HEADER VIRAL PROTEIN 18-APR-25 9UKV TITLE JM COMPLEX - E. COLI MURJ, LEVIVIRUS M LYSIS PROTEIN LYSM (SGLM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPID II FLIPPASE MURJ; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDOGLYCAN BIOSYNTHESIS PROTEIN MURJ; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: LYSIS PROTEIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MURJ, MVIN, YCEN, B1069, JW1056; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE M; SOURCE 9 ORGANISM_TAXID: 1235640; SOURCE 10 GENE: LYS; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHAGE, LYSIS PROTEIN, COMPLEX, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR H.KOHGA,N.LERTPREEDAKORN,T.TSUKAZAKI REVDAT 1 10-SEP-25 9UKV 0 JRNL AUTH H.KOHGA,N.LERTPREEDAKORN,T.TSUKAZAKI JRNL TITL JM COMPLEX - E. COLI MURJ, LEVIVIRUS M LYSIS PROTEIN LYSM JRNL TITL 2 (SGLM) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 3.050 REMARK 3 NUMBER OF PARTICLES : 371016 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 9UKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-25. REMARK 100 THE DEPOSITION ID IS D_1300058649. 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 : JM COMPLEX - E. COLI MURJ, REMARK 245 LEVIVIRUS M LYSIS PROTEIN LYSM REMARK 245 (SGLM) 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 : 8.00 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 : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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) : 5000.00 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 0 REMARK 465 VAL A 511 REMARK 465 ASP A 512 REMARK 465 TYR A 513 REMARK 465 LYS A 514 REMARK 465 ASP A 515 REMARK 465 HIS A 516 REMARK 465 ASP A 517 REMARK 465 GLY A 518 REMARK 465 ASP A 519 REMARK 465 TYR A 520 REMARK 465 LYS A 521 REMARK 465 ASP A 522 REMARK 465 HIS A 523 REMARK 465 ASP A 524 REMARK 465 ILE A 525 REMARK 465 ASP A 526 REMARK 465 TYR A 527 REMARK 465 LYS A 528 REMARK 465 ASP A 529 REMARK 465 ASP A 530 REMARK 465 ASP A 531 REMARK 465 ASP A 532 REMARK 465 LYS A 533 REMARK 465 HIS B 39 REMARK 465 HIS B 40 REMARK 465 HIS B 41 REMARK 465 HIS B 42 REMARK 465 HIS B 43 REMARK 465 HIS B 44 REMARK 465 HIS B 45 REMARK 465 HIS B 46 REMARK 465 HIS B 47 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 ALA A 59 -37.14 -131.82 REMARK 500 ALA A 178 49.94 -88.97 REMARK 500 LEU A 279 -60.71 -95.68 REMARK 500 LYS A 406 -129.13 60.50 REMARK 500 PRO A 467 -175.83 -65.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-64256 RELATED DB: EMDB REMARK 900 JM COMPLEX - E. COLI MURJ, LEVIVIRUS M LYSIS PROTEIN LYSM (SGLM) DBREF 9UKV A 2 511 UNP P0AF16 MURJ_ECOLI 2 511 DBREF 9UKV B 1 37 UNP K7QK87 K7QK87_BPM 1 37 SEQADV 9UKV MET A 0 UNP P0AF16 INITIATING METHIONINE SEQADV 9UKV ALA A 1 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 512 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV TYR A 513 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV LYS A 514 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 515 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV HIS A 516 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 517 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV GLY A 518 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 519 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV TYR A 520 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV LYS A 521 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 522 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV HIS A 523 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 524 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ILE A 525 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 526 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV TYR A 527 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV LYS A 528 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 529 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 530 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 531 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV ASP A 532 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV LYS A 533 UNP P0AF16 EXPRESSION TAG SEQADV 9UKV HIS B 38 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 39 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 40 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 41 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 42 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 