HEADER VIRUS 01-OCT-25 9YIN TITLE SF11 BACTERIOPHAGE PORTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: SF11 PORTAL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA PHAGE SF11 SMD-2017; SOURCE 3 ORGANISM_TAXID: 2282196; SOURCE 4 GENE: SF11_GP63; SOURCE 5 EXPRESSION_SYSTEM: SHIGELLA FLEXNERI Y; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 424720 KEYWDS SF11, BACTERIOPHAGE, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR S.SUBRAMANIAN,K.N.PARENT REVDAT 1 12-NOV-25 9YIN 0 JRNL AUTH S.SUBRAMANIAN,J.A.DOVER,K.N.PARENT JRNL TITL STRUCTURE OF SHIGELLA BACTERIOPHAGE SF11 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.400 REMARK 3 NUMBER OF PARTICLES : 20482 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9YIN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000300607. 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 : SHIGELLA PHAGE SF11 SMD-2017 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 : GATAN K3 BIOCONTINUUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 5045.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C12). 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 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 0.866025 -0.500000 0.000000 105.55677 REMARK 350 BIOMT2 2 0.500000 0.866025 0.000000 -60.94323 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 227.44323 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 -60.94323 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 333.00001 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 393.94324 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 105.55677 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -0.866025 -0.500000 0.000000 393.94324 REMARK 350 BIOMT2 6 0.500000 -0.866025 0.000000 227.44323 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 333.00001 REMARK 350 BIOMT2 7 0.000000 -1.000000 0.000000 333.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 -0.866025 0.500000 0.000000 227.44324 REMARK 350 BIOMT2 8 -0.500000 -0.866025 0.000000 393.94323 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 -0.500000 0.866025 0.000000 105.55678 REMARK 350 BIOMT2 9 -0.866025 -0.500000 0.000000 393.94323 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 10 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 10 -1.000000 0.000000 0.000000 333.00001 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 0.500000 0.866025 0.000000 -60.94323 REMARK 350 BIOMT2 11 -0.866025 0.500000 0.000000 227.44323 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 12 0.866025 0.500000 0.000000 -60.94323 REMARK 350 BIOMT2 12 -0.500000 0.866025 0.000000 105.55677 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 0.00000 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 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ILE A 4 REMARK 465 ASP A 5 REMARK 465 ALA A 6 REMARK 465 LEU A 7 REMARK 465 ASN A 8 REMARK 465 ALA A 9 REMARK 465 TYR A 10 REMARK 465 ILE A 11 REMARK 465 ARG A 12 REMARK 465 ASP A 13 REMARK 465 