HEADER VIRUS 23-DEC-23 8RK4 TITLE RECEPTOR BINDING PROTEIN OF BACTERIOPHAGE JBD30 COMPUTED WITH C3 TITLE 2 SYMMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF2793 DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: RECEPTOR BINDING PROTEIN; COMPND 5 OTHER_DETAILS: RECEPTOR BINDING PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE JBD30; SOURCE 3 ORGANISM_TAXID: 1223260 KEYWDS BACTERIOPHAGE, VIRION, RECEPTOR BINDING PROTEIN, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR L.VALENTOVA,T.FUZIK,P.PLEVKA REVDAT 2 28-AUG-24 8RK4 1 JRNL REVDAT 1 14-AUG-24 8RK4 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. 4.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, EPU, GCTF, COOT, RELION, REMARK 3 RELION, 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 : 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) : 4.740 REMARK 3 NUMBER OF PARTICLES : 4088 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 8RK4 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_1292135455. 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: 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 252.45680 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 67.64560 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 67.64560 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 252.45680 REMARK 350 BIOMT3 3 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 B 1 REMARK 465 THR B 2 REMARK 465 LEU B 3 REMARK 465 TYR B 4 REMARK 465 MET B 5 REMARK 465 GLY B 6 REMARK 465 PRO B 7 REMARK 465 ASN B 8 REMARK 465 THR B 9 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASP B 33 NH2 ARG B 36 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 LEU B 16 151.61 59.28 REMARK 500 LEU B 35 2.44 -68.08 REMARK 500 ASN B 68 -3.40 74.50 REMARK 500 SER B 298 -163.39 69.96 REMARK 500 THR B 303 -147.24 54.24 REMARK 500 ARG B 306 117.56 -164.29 REMARK 500 ASN B 323 35.91 71.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19259 RELATED DB: EMDB REMARK 900 RECEPTOR BINDING PROTEIN OF BACTERIOPHAGE JBD30 COMPUTED WITH C3 REMARK 900 SYMMETRY DBREF 8RK4 B 1 382 UNP L7P803 L7P803_9CAUD 1 382 SEQRES 1 B 382 MET THR LEU TYR MET GLY PRO ASN THR GLY LEU LEU ILE SEQRES 2 B 382 ASN GLY LEU PRO GLY GLU GLY HIS TYR SER ASP LEU ILE SEQRES 3 B 382 ARG MET TRP ARG TRP ASP ASP PHE LEU ARG GLN PRO VAL SEQRES 4 B 382 VAL LYS GLY ARG VAL ALA THR LEU PRO THR THR GLY GLN SEQRES 5 B 382 ALA GLU GLY ASP THR TYR ILE PHE THR GLY SER GLY SER SEQRES 6 B 382 ASN GLN ASN ARG LEU ALA ARG TRP TRP ALA THR GLY ALA SEQRES 7 B 382 THR THR ALA ILE TRP GLU TYR MET PRO PRO ARG LEU GLY SEQRES 8 B 382 TRP ARG VAL GLN VAL ALA ASN GLU THR THR PRO SER GLY SEQRES 9 B 382 GLN VAL LYS THR TYR GLU TYR SER GLY THR ALA TRP VAL SEQRES 10 B 382 GLU LEU VAL GLY GLY MET SER ASP ALA