43 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 44 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 45 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 46 UNP K7QK87 EXPRESSION TAG SEQADV 9UKV HIS B 47 UNP K7QK87 EXPRESSION TAG SEQRES 1 A 534 MET ALA ASN LEU LEU LYS SER LEU ALA ALA VAL SER SER SEQRES 2 A 534 MET THR MET PHE SER ARG VAL LEU GLY PHE ALA ARG ASP SEQRES 3 A 534 ALA ILE VAL ALA ARG ILE PHE GLY ALA GLY MET ALA THR SEQRES 4 A 534 ASP ALA PHE PHE VAL ALA PHE LYS LEU PRO ASN LEU LEU SEQRES 5 A 534 ARG ARG ILE PHE ALA GLU GLY ALA PHE SER GLN ALA PHE SEQRES 6 A 534 VAL PRO ILE LEU ALA GLU TYR LYS SER LYS GLN GLY GLU SEQRES 7 A 534 ASP ALA THR ARG VAL PHE VAL SER TYR VAL SER GLY LEU SEQRES 8 A 534 LEU THR LEU ALA LEU ALA VAL VAL THR VAL ALA GLY MET SEQRES 9 A 534 LEU ALA ALA PRO TRP VAL ILE MET VAL THR ALA PRO GLY SEQRES 10 A 534 PHE ALA ASP THR ALA ASP LYS PHE ALA LEU THR SER GLN SEQRES 11 A 534 LEU LEU LYS ILE THR PHE PRO TYR ILE LEU LEU ILE SER SEQRES 12 A 534 LEU ALA SER LEU VAL GLY ALA ILE LEU ASN THR TRP ASN SEQRES 13 A 534 ARG PHE SER ILE PRO ALA PHE ALA PRO THR LEU LEU ASN SEQRES 14 A 534 ILE SER MET ILE GLY PHE ALA LEU PHE ALA ALA PRO TYR SEQRES 15 A 534 PHE ASN PRO PRO VAL LEU ALA LEU ALA TRP ALA VAL THR SEQRES 16 A 534 VAL GLY GLY VAL LEU GLN LEU VAL TYR GLN LEU PRO HIS SEQRES 17 A 534 LEU LYS LYS ILE GLY MET LEU VAL LEU PRO ARG ILE ASN SEQRES 18 A 534 PHE HIS ASP ALA GLY ALA MET ARG VAL VAL LYS GLN MET SEQRES 19 A 534 GLY PRO ALA ILE LEU GLY VAL SER VAL SER GLN ILE SER SEQRES 20 A 534 LEU ILE ILE ASN THR ILE PHE ALA SER PHE LEU ALA SER SEQRES 21 A 534 GLY SER VAL SER TRP MET TYR TYR ALA ASP ARG LEU MET SEQRES 22 A 534 GLU PHE PRO SER GLY VAL LEU GLY VAL ALA LEU GLY THR SEQRES 23 A 534 ILE LEU LEU PRO SER LEU SER LYS SER PHE ALA SER GLY SEQRES 24 A 534 ASN HIS ASP GLU TYR ASN ARG LEU MET ASP TRP GLY LEU SEQRES 25 A 534 ARG LEU CYS PHE LEU LEU ALA LEU PRO SER ALA VAL ALA SEQRES 26 A 534 LEU GLY ILE LEU SER GLY PRO LEU THR VAL SER LEU PHE SEQRES 27 A 534 GLN TYR GLY LYS PHE THR ALA PHE ASP ALA LEU MET THR SEQRES 28 A 534 GLN ARG ALA LEU ILE ALA TYR SER VAL GLY LEU ILE GLY SEQRES 29 A 534 LEU ILE VAL VAL LYS VAL LEU ALA PRO GLY PHE TYR SER SEQRES 30 A 534 ARG GLN ASP ILE LYS THR PRO VAL LYS ILE ALA ILE VAL SEQRES 31 A 534 THR LEU ILE LEU THR GLN LEU MET ASN LEU ALA PHE ILE SEQRES 32 A 534 GLY PRO LEU LYS HIS ALA GLY LEU SER LEU SER ILE GLY SEQRES 33 A 534 LEU ALA ALA CYS LEU ASN ALA SER LEU LEU TYR TRP GLN SEQRES 34 A 534 LEU ARG LYS GLN LYS ILE PHE THR PRO GLN PRO GLY TRP SEQRES 35 A 534 MET ALA PHE LEU LEU ARG LEU VAL VAL ALA VAL LEU VAL SEQRES 36 A 534 MET SER GLY VAL LEU LEU GLY MET LEU HIS ILE MET PRO SEQRES 37 A 534 GLU TRP SER LEU GLY THR MET PRO TRP ARG LEU LEU ARG SEQRES 38 A 534 LEU MET ALA VAL VAL LEU ALA GLY ILE ALA ALA TYR PHE SEQRES 39 A 534 ALA ALA LEU ALA VAL LEU GLY PHE LYS VAL LYS GLU PHE SEQRES 40 A 534 ALA ARG ARG THR VAL ASP TYR LYS ASP HIS ASP GLY ASP SEQRES 41 A 534 TYR LYS ASP HIS ASP ILE ASP TYR LYS ASP ASP ASP ASP SEQRES 42 A 534 LYS SEQRES 1 B 47 MET LYS TYR ILE ILE ASN LEU ALA PHE CYS VAL LEU LEU SEQRES 2 B 47 LEU VAL ALA GLY ASP SER ILE ALA TYR ARG VAL SER GLN SEQRES 3 B 47 TYR LEU ALA PRO LEU VAL ASP THR PHE THR LYS HIS HIS SEQRES 4 B 47 HIS HIS HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ALA A 1 GLY A 33 1 33 HELIX 2 AA2 GLY A 35 ALA A 56 1 22 HELIX 3 AA3 ALA A 59 GLN A 75 1 17 HELIX 4 AA4 GLY A 76 ALA A 105 1 30 HELIX 5 AA5 ALA A 105 ALA A 114 1 10 HELIX 6 AA6 ALA A 114 ASP A 119 1 6 HELIX 7 AA7 THR A 120 PHE A 135 1 16 HELIX 8 AA8 PHE A 135 TRP A 154 1 20 HELIX 9 AA9 PHE A 157 ALA A 178 1 22 HELIX 10 AB1 PRO A 185 ILE A 211 1 27 HELIX 11 AB2 ASP A 223 LEU A 257 1 35 HELIX 12 AB3 GLY A 260 LEU A 279 1 20 HELIX 13 AB4 LEU A 279 GLY A 298 1 20 HELIX 14 AB5 ASN A 299 LEU A 328 1 30 HELIX 15 AB6 LEU A 328 PHE A 337 1 10 HELIX 16 AB7 THR A 343 GLY A 360 1 18 HELIX 17 AB8 GLY A 360 ARG A 377 1 18 HELIX 18 AB9 ILE A 380 LYS A 406 1 27 HELIX 19 AC1 LYS A 406 GLN A 432 1 27 HELIX 20 AC2 GLY A 440 MET A 466 1 27 HELIX 21 AC3 THR A 473 LEU A 499 1 27 HELIX 22 AC4 LYS A 502 ALA A 507 5 6 HELIX 23 AC5 LYS B 2 ALA B 16 1 15 HELIX 24 AC6 ALA B 16 GLN B 26 1 11 HELIX 25 AC7 LEU B 28 THR B 34 1 7 CISPEP 1 ASN A 183 PRO A 184 0 -0.57 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 3888 THR A 510 TER 4190 HIS B 38 MASTER 161 0 0 25 0 0 0 6 4188 2 0 46 END