ARG A 14 REMARK 465 VAL A 15 REMARK 465 ALA A 16 REMARK 465 ASN A 17 REMARK 465 ASN A 18 REMARK 465 ASN A 19 REMARK 465 ARG A 20 REMARK 465 ALA A 21 REMARK 465 ILE A 22 REMARK 465 GLN A 23 REMARK 465 GLN A 24 REMARK 465 GLN A 25 REMARK 465 ARG A 26 REMARK 465 LEU A 27 REMARK 465 CYS A 28 REMARK 465 ASP A 411 REMARK 465 LYS A 412 REMARK 465 ALA A 413 REMARK 465 GLU A 414 REMARK 465 LEU A 415 REMARK 465 ILE A 416 REMARK 465 VAL A 417 REMARK 465 LYS A 418 REMARK 465 LEU A 419 REMARK 465 ALA A 420 REMARK 465 GLN A 421 REMARK 465 ALA A 422 REMARK 465 ALA A 423 REMARK 465 GLN A 424 REMARK 465 SER A 425 REMARK 465 ALA A 426 REMARK 465 ALA A 427 REMARK 465 ASN A 428 REMARK 465 ALA A 429 REMARK 465 GLY A 430 REMARK 465 VAL A 431 REMARK 465 GLY A 432 REMARK 465 GLN A 433 REMARK 465 ILE A 434 REMARK 465 LEU A 435 REMARK 465 THR A 436 REMARK 465 ASP A 437 REMARK 465 ASP A 438 REMARK 465 GLU A 439 REMARK 465 ILE A 440 REMARK 465 ARG A 441 REMARK 465 GLY A 442 REMARK 465 PHE A 443 REMARK 465 LEU A 444 REMARK 465 GLY A 445 REMARK 465 LEU A 446 REMARK 465 GLU A 447 REMARK 465 PRO A 448 REMARK 465 ILE A 449 REMARK 465 GLU A 450 REMARK 465 MET A 451 REMARK 465 PRO A 452 REMARK 465 ASP A 453 REMARK 465 GLY A 454 REMARK 465 TYR A 455 REMARK 465 MET A 456 REMARK 465 GLU A 457 REMARK 465 ASP A 458 REMARK 465 THR A 459 REMARK 465 PRO A 460 REMARK 465 PRO A 461 REMARK 465 GLU A 462 REMARK 465 GLY A 463 REMARK 465 GLU A 464 REMARK 465 ASP A 465 REMARK 465 GLU A 466 REMARK 465 ASP A 467 REMARK 465 THR A 468 REMARK 465 PRO A 469 REMARK 465 VAL A 470 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 GLU A 186 CG CD OE1 OE2 REMARK 470 SER A 346 OG REMARK 470 ARG A 347 CG CD NE CZ NH1 NH2 REMARK 470 SER A 348 OG REMARK 470 VAL A 350 CG1 CG2 REMARK 470 LEU A 351 CG CD1 CD2 REMARK 470 SER A 353 OG REMARK 470 ASN A 355 CG OD1 ND2 REMARK 470 GLU A 357 CG CD OE1 OE2 REMARK 470 GLU A 406 CG CD OE1 OE2 REMARK 470 THR A 408 OG1 CG2 REMARK 470 GLN A 409 CG CD OE1 NE2 REMARK 470 ASN A 410 CG OD1 ND2 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 MET A 81 148.47 66.55 REMARK 500 ASP A 90 -169.30 -79.21 REMARK 500 THR A 408 -166.83 -124.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-72999 RELATED DB: EMDB REMARK 900 SF11 BACTERIOPHAGE PORTAL DBREF1 9YIN A 1 470 UNP A0A291AXK9_9CAUD DBREF2 9YIN A A0A291AXK9 1 470 SEQRES 1 A 470 MET SER LYS ILE ASP ALA LEU ASN ALA TYR ILE ARG ASP SEQRES 2 A 470 ARG VAL ALA ASN ASN ASN ARG ALA ILE GLN GLN GLN ARG SEQRES 3 A 470 LEU CYS ALA GLY GLY LYS ASN LEU ASP GLN LYS HIS ASP SEQRES 4 A 470 ARG LEU TRP THR GLU CYS GLY TYR LYS GLN GLU ILE ASN SEQRES 5 A 470 ALA GLU ASP PHE ARG PHE ALA TYR GLU ARG TYR PRO LEU SEQRES 6 A 470 ALA ASN ALA ALA VAL ASN ILE VAL LEU ASN LYS SER TRP SEQRES 7 A 470 HIS GLY MET PRO THR VAL LEU GLU ASN ASP ALA ASP ASP SEQRES 8 A 470 GLU ALA THR SER PRO TRP GLU LYS SER VAL ASN ASP ILE SEQRES 9 A 470 LEU LYS LYS ALA LEU PRO PHE ILE ARG ASP ALA ASP LYS SEQRES 10 A 470 ARG ASN LEU ILE ASN ARG TYR SER ALA LEU ILE LEU