -25 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 HIS A -24 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 HIS A -23 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 HIS A -22 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 HIS A -21 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 HIS A -20 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 PRO A -19 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 MET A -18 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 SER A -17 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 ASP A -16 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 TYR A -15 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 ASP A -14 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 ILE A -13 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 PRO A -12 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 THR A -11 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 THR A -10 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 GLU A -9 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 ASN A -8 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 LEU A -7 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 TYR A -6 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 PHE A -5 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 GLN A -4 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 GLY A -3 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 ALA A -2 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 MET A -1 UNP C8CGY8 EXPRESSION TAG SEQADV 8PQ8 GLY A 0 UNP C8CGY8 EXPRESSION TAG SEQRES 1 A 169 MET LYS HIS HIS HIS HIS HIS HIS PRO MET SER ASP TYR SEQRES 2 A 169 ASP ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY ALA SEQRES 3 A 169 MET GLY MET THR GLU GLN THR LEU PHE GLU GLN LEU ASN SEQRES 4 A 169 SER LYS ASN VAL ASN ASP HIS THR GLU GLN LYS ASN GLY SEQRES 5 A 169 LEU THR TYR LEU ALA TRP SER TYR ALA HIS GLN GLU LEU SEQRES 6 A 169 LYS LYS ILE ASP PRO ASN TYR THR VAL LYS VAL HIS GLU SEQRES 7 A 169 PHE PRO HIS PRO ASP ILE ASN THR GLU ASN TYR PHE VAL SEQRES 8 A 169 PRO TYR LEU ALA THR PRO GLU GLY TYR PHE VAL GLN VAL SEQRES 9 A 169 SER VAL THR VAL LYS ASP SER THR GLU THR GLU TRP LEU SEQRES 10 A 169 PRO VAL LEU ASP PHE ARG ASN LYS SER LEU ALA LYS GLY SEQRES 11 A 169 SER ALA THR THR PHE ASP ILE ASN LYS ALA GLN LYS ARG SEQRES 12 A 169 CYS PHE VAL LYS ALA SER ALA LEU HIS GLY LEU GLY LEU SEQRES 13 A 169 TYR ILE TYR ASN GLY GLU GLU LEU PRO SER ALA SER ASP FORMUL 2 HOH *9(H2 O) HELIX 1 AA1 THR A 5 SER A 12 1 8 HELIX 2 AA2 ALA A 29 ASP A 41 1 13 HELIX 3 AA3 THR A 105 ALA A 122 1 18 HELIX 4 AA4 GLY A 127 TYR A 131 5 5 SHEET 1 AA1 2 THR A 19 LYS A 22 0 SHEET 2 AA1 2 LEU A 25 LEU A 28 -1 O TYR A 27 N GLU A 20 SHEET 1 AA2 3 THR A 45 VAL A 48 0 SHEET 2 AA2 3 GLY A 71 VAL A 80 -1 O SER A 77 N LYS A 47 SHEET 3 AA2 3 LEU A 66 THR A 68 -1 N LEU A 66 O PHE A 73 SHEET 1 AA3 3 THR A 45 VAL A 48 0 SHEET 2 AA3 3 GLY A 71 VAL A 80 -1 O SER A 77 N LYS A 47 SHEET 3 AA3 3 SER A 83 PRO A 90 -1 O GLU A 85 N VAL A 78 SHEET 1 AA4 2 PHE A 51 PRO A 52 0 SHEET 2 AA4 2 PHE A 62 VAL A 63 -1 O VAL A 63 N PHE A 51 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000