HEADER VIRUS 14-OCT-25 9SZB TITLE STRUCTURE OF THE PORTAL AND HEAD-TAIL CONNECTOR OF LACTOCOCCUS PHAGE TITLE 2 NOCTURNE116 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PORTAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: DNA PACKAGING PROTEIN; COMPND 6 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE NOCTURNE116; SOURCE 3 ORGANISM_TAXID: 2831179; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: LACTOCOCCUS PHAGE NOCTURNE116; SOURCE 6 ORGANISM_TAXID: 2831179 KEYWDS BACTERIOPHAGE, PORTAL, HEAD-TAIL CONNECTOR, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR J.RUMNIEKS,K.TARS REVDAT 1 26-AUG-26 9SZB 0 JRNL AUTH J.RUMNIEKS,K.TARS JRNL TITL THREE-DIMENSIONAL STRUCTURE OF LACTOCOCCUS BACTERIOPHAGE JRNL TITL 2 NOCTURNE116 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, PHENIX, RELION 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) : 2.780 REMARK 3 NUMBER OF PARTICLES : 27997 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 9SZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1292151364. 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 : LACTOCOCCUS PHAGE NOCTURNE116; REMARK 245 PORTAL AND HEAD-TAIL CONNECTOR REMARK 245 COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 3.00 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 : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: 24-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 24-MERIC REMARK 350 SOFTWARE USED: PISA 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 350 BIOMT1 2 0.866025 -0.500000 0.000000 111.19407 REMARK 350 BIOMT2 2 0.500000 0.866025 0.000000 -64.19793 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 239.58993 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 -64.19793 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 350.78400 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 414.98193 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 111.19407 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -0.866025 -0.500000 0.000000 414.98193 REMARK 350 BIOMT2 6 0.500000 -0.866025 0.000000 239.58993 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 350.78400 REMARK 350 BIOMT2 7 0.000000 -1.000000 0.000000 350.78400 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 -0.866025 0.500000 0.000000 239.58993 REMARK 350 BIOMT2 8 -0.500000 -0.866025 0.000000 414.98193 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 -0.500000 0.866025 0.000000 111.19407 REMARK 350 BIOMT2 9 -0.866025 -0.500000 0.000000 414.98193 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 350.78400 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 11 0.500000 0.866025 0.000000 -64.19793 REMARK 350 BIOMT2 11 -0.866025 0.500000 0.000000 239.58993 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 12 0.866025 0.500000 0.000000 -64.19793 REMARK 350 BIOMT2 12 -0.500000 0.866025 0.000000 111.19407 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 GLY A 2 REMARK 465 ILE A 3 REMARK 465 PHE A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 ARG A 7 REMARK 465 GLU A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 GLN A 11 REMARK 465 PRO A 12 REMARK 465 VAL A 13 REMARK 465 PRO A 14 REMARK 465 GLN A 15 REMARK 465 THR A 16 REMARK 465 VAL A 17 REMARK 465 ASN A 18 REMARK 465 THR A 19 REMARK 465 ILE A 20 REMARK 465 ASN A 21 REMARK 465 GLN A 22 REMARK 465 VAL A 23 REMARK 465 THR A 24 REMARK 465 ILE A 25 REMARK 465 LYS A 26 REMARK 465 ASP A 27 REMARK 465 ASN A 28 REMARK 465 THR A 29 REMARK 465 ILE A 30 REMARK 465 VAL A 31 REMARK 465 ALA A 32 REMARK 465 ALA A 33 REMARK 465 ILE A 34 REMARK 465 LYS A 303 REMARK 465 GLU A 304 REMARK 465 LYS A 305 REMARK 465 THR A 306 REMARK 465 ILE A 307 REMARK 465 ASN A 308 REMARK 465 ASP A 309 REMARK 465 ARG A 310 REMARK 465 ALA A 311 REMARK 465 SER A 312 REMARK 465 GLN A 313 REMARK 465 VAL A 314 REMARK 465 MET B 1 REMARK 465 LEU B 65 REMARK 465 GLY B 66 REMARK 465 ASP B 67 REMARK 465 GLU B 68 REMARK 465 LEU B 69 REMARK 465 TRP B 70 REMARK 465 GLY B 94 REMARK 465 ASN B 95 REMARK 465 GLU B 96 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 PRO A 113 -179.19 -68.17 REMARK 500 TYR A 300 40.08 -109.98 REMARK 500 GLU B 47 -134.41 60.