HEADER VIRUS 23-DEC-23 8RK8 TITLE TAIL OF BACTERIOPHAGE JBD30 COMPUTED IN C6 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR TAIL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MAJOR TAIL PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE JBD30; SOURCE 3 ORGANISM_TAXID: 1223260 KEYWDS BACTERIOPHAGE JBD30, VIRION, TAIL, MAJOR TAIL PROTEIN, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR L.VALENTOVA,T.FUZIK,P.PLEVKA REVDAT 2 28-AUG-24 8RK8 1 JRNL REVDAT 1 14-AUG-24 8RK8 0 JRNL AUTH L.VALENTOVA,T.FUZIK,J.NOVACEK,Z.HLAVENKOVA,J.POSPISIL, JRNL AUTH 2 P.PLEVKA JRNL TITL STRUCTURE AND REPLICATION OF PSEUDOMONAS AERUGINOSA PHAGE JRNL TITL 2 JBD30. JRNL REF EMBO J. 2024 JRNL REFN ESSN 1460-2075 JRNL PMID 39143239 JRNL DOI 10.1038/S44318-024-00195-1 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.VALENTOVA,P.PLEVKA,T.FUZIK,J.NOVACEK,J.POSPISIL REMARK 1 TITL STRUCTURE AND REPLICATION OF PSEUDOMONAS AERUGINOSA PHAGE REMARK 1 TITL 2 JBD30 REMARK 1 REF EMBO J. 2024 REMARK 1 REFN ESSN 1460-2075 REMARK 1 DOI 10.1038/S44318-024-0 REMARK 2 REMARK 2 RESOLUTION. 3.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN2, EPU, GCTF, COOT, RELION, RELION, REMARK 3 RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER 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) : 3.880 REMARK 3 NUMBER OF PARTICLES : 1759 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8RK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292135489. 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 : PSEUDOMONAS PHAGE JBD30 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : GATAN SOLARIS II REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOTTING FORCE 0, BLOTTING TIME REMARK 245 2S, WAITING TIME 15S REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : PHAGE JBD30 WAS PROPAGATED IN REMARK 245 P. AERUGINOSA STRAIN BAA-28 AND PURIFIED USING CSCL GRADIENT. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 12356 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) : 600.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3400.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 0.500000 -0.866025 0.000000 145.75600 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -39.05520 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 252.45680 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 67.64560 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 213.40160 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 213.40160 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 5 -0.500000 0.866025 0.000000 67.64560 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 252.45680 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -39.05520 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 145.75600 REMARK 350 BIOMT3 6 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 ALA A 2 REMARK 465 GLN A 3 REMARK 465 GLU A 4 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 GLN A 30 -158.07 70.09 REMARK 500 ALA A 103 -169.70 -78.58 REMARK 500 ASP A 104 39.86 39.44 REMARK 500 ASP A 143 41.21 36.24 REMARK 500 PRO A 212 157.62 -45.