GLN SEQRES 11 A 470 ILE ARG ASP GLY LYS GLN TRP SER GLU PRO VAL ASP ILE SEQRES 12 A 470 THR LYS THR ARG ARG ILE LYS ASP LYS SER ILE VAL ARG SEQRES 13 A 470 PHE ILE PRO VAL TRP GLU GLU GLN LEU ARG VAL SER ALA SEQRES 14 A 470 TRP ASN ASN ASP GLU THR SER GLU ASP TYR GLY MET PRO SEQRES 15 A 470 GLU MET TYR GLU TYR GLN GLU SER ALA VAL GLU ASP PHE SEQRES 16 A 470 ASP SER ASP GLY LYS PRO GLU ARG SER VAL GLN ILE HIS SEQRES 17 A 470 PRO ASP ARG ILE ILE ILE LEU ALA GLU GLY SER PHE ASP SEQRES 18 A 470 GLY SER MET PHE SER GLY VAL PRO LEU LEU ARG ALA GLY SEQRES 19 A 470 PHE ASN SER LEU ILE ASP CYS ALA LYS VAL SER GLY SER SEQRES 20 A 470 SER ALA GLU GLY LEU LEU LYS ASN SER SER ARG GLN LEU SEQRES 21 A 470 ASN VAL SER PHE ASN LYS ASP ASN VAL SER ALA GLN SER SEQRES 22 A 470 LEU ALA GLN GLN MET GLN VAL PRO VAL ASP GLU LEU ALA SEQRES 23 A 470 ASP LEU LEU ASN GLU ASN ILE GLU MET LEU ASN SER GLY SEQRES 24 A 470 ILE ASP ALA ALA MET PHE SER PHE GLY SER ASP VAL SER SEQRES 25 A 470 VAL LEU SER THR SER MET SER ASP PRO GLU PRO PHE MET SEQRES 26 A 470 TYR VAL ALA ALA SER GLN PHE ALA ALA SER VAL ASN ILE SEQRES 27 A 470 PRO LEU ASN SER LEU LEU GLY SER ARG SER GLY VAL LEU SEQRES 28 A 470 ALA SER ALA ASN ASP GLU GLN SER LEU ALA MET MET ALA SEQRES 29 A 470 MET GLN ARG ARG ASP GLY TRP LEU ASP TYR LEU VAL GLY SEQRES 30 A 470 SER PHE VAL GLU ARG LEU ILE THR PHE GLY ILE VAL ASP SEQRES 31 A 470 LYS ALA PRO ALA ALA GLY TYR TYR CYS LYS TRP ASN ASP SEQRES 32 A 470 LEU LEU GLU PRO THR GLN ASN ASP LYS ALA GLU LEU ILE SEQRES 33 A 470 VAL LYS LEU ALA GLN ALA ALA GLN SER ALA ALA ASN ALA SEQRES 34 A 470 GLY VAL GLY GLN ILE LEU THR ASP ASP GLU ILE ARG GLY SEQRES 35 A 470 PHE LEU GLY LEU GLU PRO ILE GLU MET PRO ASP GLY TYR SEQRES 36 A 470 MET GLU ASP THR PRO PRO GLU GLY GLU ASP GLU ASP THR SEQRES 37 A 470 PRO VAL HELIX 1 AA1 ARG A 40 GLY A 46 1 7 HELIX 2 AA2 ASN A 52 TYR A 63 1 12 HELIX 3 AA3 TYR A 63 HIS A 79 1 17 HELIX 4 AA4 SER A 95 ASN A 122 1 28 HELIX 5 AA5 ASP A 142 ILE A 149 1 8 HELIX 6 AA6 LYS A 150 LYS A 152 5 3 HELIX 7 AA7 SER A 190 VAL A 192 5 3 HELIX 8 AA8 HIS A 208 ASP A 210 5 3 HELIX 9 AA9 SER A 223 GLY A 227 5 5 HELIX 10 AB1 GLY A 234 SER A 256 1 23 HELIX 11 AB2 SER A 270 MET A 278 1 9 HELIX 12 AB3 PRO A 281 GLY A 299 1 19 HELIX 13 AB4 ASP A 320 VAL A 336 1 17 HELIX 14 AB5 PRO A 339 LEU A 344 1 6 HELIX 15 AB6 VAL A 350 TRP A 371 1 22 HELIX 16 AB7 TRP A 371 PHE A 386 1 16 SHEET 1 AA1 2 THR A 83 GLU A 86 0 SHEET 2 AA1 2 TYR A 397 LYS A 400 -1 O LYS A 400 N THR A 83 SHEET 1 AA2 3 ILE A 154 VAL A 160 0 SHEET 2 AA2 3 SER A 125 ILE A 131 -1 N GLN A 130 O VAL A 155 SHEET 3 AA2 3 ILE A 212 LEU A 215 -1 O LEU A 215 N SER A 125 SHEET 1 AA3 3 LEU A 165 TRP A 170 0 SHEET 2 AA3 3 PRO A 182 GLN A 188 -1 O GLU A 186 N ARG A 166 SHEET 3 AA3 3 SER A 204 ILE A 207 -1 O VAL A 205 N TYR A 187 SHEET 1 AA4 2 LEU A 260 SER A 263 0 SHEET 2 AA4 2 ASP A 310 VAL A 313 -1 O ASP A 310 N SER A 263 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 TER 2965 ASN A 410 MASTER 265 0 0 16 10 0 0 6 2964 1 0 37 END