HEADER VIRAL PROTEIN 23-DEC-23 8RK9 TITLE STOPPER PROTEIN OF BACTERIOPHAGE JBD30 COMPUTED IN C6 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: STOPPER PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE JBD30; SOURCE 3 ORGANISM_TAXID: 1223260 KEYWDS BACTERIOPHAGE JBD30, VIRION, CONNECTOR, STOPPER, HEAD COMPLETION KEYWDS 2 PROTEIN 2, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR L.VALENTOVA,T.FUZIK,P.PLEVKA REVDAT 2 28-AUG-24 8RK9 1 JRNL REVDAT 1 14-AUG-24 8RK9 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. 3.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, EPU, GCTF, COOT, RELION, REMARK 3 RELION, RELION, RELION, RELION 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 : AB INITIO MODEL 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) : 3.950 REMARK 3 NUMBER OF PARTICLES : 3559 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 8RK9 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_1292135488. 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 SOLARUS II REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOTTING FORCE 0, BLOTTING TIME REMARK 245 2 S, WAITING TIME 15 S 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 291.51201 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -78.11041 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 504.91361 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 135.29119 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 426.80320 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 426.80320 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 135.29119 REMARK 350 BIOMT2 5 -0.866025 -0.500000 0.000000 504.91361 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 -78.11041 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 291.51201 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 SER A 2 REMARK 465 ASP A 3 REMARK 465 PRO A 4 REMARK 465 PHE A 5 REMARK 465 ASP A 6 REMARK 465 TYR A 7 REMARK 465 LEU A 8 REMARK 465 ASP A 33 REMARK 465 LEU A 34 REMARK 465 ALA A 35 REMARK 465 VAL A 148 REMARK 465 TYR A 149 REMARK 465 PRO A 150 REMARK 465 ARG A 151 REMARK 465 ILE A 152 REMARK 465 LYS A 153 REMARK 465 SER A 154 REMARK 465 TRP A 155 REMARK 465 LYS A 156 REMARK 465 PRO A 157 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 SER A 20 30.38 -140.43 REMARK 500 ALA A 60 -169.37 -160.19 REMARK 500 GLN A 66 172.16 -58.76 REMARK 500 ARG A 67 -0.97 61.09 REMARK 500 THR A 71 98.26 -68.24 REMARK 500 SER A 88 11.53 81.66 REMARK 500 SER A 134 -1.47 72.08 REMARK 500 LEU A 137 129.92 -170.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19265 RELATED DB: EMDB REMARK 900 STOPPER PROTEIN OF BACTERIOPHAGE JBD30 COMPUTED IN C6 SYMMETRY DBREF 8RK9 A 1 157 UNP L7P7R4 L7P7R4_9CAUD 1 157 SEQRES 1 A 157 MET SER ASP PRO PHE ASP TYR LEU PHE LEU GLU PRO LEU SEQRES 2 A 157 LEU ILE GLU ARG ILE ARG SER GLU VAL PRO GLY LEU ALA SEQRES 3 A 157 ILE VAL SER GLY VAL PRO ASP LEU ALA THR LEU SER GLU SEQRES 4 A 157 GLN ASP GLN PRO ALA PRO SER ALA TYR VAL VAL TYR LEU SEQRES 5 A 157 GLY ASP GLU THR GLY THR GLY ALA ASP HIS GLN GLY GLY SEQRES 6 A 157 GLN ARG ALA ILE GLN THR VAL GLY GLN GLN TRP ALA VAL SEQRES 7 A 157 VAL LEU VAL VAL HIS TYR ALA ASP SER SER ASN SER GLY SEQRES 8 A 157 GLU GLY ALA ARG ARG GLU ALA GLY PRO LEU LEU GLY ARG SEQRES 9 A 157 LEU VAL LYS ALA LEU THR GLY TRP ALA PRO ALA ILE ASP SEQRES 10 A 157 VAL ALA PRO LEU ALA ARG SER ALA ARG GLN SER PRO ALA SEQRES 11 A 157 THR TYR ALA SER GLY TYR LEU TYR PHE PRO LEU VAL PHE SEQRES 12 A 157 THR ALA ARG PHE VAL TYR PRO ARG ILE LYS SER TRP LYS SEQRES 13 A 157 PRO HELIX 1 AA1 GLU A 11 ARG A 19 1 9 HELIX 2 AA2 GLY A 65 ILE A 69 5 5 HELIX 3 AA3 GLU A 97 LEU A 109 1 13 SHEET 1 AA1 3 VAL A 49 VAL A 50 0 SHEET 2 AA1 3 GLY A 73 VAL A 78 -1 O ALA A 77 N VAL A 50 SHEET 3 AA1 3 ASP A 54 GLU A 55 -1 N GLU A 55 O GLY A 73 SHEET 1 AA2 3 VAL A 49 VAL A 50 0 SHEET 2 AA2 3 GLY A 73 VAL A 78 -1 O ALA A 77 N VAL A 50 SHEET 3 AA2 3 PHE A 143 THR A 144 -1 O PHE A 143 N TRP A 76 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