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-55364 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE PORTAL AND HEAD-TAIL CONNECTOR OF LACTOCOCCUS REMARK 900 PHAGE NOCTURNE116 DBREF1 9SZB A 1 314 UNP A0A8E5NQ91_9CAUD DBREF2 9SZB A A0A8E5NQ91 1 314 DBREF1 9SZB B 1 96 UNP A0A8E5K7F6_9CAUD DBREF2 9SZB B A0A8E5K7F6 1 96 SEQRES 1 A 314 MET GLY ILE PHE LYS LYS ARG GLU ALA ALA GLN PRO VAL SEQRES 2 A 314 PRO GLN THR VAL ASN THR ILE ASN GLN VAL THR ILE LYS SEQRES 3 A 314 ASP ASN THR ILE VAL ALA ALA ILE ASP PHE ASN VAL ARG SEQRES 4 A 314 ASN GLU VAL ALA GLU SER VAL SER SER TYR LEU GLY ALA SEQRES 5 A 314 TYR SER LEU SER SER ASP ARG LEU SER LYS ILE THR ASN SEQRES 6 A 314 ASN THR SER PHE LEU HIS ARG LEU VAL LYS HIS VAL LEU SEQRES 7 A 314 LYS HIS GLU GLN THR PHE ILE TYR ASN SER GLU THR TYR SEQRES 8 A 314 GLY TRP VAL MET THR ASP THR VAL VAL LEU ASN GLN THR SEQRES 9 A 314 ARG VAL THR MET THR ILE GLN LEU PRO ASN PRO TYR ASN SEQRES 10 A 314 SER SER ILE TYR LEU SER VAL PRO LEU LYS ASP VAL GLY SEQRES 11 A 314 VAL ILE ASP THR THR MET MET ASN VAL ASP THR GLU ALA SEQRES 12 A 314 ALA ASN LYS MET LEU GLU ALA ALA TYR GLU ALA VAL ILE SEQRES 13 A 314 LYS LYS LEU ASN ASN THR GLY ALA ILE LYS ALA PHE ILE SEQRES 14 A 314 SER SER ASN VAL ASP VAL GLY LEU ASN LYS MET ALA GLU SEQRES 15 A 314 ASP ALA ASN ASP LYS ILE LYS THR MET LEU LYS THR ALA SEQRES 16 A 314 SER GLU LEU ALA GLY TYR THR PHE LEU ASN LYS GLY ASP SEQRES 17 A 314 GLU VAL THR GLN MET MET PRO ASP TYR THR THR SER ASN SEQRES 18 A 314 THR ALA ASP PHE ALA ALA MET ARG ALA PHE ALA ALA SER SEQRES 19 A 314 GLN LEU SER VAL SER GLU LYS ILE LEU ASP GLY SER ALA SEQRES 20 A 314 THR ASP GLY GLU LYS VAL ALA VAL MET PHE ARG PHE LEU SEQRES 21 A 314 ASP PRO ILE LEU GLN GLN PHE LYS GLU TYR GLU PRO THR SEQRES 22 A 314 LEU ASN TYR SER ILE ARG ASP GLU MET PHE VAL ALA PHE SEQRES 23 A 314 MET THR THR GLY GLY LEU LEU ASN SER ASN LYS ILE GLU SEQRES 24 A 314 TYR TRP GLY LYS GLU LYS THR ILE ASN ASP ARG ALA SER SEQRES 25 A 314 GLN VAL SEQRES 1 B 96 MET VAL THR ILE LEU GLU GLN ALA ALA ARG GLN ALA ARG SEQRES 2 B 96 VAL SER THR SER ILE LEU GLU SER VAL ILE ASP ASN SER SEQRES 3 B 96 ILE PHE ARG LEU LYS THR ALA GLY VAL ILE VAL LYS ALA SEQRES 4 B 96 ASP ASP GLU TYR LEU PRO ASN GLU LEU LEU PRO ILE VAL SEQRES 5 B 96 VAL GLN PHE ILE ALA ILE ASP ALA ARG ILE THR LEU LEU SEQRES 6 B 96 GLY ASP GLU LEU TRP ALA PRO SER VAL ALA ASN MET GLN SEQRES 7 B 96 GLN LYS ARG GLN GLY LEU ILE ASN THR ILE GLU LEU LEU SEQRES 8 B 96 SER LYS GLY ASN GLU HELIX 1 AA1 ASN A 37 TYR A 49 1 13 HELIX 2 AA2 ASN A 65 HIS A 80 1 16 HELIX 3 AA3 THR A 141 THR A 162 1 22 HELIX 4 AA4 GLY A 176 LEU A 198 1 23 HELIX 5 AA5 ASN A 221 LEU A 236 1 16 HELIX 6 AA6 SER A 239 ASP A 244 1 6 HELIX 7 AA7 THR A 248 PHE A 259 1 12 HELIX 8 AA8 LEU A 260 GLU A 271 1 12 HELIX 9 AA9 ASP A 280 MET A 282 5 3 HELIX 10 AB1 PHE A 283 THR A 289 1 7 HELIX 11 AB2 LEU A 293 ILE A 298 1 6 HELIX 12 AB3 THR B 3 ARG B 13 1 11 HELIX 13 AB4 SER B 15 ALA B 33 1 19 HELIX 14 AB5 LEU B 48 LEU B 64 1 17 HELIX 15 AB6 PRO B 72 LYS B 93 1 22 SHEET 1 AA1 2 TYR A 53 SER A 56 0 SHEET 2 AA1 2 ASN A 275 ILE A 278 -1 O SER A 277 N SER A 54 SHEET 1 AA2 3 GLY A 92 THR A 96 0 SHEET 2 AA2 3 GLN A 82 SER A 88 -1 N PHE A 84 O THR A 96 SHEET 3 AA2 3 GLY A 130 ASP A 133 -1 O ILE A 132 N THR A 83 SHEET 1 AA3 3 VAL A 99 LEU A 101 0 SHEET 2 AA3 3 ARG A 105 GLN A 111 -1 O THR A 107 N VAL A 100 SHEET 3 AA3 3 SER A 119 PRO A 125 -1 O VAL A 124 N VAL A 106 SHEET 1 AA4 2 ALA A 167 ILE A 169 0 SHEET 2 AA4 2 VAL A 210 GLN A 212 -1 O THR A 211 N PHE A 168 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 218 0 0 15 10 0 0 6 2763 2 0 33 END