HEADER VIRUS 16-SEP-22 8EJ5 TITLE TAIL TIP STRUCTURE OF STAPHYLOCOCCUS PHAGE ANDHRA COMPND MOL_ID: 1; COMPND 2 MOLECULE: GP10, TAIL TIP LYSIN (SPIKE); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GP1, TAIL TIP PROTEIN; COMPND 7 CHAIN: B, C, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS PHAGE ANDHRA; SOURCE 3 ORGANISM_TAXID: 1958907; SOURCE 4 GENE: ANDHRA_10; SOURCE 5 EXPRESSION_SYSTEM: STAPHYLOCOCCUS PHAGE ANDHRA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1958907; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS PHAGE ANDHRA; SOURCE 9 ORGANISM_TAXID: 1958907; SOURCE 10 EXPRESSION_SYSTEM: STAPHYLOCOCCUS PHAGE ANDHRA; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 1958907 KEYWDS PHAGE TAIL, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR J.L.KIZZIAH,N.C.HAWKINS,T.DOKLAND REVDAT 2 19-JUN-24 8EJ5 1 REMARK REVDAT 1 14-DEC-22 8EJ5 0 JRNL AUTH N.C.HAWKINS,J.L.KIZZIAH,A.HATOUM-ASLAN,T.DOKLAND JRNL TITL STRUCTURE AND HOST SPECIFICITY OF STAPHYLOCOCCUS EPIDERMIDIS JRNL TITL 2 BACTERIOPHAGE ANDHRA. JRNL REF SCI ADV V. 8 E0459 2022 JRNL REFN ESSN 2375-2548 JRNL PMID 36449623 JRNL DOI 10.1126/SCIADV.ADE0459 REMARK 2 REMARK 2 RESOLUTION. 4.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 4.900 REMARK 3 NUMBER OF PARTICLES : 98203 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 8EJ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1000268315. 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 : STAPHYLOCOCCUS PHAGE ANDHRA 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 : 7.80 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 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) : 3900.00 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 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 LYS A 195 REMARK 465 GLY A 196 REMARK 465 GLY A 197 REMARK 465 SER A 198 REMARK 465 SER A 199 REMARK 465 SER A 200 REMARK 465 GLY A 201 REMARK 465 SER A 202 REMARK 465 SER A 203 REMARK 465 SER A 204 REMARK 465 SER A 205 REMARK 465 SER A 206 REMARK 465 SER A 207 REMARK 465 GLY A 208 REMARK 465 THR A 209 REMARK 465 SER A 210 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 VAL A 171 -67.07 -120.53 REMARK 500 THR A 240 -140.75 -107.01 REMARK 500 PHE A 244 71.65 -150.36 REMARK 500 ASN A 246 -112.63 -115.22 REMARK 500 ALA A 299 -169.85 173.38 REMARK 500 LYS A 308 64.74 38.58 REMARK 500 ARG A 311 -141.81 178.44 REMARK 500 ARG A 393 -101.56 67.67 REMARK 500 VAL A 394 145.36 91.85 REMARK 500 ASN A 409 -21.66 100.14 REMARK 500 GLN A 412 8.89 81.36 REMARK 500 PRO A 446 33.28 -96.