HEADER DNA BINDING PROTEIN 19-AUG-25 9SF8 TITLE MONOMERIC FORM OF THE STREPTOCOCCUS PYOGENES NUCLEASE A (SPNA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE/EXONUCLEASE/PHOSPHATASE DOMAIN-CONTAINING COMPND 3 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 GENE: SPY_0747; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STREPTOCOCCUS PYOGENES, NUCLEASE, SPNA, DNA BINDING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR I.A.BENNIG,J.STROBAEK,R.MARMEDE,A.SELLERBERG,A.NEUMANN,A.FRIAES, AUTHOR 2 M.RAMIREZ,M.HALL,M.COLLIN,L.MALMSTROM,S.EKSTROM,I.FRICK,L.BJORCK, AUTHOR 3 L.J.HAPPONEN REVDAT 1 02-SEP-26 9SF8 0 JRNL AUTH I.A.BENNIG,J.STROBAEK,R.MARMEDE,A.NEUMANN,A.FRIAES, JRNL AUTH 2 M.RAMIREZ,M.HALL,M.COLLIN,L.MALMSTROM,S.EKSTROM,I.FRICK, JRNL AUTH 3 L.BJORCK,H.J.HAPPONEN JRNL TITL STREPTOCOCCUS PYOGENES NUCLEASE A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, 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 : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL 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) : 2.600 REMARK 3 NUMBER OF PARTICLES : 134130 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: NULL REMARK 4 REMARK 4 9SF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1292149094. 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 : STREPTOCOCCUS PYOGENES NUCLEASE REMARK 245 A, SPNA; STREPTOCOCCUS PYOGENES REMARK 245 NUCLEASE A, SPNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 10.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 380 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 124 -8.33 73.39 REMARK 500 ASP A 127 118.47 -161.25 REMARK 500 ALA A 296 75.48 52.55 REMARK 500 ASN A 348 19.71 59.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-54816 RELATED DB: EMDB REMARK 900 MONOMERIC FORM OF THE STREPTOCOCCUS PYOGENES NUCLEASE A (SPNA) DBREF 9SF8 A 1 562 UNP Q9A0J7 Q9A0J7_STRP1 289 850 SEQRES 1 A 562 ILE VAL LYS ILE GLY GLU ILE GLN GLY ALA SER HIS THR SEQRES 2 A 562 SER PRO LEU LEU LYS LYS ALA VAL THR VAL GLU GLN VAL SEQRES 3 A 562 VAL VAL THR TYR LEU ASP ASP SER THR HIS PHE TYR VAL SEQRES 4 A 562 GLN ASP LEU ASN GLY ASP GLY ASP LEU ALA THR SER ASP SEQRES 5 A 562 GLY ILE ARG VAL PHE ALA LYS ASN ALA LYS VAL GLN VAL SEQRES 6 A 562 GLY ASP VAL LEU THR ILE SER GLY GLU VAL GLU GLU PHE SEQRES 7 A 562 PHE GLY ARG GLY TYR GLU GLU ARG LYS GLN THR ASP LEU SEQRES 8 A 562 THR ILE THR GLN