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19264 RELATED DB: EMDB REMARK 900 TAIL OF BACTERIOPHAGE JBD30 COMPUTED IN C6 SYMMETRY DBREF 8RK8 A 1 256 UNP L7P801 L7P801_9CAUD 1 256 SEQRES 1 A 256 MET ALA GLN GLU THR TYR PHE TYR GLY GLN GLY GLU ILE SEQRES 2 A 256 ASP ALA ALA PRO ILE VAL ASN GLY VAL LEU GLY LYS TRP SEQRES 3 A 256 ARG TRP ILE GLN ASP VAL SER ALA MET SER ILE GLN LEU SEQRES 4 A 256 ALA VAL GLU LYS VAL GLU HIS LYS GLU SER TYR SER GLY SEQRES 5 A 256 GLN LYS ALA LEU VAL ARG SER PHE PRO ILE GLY LYS THR SEQRES 6 A 256 ALA THR VAL ASN ILE THR LEU HIS SER ILE GLY PRO ASP SEQRES 7 A 256 ASN LEU ALA LEU THR LEU TYR GLY LYS VAL VAL ALA LYS SEQRES 8 A 256 ALA ALA GLY SER VAL THR GLY GLU VAL LEU PRO ALA ASP SEQRES 9 A 256 LEU VAL ALA GLY ASP VAL ILE ARG LEU ALA ASN PHE GLY SEQRES 10 A 256 VAL SER GLU LEU VAL ILE THR ASP SER ALA SER SER PRO SEQRES 11 A 256 ALA PRO LEU ASP PRO GLN TYR TYR ALA LEU ARG ALA ASP SEQRES 12 A 256 GLY ALA TYR GLY GLU VAL GLN LEU LEU GLY LEU PRO THR SEQRES 13 A 256 PRO ALA PRO THR GLN PRO PHE LYS ALA ALA TYR GLU TYR SEQRES 14 A 256 ALA ALA THR LYS GLN VAL GLY MET PHE THR ALA PRO GLN SEQRES 15 A 256 PRO THR VAL ALA LEU ARG TYR LYS GLY ILE ASN LEU ALA SEQRES 16 A 256 GLU GLY GLY ALA PRO VAL ILE VAL GLU LEU TYR LYS VAL SEQRES 17 A 256 ALA THR ASP PRO LEU GLN GLU LEU ALA LEU ILE SER ASP SEQRES 18 A 256 GLY ASN THR VAL ALA GLY MET GLN ILE SER GLY GLY ILE SEQRES 19 A 256 LEU LEU ASP THR SER LYS PRO ASP THR GLY ASP LEU GLY SEQRES 20 A 256 ARG PHE GLY ARG ILE ILE GLN LEU GLY HELIX 1 AA1 GLY A 76 LEU A 84 1 9 HELIX 2 AA2 ASP A 134 GLN A 136 5 3 HELIX 3 AA3 ALA A 142 ALA A 145 5 4 SHEET 1 AA1 7 VAL A 22 LEU A 23 0 SHEET 2 AA1 7 GLY A 9 VAL A 19 -1 N VAL A 19 O VAL A 22 SHEET 3 AA1 7 THR A 184 ASN A 193 -1 O THR A 184 N ILE A 18 SHEET 4 AA1 7 ALA A 199 ASP A 211 -1 O LEU A 205 N LEU A 187 SHEET 5 AA1 7 MET A 228 ILE A 234 -1 O SER A 231 N ASP A 211 SHEET 6 AA1 7 LEU A 56 LEU A 72 -1 N ILE A 70 O ILE A 230 SHEET 7 AA1 7 VAL A 32 LYS A 47 -1 N GLU A 42 O ILE A 62 SHEET 1 AA2 5 ARG A 27 TRP A 28 0 SHEET 2 AA2 5 GLY A 9 VAL A 19 -1 N ALA A 15 O ARG A 27 SHEET 3 AA2 5 THR A 184 ASN A 193 -1 O THR A 184 N ILE A 18 SHEET 4 AA2 5 ALA A 199 ASP A 211 -1 O LEU A 205 N LEU A 187 SHEET 5 AA2 5 GLY A 250 GLN A 254 -1 O ILE A 253 N ILE A 202 SHEET 1 AA3 2 VAL A 88 LYS A 91 0 SHEET 2 AA3 2 THR A 172 VAL A 175 -1 O THR A 172 N LYS A 91 SHEET 1 AA4 3 GLY A 94 VAL A 100 0 SHEET 2 AA4 3 PHE A 163 TYR A 169 -1 O ALA A 165 N GLU A 99 SHEET 3 AA4 3 SER A 119 ASP A 125 -1 N VAL A 122 O ALA A 166 SHEET 1 AA5 3 VAL A 110 ARG A 112 0 SHEET 2 AA5 3 GLU A 148 LEU A 151 -1 O VAL A 149 N ILE A 111 SHEET 3 AA5 3 TYR A 138 ARG A 141 -1 N ALA A 139 O GLN A 150 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