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-28128 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-28129 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-28130 RELATED DB: EMDB REMARK 900 RELATED ID: 8EGR RELATED DB: PDB REMARK 900 RELATED ID: 8EGS RELATED DB: PDB REMARK 900 RELATED ID: 8EGT RELATED DB: PDB REMARK 900 RELATED ID: EMD-28176 RELATED DB: EMDB REMARK 900 TAIL TIP STRUCTURE OF STAPHYLOCOCCUS PHAGE ANDHRA DBREF1 8EJ5 A 1 473 UNP A0A1S6L1H0_9CAUD DBREF2 8EJ5 A A0A1S6L1H0 1 473 DBREF 8EJ5 B 1 90 PDB 8EJ5 8EJ5 1 90 DBREF 8EJ5 C 1 90 PDB 8EJ5 8EJ5 1 90 DBREF 8EJ5 D 1 90 PDB 8EJ5 8EJ5 1 90 SEQRES 1 A 473 MET ASN ASP LYS GLU LYS ILE ASP LYS PHE ILE HIS SER SEQRES 2 A 473 ASN LEU ASN ASP ASP PHE GLY LEU SER VAL ASP ASP LEU SEQRES 3 A 473 VAL GLY LYS VAL LYS GLY ILE GLY ARG PHE SER ALA TRP SEQRES 4 A 473 CYS GLY ASN SER SER THR LYS ILE LYS GLN VAL LEU ASN SEQRES 5 A 473 ALA VAL LYS SER ILE GLY VAL SER PRO ALA LEU PHE ALA SEQRES 6 A 473 ALA TYR GLU LYS ASN GLU GLY TYR ASN GLY SER TRP GLY SEQRES 7 A 473 TRP LEU ASN HIS THR SER PRO GLN GLY ASN TYR LEU THR SEQRES 8 A 473 ASP ALA GLN PHE VAL ALA ARG LYS LEU VAL SER GLN SER SEQRES 9 A 473 ARG GLN ALA GLY THR PRO SER TRP ILE ASP ALA GLY ASN SEQRES 10 A 473 PRO VAL ASP PHE VAL PRO ALA SER VAL LYS ARG LYS GLY SEQRES 11 A 473 ASN TYR ASP PHE SER HIS ASN MET LYS ASN GLY LYS VAL SEQRES 12 A 473 GLY ARG ALA TYR ILE PRO LEU THR ALA ALA ALA THR TRP SEQRES 13 A 473 ALA ALA TYR TYR PRO GLU GLY LEU GLN ALA SER TYR ASN SEQRES 14 A 473 ARG VAL GLN ASN TYR GLY ASN PRO PHE LEU ASP ALA ALA SEQRES 15 A 473 ASN THR ILE LEU GLY TRP GLY GLY LYS ILE ASP GLY LYS SEQRES 16 A 473 GLY GLY SER SER SER GLY SER SER SER SER SER SER GLY SEQRES 17 A 473 THR SER GLY GLY LEU ASP VAL VAL ALA ARG ALA PHE GLU SEQRES 18 A 473 GLU PHE LEU LYS LYS LEU GLN ASP SER MET GLN TRP ASP SEQRES 19 A 473 LEU HIS SER ILE GLY THR ASP LYS PHE PHE SER ASN GLN SEQRES 20 A 473 MET PHE THR ILE THR LYS THR TYR ASN ASN THR TYR ARG SEQRES 21 A 473 LEU ASN MET ASN GLN LYS LEU LEU ASP GLU MET LYS ASP SEQRES 22 A 473 LEU ILE SER ARG ILE ASP GLY GLY SER GLY ASN ASP THR SEQRES 23 A 473 GLY ALA ASP ASP SER ASP GLY ASP HIS GLY GLY LYS ALA SEQRES 24 A 473 GLY LYS SER VAL ALA PRO ASN GLY LYS SER GLY ARG LYS SEQRES 25 A 473 ILE GLY GLY ASN TRP THR TYR SER ASN LEU PRO GLN LYS SEQRES 26 A 473 TYR LYS ASP ALA ILE GLU VAL PRO LYS PHE ASP PRO LYS SEQRES 27 A 473 TYR LEU ALA GLY SER PRO PHE VAL ASN THR GLY ASP THR SEQRES 28 A 473 GLY GLN CYS THR GLU LEU THR TRP ALA TYR MET HIS GLN SEQRES 29 A 473 ILE TRP GLY LYS ARG GLN PRO ALA TRP ASP ASN GLN VAL SEQRES 30 A 473 THR ASN GLY GLN ARG VAL TRP VAL VAL TYR ARG ASN GLN SEQRES 31 A 473 GLY ALA ARG VAL THR HIS ARG PRO THR VAL GLY TYR GLY SEQRES 32 A 473 PHE SER SER LYS PRO ASN TYR LEU GLN ALA MET LEU PRO SEQRES 33 A 473 GLY VAL GLY HIS THR GLY VAL VAL VAL ALA VAL PHE LYS SEQRES 34 A 473 ASP GLY SER PHE LEU THR ALA ASN TYR ASN VAL PRO PRO SEQRES 35 A 473 TYR TRP ALA PRO SER ARG VAL VAL GLU TYR ALA LEU ILE SEQRES 36 A 473 ASP GLY VAL PRO GLU ASN ALA GLY ASP ASN ILE MET PHE SEQRES 37 A 473 PHE SER GLY ILE LYS SEQRES 1 B 90 VAL THR ASN GLU LYS GLY GLN ALA TYR THR GLU MET LEU SEQRES 2 B 90 GLN LEU PHE ASN LEU LEU GLN GLN TRP ASN ASP PHE TYR SEQRES 3 B 90 THR ALA GLU ASN ALA ASN ASN LEU LEU VAL ALA CYS GLN SEQRES 4 B 90 GLN LEU LEU