ILE VAL ALA LYS ALA VAL THR LYS THR SEQRES 9 A 562 GLY THR ALA GLN VAL PRO SER PRO LEU VAL LEU GLY LYS SEQRES 10 A 562 ASP ARG ILE ALA PRO ALA ASN ILE ILE ASP ASN ASP GLY SEQRES 11 A 562 LEU ARG VAL PHE ASP PRO GLU GLU ASP ALA ILE ASP TYR SEQRES 12 A 562 TRP GLU SER MET GLU GLY MET LEU VAL ALA VAL ASP ASP SEQRES 13 A 562 ALA LYS ILE LEU GLY PRO MET LYS ASN LYS GLU ILE TYR SEQRES 14 A 562 VAL LEU PRO GLY SER SER THR ARG PRO LEU ASN ASN SER SEQRES 15 A 562 GLY GLY VAL LEU LEU PRO ALA ASN SER TYR ASN THR ASP SEQRES 16 A 562 VAL ILE PRO VAL LEU PHE LYS LYS GLY LYS GLN ILE ILE SEQRES 17 A 562 LYS ALA GLY ASP SER TYR LYS GLY ARG LEU ALA GLY PRO SEQRES 18 A 562 VAL SER TYR SER TYR GLY ASN TYR LYS VAL PHE VAL ASP SEQRES 19 A 562 ASP SER LYS ASN MET PRO SER LEU MET ASP GLY HIS LEU SEQRES 20 A 562 LYS PRO GLU LYS THR ASN LEU GLN LYS ASP LEU SER LYS SEQRES 21 A 562 LEU SER ILE ALA SER TYR ASN ILE GLU ASN PHE SER ALA SEQRES 22 A 562 ASN PRO SER SER THR LYS ASP GLU LYS VAL LYS ARG ILE SEQRES 23 A 562 ALA GLU SER PHE ILE HIS ASP LEU ASN ALA PRO ASP ILE SEQRES 24 A 562 ILE GLY LEU ILE GLU VAL GLN ASP ASN ASN GLY PRO THR SEQRES 25 A 562 ASP ASP GLY THR THR ASP ALA THR GLN SER ALA GLN ARG SEQRES 26 A 562 LEU ILE ASP ALA ILE LYS LYS LEU GLY GLY PRO THR TYR SEQRES 27 A 562 ARG TYR VAL ASP ILE ALA PRO GLU ASN ASN VAL ASP GLY SEQRES 28 A 562 GLY GLN PRO GLY GLY ASN ILE ARG THR GLY PHE LEU TYR SEQRES 29 A 562 GLN PRO GLU ARG VAL SER LEU SER ASP LYS PRO LYS GLY SEQRES 30 A 562 GLY ALA ARG ASP ALA LEU THR TRP VAL ASN GLY GLU LEU SEQRES 31 A 562 ASN LEU SER VAL GLY ARG ILE ASP PRO THR ASN ALA ALA SEQRES 32 A 562 TRP LYS ASP VAL ARG LYS SER LEU ALA ALA GLU PHE ILE SEQRES 33 A 562 PHE GLN GLY ARG LYS VAL VAL VAL VAL ALA ASN HIS LEU SEQRES 34 A 562 ASN SER LYS ARG GLY ASP ASN ALA LEU TYR GLY CYS VAL SEQRES 35 A 562 GLN PRO VAL THR PHE LYS SER GLU GLN ARG ARG HIS VAL SEQRES 36 A 562 LEU ALA ASN MET LEU ALA GLN PHE ALA LYS GLU GLY ALA SEQRES 37 A 562 LYS HIS GLN ALA ASN ILE VAL MET LEU GLY ASP PHE ASN SEQRES 38 A 562 ASP PHE GLU PHE THR LYS THR ILE GLN LEU ILE GLU GLU SEQRES 39 A 562 GLY ASP MET VAL ASN LEU VAL SER ARG HIS ASP ILE SER SEQRES 40 A 562 ASP ARG TYR SER TYR PHE HIS GLN GLY ASN ASN GLN THR SEQRES 41 A 562 LEU ASP ASN ILE LEU VAL SER ARG HIS LEU LEU ASP HIS SEQRES 42 A 562 TYR GLU PHE ASP MET VAL HIS VAL ASN SER PRO PHE MET SEQRES 43 A 562 GLU ALA HIS GLY ARG ALA SER