PRO SER ASP GLY SEQRES 11 B 382 LYS ALA TYR ALA ARG GLU SER GLY ALA TRP THR GLU LEU SEQRES 12 B 382 GLY SER ALA ALA LYS SER ALA LEU ASN VAL LEU PRO PHE SEQRES 13 B 382 MET ASN LEU MET PRO ASP MET GLY ARG PHE ALA GLY THR SEQRES 14 B 382 ALA ALA ASN PRO LEU ALA THR MET PHE THR THR SER TRP SEQRES 15 B 382 THR PRO SER SER PHE LEU ASN GLY TRP ASN GLY ALA THR SEQRES 16 B 382 VAL ALA ASP GLY GLY LYS PHE ALA PHE ASP ASN SER THR SEQRES 17 B 382 ASN GLY GLY ALA GLY PRO ALA LEU ASN ALA ARG VAL GLN SEQRES 18 B 382 ALA LEU LEU ALA ALA MET GLY ARG THR TRP THR SER VAL SEQRES 19 B 382 SER ARG TYR GLY VAL GLU PHE PHE THR ALA VAL LEU THR SEQRES 20 B 382 ALA GLY SER GLN THR THR THR GLY SER ALA GLY ALA ASP SEQRES 21 B 382 GLY VAL THR ARG TYR LEU CYS CYS SER ASN GLY SER LYS SEQRES 22 B 382 THR VAL PHE ASN ALA GLY GLY TRP ALA THR VAL VAL MET SEQRES 23 B 382 TRP LEU ARG VAL GLU SER GLY SER ALA HIS ILE SER SER SEQRES 24 B 382 ALA PRO TYR THR THR HIS ARG LEU TRP ILE ASN GLY ALA SEQRES 25 B 382 VAL ALA ALA PRO GLY VAL VAL LEU PRO ALA ASN GLN TRP SEQRES 26 B 382 VAL HIS LEU ARG PHE SER MET GLN SER TYR ASN GLY TYR SEQRES 27 B 382 ASP ASN ALA CYS PRO TYR ILE TYR ALA SER ALA GLY ALA SEQRES 28 B 382 GLN ILE ALA PHE ALA CYS PRO ALA TRP PHE GLY GLY LEU SEQRES 29 B 382 VAL ASP PRO GLY ILE HIS VAL ALA PRO ILE LEU THR ILE SEQRES 30 B 382 ASN GLY ALA SER ALA HELIX 1 AA1 PRO B 17 GLU B 19 5 3 HELIX 2 AA2 GLY B 20 LEU B 35 1 16 HELIX 3 AA3 GLY B 144 LYS B 148 5 5 HELIX 4 AA4 ASN B 217 GLY B 228 1 12 HELIX 5 AA5 TRP B 231 ARG B 236 1 6 SHEET 1 AA1 3 GLY B 42 VAL B 44 0 SHEET 2 AA1 3 TYR B 58 PHE B 60 1 O ILE B 59 N VAL B 44 SHEET 3 AA1 3 ARG B 69 LEU B 70 -1 O ARG B 69 N PHE B 60 SHEET 1 AA2 2 ARG B 72 TRP B 73 0 SHEET 2 AA2 2 TRP B 83 GLU B 84 -1 O GLU B 84 N ARG B 72 SHEET 1 AA3 3 GLN B 95 THR B 100 0 SHEET 2 AA3 3 VAL B 106 TYR B 111 -1 O LYS B 107 N VAL B 96 SHEET 3 AA3 3 TRP B 116 GLU B 118 -1 O VAL B 117 N GLU B 110 SHEET 1 AA4 2 TYR B 133 GLU B 136 0 SHEET 2 AA4 2 ALA B 139 GLU B 142 -1 O ALA B 139 N GLU B 136 SHEET 1 AA5 2 ASN B 189 GLY B 190 0 SHEET 2 AA5 2 CYS B 268 SER B 269 -1 O SER B 269 N ASN B 189 SHEET 1 AA6 7 THR B 195 PHE B 202 0 SHEET 2 AA6 7 PHE B 241 THR B 247 -1 O THR B 243 N GLY B 199 SHEET 3 AA6 7 GLN B 352 PHE B 361 -1 O ILE B 353 N LEU B 246 SHEET 4 AA6 7 TRP B 281 VAL B 290 -1 N ARG B 289 O ALA B 354 SHEET 5 AA6 7 VAL B 326 GLN B 333 -1 O MET B 332 N ALA B 282 SHEET 6 AA6 7 ARG B 306 ILE B 309 -1 N ARG B 306 O SER B 331 SHEET 7 AA6 7 ALA B 312 ALA B 314 -1 O ALA B 312 N ILE B 309 SHEET 1 AA7 4 GLY B 255 ALA B 257 0 SHEET 2 AA7 4 THR B 263 LEU B 266 -1 O ARG B 264 N SER B 256 SHEET 3 AA7 4 ILE B 345 ALA B 347 -1 O ALA B 347 N TYR B 265 SHEET 4 AA7 4 ALA B 295 ILE B 297 -1 N HIS B 296 O TYR B 346 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