HEADER VIRAL PROTEIN 04-FEB-25 9I8C TITLE GBSV1 PORTAL PROTEIN WITHOUT THE N-TERMINAL TAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHAGE PORTAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS PHAGE GBSV1; SOURCE 3 ORGANISM_TAXID: 365048; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GBSV1, PORTAL PROTEIN, GEOBACILLUS PHAGE GSBV1, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR P.J.CHONG,M.CHECHIK,H.JENKINS,S.GREIVE,F.ANTSON REVDAT 1 18-FEB-26 9I8C 0 JRNL AUTH P.J.CHONG,M.CHECHIK,H.JENKINS,S.GREIVE,F.ANTSON JRNL TITL GBSV1 PORTAL PROTEIN WITHOUT THE N-TERMINAL TAIL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, CTFFIND, COOT, PHENIX, REMARK 3 RELION, RELION, RELION, 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 : 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) : 2.700 REMARK 3 NUMBER OF PARTICLES : 21727 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 9I8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1292145285. 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 : GBSV1 PORTAL PROTEIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.30 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT TIME 1S, FORCE -10, WAIT REMARK 245 TIME 5S REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : THE N-TERMINAL TAIL (M1-V40) REMARK 245 WAS REMOVED DURING CLONING. THE C-TERMINAL END (E379-D406) COULD REMARK 245 NOT BE MODELLED, SO HAS BEEN OMITTED FROM THE COORDINATE FILE. 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 : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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 : OTHER REMARK 245 NOMINAL MAGNIFICATION : 240000 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: 12-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 12-MERIC REMARK 350 SOFTWARE USED: PISA 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 BIOMT1 2 0.866025 0.500000 0.000000 -47.06208 REMARK 350 BIOMT2 2 -0.500000 0.866025 0.000000 81.51392 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -0.00001 REMARK 350 BIOMT1 3 0.866025 -0.500000 0.000000 81.51398 REMARK 350 BIOMT2 3 0.500000 0.866025 0.000000 -47.06206 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -0.00006 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 175.63808 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 -47.06208 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -0.00001 REMARK 350 BIOMT1 5 0.000000 -1.000000 0.000000 257.15199 REMARK 350 BIOMT2 5 1.000000 0.000000 0.000000 -0.00001 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 304.21406 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 81.51398 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -0.00005 REMARK 350 BIOMT1 7 -0.866025 -0.500000 0.000000 304.21408 REMARK 350 BIOMT2 7 0.500000 -0.866025 0.000000 175.63808 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -0.00001 REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 257.15204 REMARK 350 BIOMT2 8 0.000000 -1.000000 0.000000 257.15199 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00001 REMARK 350 BIOMT1 9 -0.866025 0.500000 0.000000 175.63803 REMARK 350 BIOMT2 9 -0.500000 -0.866025 0.000000 304.21406 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -0.00005 REMARK 350 BIOMT1 10 -0.500000 0.866025 0.000000 81.51392 REMARK 350 BIOMT2 10 -0.866025 -0.500000 0.000000 304.21408 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -0.00001 REMARK 350 BIOMT1 11 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 11 -1.000000 0.000000 0.000000 257.15204 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 0.00001 REMARK 350 BIOMT1 12 0.500000 0.866025 0.000000 -47.06206 REMARK 350 BIOMT2 12 -0.866025 0.500000 0.000000 175.63804 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 -0.00006 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 ARG A 78 73.21 -100.30 REMARK 500 ASN A 166 73.81 52.63 REMARK 500 LEU A 248 -70.33 -80.