ASP HIS ASP PRO LEU LEU SEQRES 44 A 562 LEU GLN LEU HELIX 1 AA1 LYS A 3 GLY A 9 1 7 HELIX 2 AA2 ASP A 139 SER A 146 1 8 HELIX 3 AA3 LYS A 279 ASP A 293 1 15 HELIX 4 AA4 ALA A 319 LEU A 333 1 15 HELIX 5 AA5 ASN A 401 LYS A 405 5 5 HELIX 6 AA6 PHE A 447 LYS A 469 1 23 HELIX 7 AA7 THR A 486 GLU A 494 1 9 HELIX 8 AA8 ASP A 505 ARG A 509 5 5 HELIX 9 AA9 HIS A 529 LEU A 531 5 3 HELIX 10 AB1 MET A 546 GLY A 550 5 5 SHEET 1 AA1 6 ALA A 20 LEU A 31 0 SHEET 2 AA1 6 HIS A 36 ASP A 41 -1 O GLN A 40 N VAL A 27 SHEET 3 AA1 6 GLY A 53 ALA A 58 -1 O ILE A 54 N VAL A 39 SHEET 4 AA1 6 ILE A 93 THR A 106 1 O ALA A 98 N PHE A 57 SHEET 5 AA1 6 ASP A 67 PHE A 78 -1 N PHE A 78 O ILE A 93 SHEET 6 AA1 6 ALA A 20 LEU A 31 -1 N VAL A 26 O LEU A 69 SHEET 1 AA2 7 LEU A 113 VAL A 114 0 SHEET 2 AA2 7 LEU A 151 ASP A 155 1 O ALA A 153 N LEU A 113 SHEET 3 AA2 7 ARG A 217 SER A 225 -1 O GLY A 220 N VAL A 152 SHEET 4 AA2 7 ASN A 228 VAL A 233 -1 O PHE A 232 N PRO A 221 SHEET 5 AA2 7 ILE A 197 PHE A 201 1 N LEU A 200 O VAL A 233 SHEET 6 AA2 7 GLU A 167 LEU A 171 -1 N ILE A 168 O VAL A 199 SHEET 7 AA2 7 LYS A 158 ILE A 159 -1 N LYS A 158 O LEU A 171 SHEET 1 AA3 2 SER A 213 LYS A 215 0 SHEET 2 AA3 2 SER A 241 MET A 243 -1 O SER A 241 N LYS A 215 SHEET 1 AA4 6 ARG A 339 VAL A 341 0 SHEET 2 AA4 6 ARG A 359 TYR A 364 -1 O PHE A 362 N VAL A 341 SHEET 3 AA4 6 ILE A 299 VAL A 305 -1 N VAL A 305 O ARG A 359 SHEET 4 AA4 6 LEU A 261 PHE A 271 1 N ALA A 264 O GLY A 301 SHEET 5 AA4 6 LEU A 558 LEU A 562 -1 O LEU A 560 N ILE A 263 SHEET 6 AA4 6 GLU A 535 MET A 538 -1 N ASP A 537 O LEU A 559 SHEET 1 AA5 3 SER A 370 LEU A 371 0 SHEET 2 AA5 3 LEU A 411 PHE A 417 -1 O ILE A 416 N SER A 370 SHEET 3 AA5 3 VAL A 394 ARG A 396 -1 N GLY A 395 O ALA A 412 SHEET 1 AA6 6 SER A 370 LEU A 371 0 SHEET 2 AA6 6 LEU A 411 PHE A 417 -1 O ILE A 416 N SER A 370 SHEET 3 AA6 6 ARG A 420 HIS A 428 -1 O ALA A 426 N LEU A 411 SHEET 4 AA6 6 ASN A 473 ASP A 479 1 O ASN A 473 N VAL A 423 SHEET 5 AA6 6 ASP A 522 SER A 527 -1 O LEU A 525 N MET A 476 SHEET 6 AA6 6 MET A 497 ASN A 499 -1 N VAL A 498 O VAL A 526 SHEET 1 AA7 2 TRP A 385 VAL A 386 0 SHEET 2 AA7 2 GLU A 389 LEU A 390 -1 O GLU A 389 N VAL A 386 SHEET 1 AA8 2 TYR A 512 HIS A 514 0 SHEET 2 AA8 2 ASN A 517 GLN A 519 -1 O ASN A 517 N HIS A 514 CISPEP 1 GLN A 443 PRO A 444 0 2.73 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 MASTER 129 0 0 10 34 0 0 6 4355 1 0 44 END