ILE ASN TYR ASN GLU PRO VAL ILE LYS PHE SEQRES 5 B 90 ILE ASN ASP GLU ASN GLU ASP LYS SER LEU LEU GLN TYR SEQRES 6 B 90 LEU ALA GLY ASP ASP GLY LEU ALA GLN TRP GLN PHE TYR SEQRES 7 B 90 LYS GLY PHE TYR ASN ASN TYR ASN VAL HIS ILE PHE SEQRES 1 C 90 VAL THR ASN GLU LYS GLY GLN ALA TYR THR GLU MET LEU SEQRES 2 C 90 GLN LEU PHE ASN LEU LEU GLN GLN TRP ASN ASP PHE TYR SEQRES 3 C 90 THR ALA GLU ASN ALA ASN ASN LEU LEU VAL ALA CYS GLN SEQRES 4 C 90 GLN LEU LEU ILE ASN TYR ASN GLU PRO VAL ILE LYS PHE SEQRES 5 C 90 ILE ASN ASP GLU ASN GLU ASP LYS SER LEU LEU GLN TYR SEQRES 6 C 90 LEU ALA GLY ASP ASP GLY LEU ALA GLN TRP GLN PHE TYR SEQRES 7 C 90 LYS GLY PHE TYR ASN ASN TYR ASN VAL HIS ILE PHE SEQRES 1 D 90 VAL THR ASN GLU LYS GLY GLN ALA TYR THR GLU MET LEU SEQRES 2 D 90 GLN LEU PHE ASN LEU LEU GLN GLN TRP ASN ASP PHE TYR SEQRES 3 D 90 THR ALA GLU ASN ALA ASN ASN LEU LEU VAL ALA CYS GLN SEQRES 4 D 90 GLN LEU LEU ILE ASN TYR ASN GLU PRO VAL ILE LYS PHE SEQRES 5 D 90 ILE ASN ASP GLU ASN GLU ASP LYS SER LEU LEU GLN TYR SEQRES 6 D 90 LEU ALA GLY ASP ASP GLY LEU ALA GLN TRP GLN PHE TYR SEQRES 7 D 90 LYS GLY PHE TYR ASN ASN TYR ASN VAL HIS ILE PHE HELIX 1 AA1 ASN A 2 HIS A 12 1 11 HELIX 2 AA2 SER A 22 VAL A 30 1 9 HELIX 3 AA3 ILE A 33 TRP A 39 1 7 HELIX 4 AA4 SER A 43 GLY A 58 1 16 HELIX 5 AA5 SER A 60 GLY A 72 1 13 HELIX 6 AA6 ASN A 88 GLN A 106 1 19 HELIX 7 AA7 PRO A 123 ASN A 137 1 15 HELIX 8 AA8 LYS A 142 ILE A 148 1 7 HELIX 9 AA9 THR A 151 TYR A 160 1 10 HELIX 10 AB1 PRO A 161 LEU A 164 5 4 HELIX 11 AB2 GLN A 165 ARG A 170 1 6 HELIX 12 AB3 ASN A 176 GLY A 189 1 14 HELIX 13 AB4 GLY A 212 TRP A 233 1 22 HELIX 14 AB5 ASN A 264 ARG A 277 1 14 HELIX 15 AB6 PRO A 323 ALA A 329 1 7 HELIX 16 AB7 ASP A 336 LEU A 340 5 5 HELIX 17 AB8 GLN A 353 GLY A 367 1 15 HELIX 18 AB9 ARG A 382 GLN A 390 1 9 HELIX 19 AC1 ALA A 462 ASP A 464 5 3 HELIX 20 AC2 THR B 2 GLN B 21 1 20 HELIX 21 AC3 THR B 27 TYR B 45 1 19 HELIX 22 AC4 TYR B 45 ASP B 55 1 11 HELIX 23 AC5 SER B 61 GLY B 68 1 8 HELIX 24 AC6 ASP B 70 ASN B 86 1 17 HELIX 25 AC7 THR C 2 GLN C 21 1 20 HELIX 26 AC8 THR C 27 TYR C 45 1 19 HELIX 27 AC9 TYR C 45 ASP C 55 1 11 HELIX 28 AD1 SER C 61 GLY C 68 1 8 HELIX 29 AD2 ASP C 70 ASN C 86 1 17 HELIX 30 AD3 THR D 2 GLN D 21 1 20 HELIX 31 AD4 THR D 27 TYR D 45 1 19 HELIX 32 AD5 TYR D 45 ASP D 55 1 11 HELIX 33 AD6 SER D 61 GLY D 68 1 8 HELIX 34 AD7 ASP D 70 ASN D 86 1 17 SHEET 1 AA1 2 PHE A 249 TYR A 255 0 SHEET 2 AA1 2 THR A 258 MET A 263 -1 O THR A 258 N THR A 254 SHEET 1 AA2 6 LYS A 312 TRP A 317 0 SHEET 2 AA2 6 GLU A 451 ILE A 455 -1 O TYR A 452 N TRP A 317 SHEET 3 AA2 6 PHE A 433 ASN A 437 -1 N PHE A 433 O ILE A 455 SHEET 4 AA2 6 HIS A 420 VAL A 427 -1 N VAL A 423 O ALA A 436 SHEET 5 AA2 6 GLY A 403 SER A 406 -1 N SER A 406 O HIS A 420 SHEET 6 AA2 6 ILE A 466 PHE A 469 -1 O MET A 467 N SER A 405 CISPEP 1 PRO A 441 PRO A 442 0 4.10 CISPEP 2 ALA A 445 PRO A 446 0 4.60 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