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-52713 RELATED DB: EMDB REMARK 900 GBSV1 PORTAL PROTEIN WITHOUT THE N-TERMINAL TAIL DBREF 9I8C A 41 378 UNP Q0H263 Q0H263_9CAUD 41 378 SEQRES 1 A 338 ARG LEU SER ASP ASN PRO GLU VAL ARG MET ALA VAL HIS SEQRES 2 A 338 LYS ILE ALA ASP LEU ILE SER SER MET THR ILE TYR LEU SEQRES 3 A 338 MET GLN ASN THR GLU ASP GLY ASP ILE ARG ILE ARG ASN SEQRES 4 A 338 GLU LEU SER ARG LYS ILE ASP ILE THR PRO TYR SER LEU SEQRES 5 A 338 MET THR ARG LYS SER TRP MET TYR ASN ILE VAL TYR THR SEQRES 6 A 338 MET LEU LEU ASP GLY GLU GLY ASN SER VAL VAL PHE PRO SEQRES 7 A 338 LYS TYR THR ALA ASP GLY LEU ILE ASP GLU LEU VAL PRO SEQRES 8 A 338 LEU THR PRO SER LYS VAL ASN PHE LEU ASP THR PRO ASP SEQRES 9 A 338 GLY TYR GLN VAL LEU TYR GLY GLY GLN THR PHE ASN TYR SEQRES 10 A 338 ASP GLU VAL LEU HIS PHE ILE TYR ASN PRO ASP PRO GLU SEQRES 11 A 338 ARG PRO TYR ILE GLY ARG GLY TYR ARG VAL VAL LEU LYS SEQRES 12 A 338 ASP ILE ALA ASP ASN LEU LYS GLN ALA THR ALA THR LYS SEQRES 13 A 338 LYS SER PHE MET SER GLY LYS TYR MET PRO SER LEU ILE SEQRES 14 A 338 VAL LYS VAL ASP ALA ALA THR ALA GLU LEU SER SER GLU SEQRES 15 A 338 GLU GLY ARG ASN ALA VAL PHE LYS LYS TYR LEU GLN ALA SEQRES 16 A 338 THR GLU ALA GLY GLN PRO TRP ILE ILE PRO ALA GLU LEU SEQRES 17 A 338 LEU GLU VAL GLU GLN VAL LYS PRO LEU SER LEU LYS ASP SEQRES 18 A 338 ILE ALA ILE ASN GLU ALA VAL GLU LEU ASP LYS ARG THR SEQRES 19 A 338 VAL ALA GLY MET PHE GLY VAL PRO ALA PHE LEU LEU GLY SEQRES 20 A 338 ILE GLY GLU PHE ASN ARG ASP GLU TYR ASN ASN PHE ILE SEQRES 21 A 338 ASN SER THR ILE LEU PRO ILE ALA LYS GLY ILE GLU GLN SEQRES 22 A 338 GLU LEU THR ARG LYS LEU LEU ILE SER PRO ASP LEU TYR SEQRES 23 A 338 PHE LYS PHE ASN PRO ARG SER LEU TYR ALA TYR ASP LEU SEQRES 24 A 338 LYS GLU LEU ALA GLU VAL GLY SER ASN MET TYR VAL ARG SEQRES 25 A 338 GLY ILE MET GLU GLY ASN GLU VAL ARG ASP TRP LEU GLY SEQRES 26 A 338 LEU SER PRO LYS GLU GLY LEU SER GLU LEU VAL ILE LEU HELIX 1 AA1 ARG A 41 ASP A 44 5 4 HELIX 2 AA2 ASN A 45 MET A 62 1 18 HELIX 3 AA3 ASN A 79 ILE A 87 1 9 HELIX 4 AA4 THR A 94 LEU A 108 1 15 HELIX 5 AA5 THR A 133 SER A 135 5 3 HELIX 6 AA6 ASP A 158 VAL A 160 5 3 HELIX 7 AA7 LEU A 182 SER A 201 1 20 HELIX 8 AA8 SER A 221 LEU A 233 1 13 HELIX 9 AA9 SER A 258 ALA A 263 1 6 HELIX 10 AB1 ILE A 264 GLY A 280 1 17 HELIX 11 AB2 PRO A 282 GLY A 287 5 6 HELIX 12 AB3 ASN A 292 THR A 303 1 12 HELIX 13 AB4 THR A 303 LEU A 320 1 18 HELIX 14 AB5 PRO A 331 TYR A 335 5 5 HELIX 15 AB6 ASP A 338 ARG A 352 1 15 HELIX 16 AB7 GLU A 356 LEU A 364 1 9 SHEET 1 AA1 3 ASP A 74 ARG A 76 0 SHEET 2 AA1 3 ILE A 64 ASN A 69 -1 N GLN A 68 O ILE A 75 SHEET 3 AA1 3 LEU A 325 PHE A 329 -1 O LYS A 328 N TYR A 65 SHEET 1 AA2 3 ILE A 126 PRO A 131 0 SHEET 2 AA2 3 ASN A 113 TYR A 120 -1 N LYS A 119 O GLU A 128 SHEET 3 AA2 3 LEU A 161 ILE A 164 -1 O LEU A 161 N VAL A 116 SHEET 1 AA3 3 VAL A 137 ASP A 141 0 SHEET 2 AA3 3 TYR A 146 TYR A 150 -1 O LEU A 149 N ASN A 138 SHEET 3 AA3 3 GLN A 153 ASN A 156 -1 O PHE A 155 N VAL A 148 SHEET 1 AA4 2 PRO A 167 ASP A 168 0 SHEET 2 AA4 2 ARG A 171 GLY A 175 -1 O ILE A 174 N ASP A 168 SHEET 1 AA5 2 LEU A 208 VAL A 212 0 SHEET 2 AA5 2 LEU A 249 GLN A 253 -1 O GLU A 252 N ILE A 209 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 156 0 0 16 13 0 0 6 2693 1 0 26 END