HEADER VIRUS 26-MAY-22 8A05 TITLE BACTERIOPHAGE PHICJT23 SPIKE PROTEIN PENTON DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN P13 N-TERMINAL, CAPSID INTERNAL DOMAIN; COMPND 3 CHAIN: P; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: UNKNOWN VERTEX PROTEIN; COMPND 6 CHAIN: X SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FLAVOBACTERIUM PHAGE; SOURCE 3 ORGANISM_TAXID: 908820; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 6 ORGANISM_TAXID: 32644 KEYWDS BACTERIOPHAGE, PHICJT23, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR I.RISSANEN,J.T.HUISKONEN REVDAT 1 14-DEC-22 8A05 0 JRNL AUTH N.KEJZAR,E.LAANTO,I.RISSANEN,V.ABRISHAMI,M.SELVARAJ, JRNL AUTH 2 S.MOINEAU,J.RAVANTTI,L.R.SUNDBERG,J.T.HUISKONEN JRNL TITL CRYO-EM STRUCTURE OF SSDNA BACTERIOPHAGE PHI CJT23 PROVIDES JRNL TITL 2 INSIGHT INTO EARLY VIRUS EVOLUTION. JRNL REF NAT COMMUN V. 13 7478 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36463224 JRNL DOI 10.1038/S41467-022-35123-6 REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : COOT, PHENIX 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 18122 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 8A05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292123203. 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 : UNIDENTIFIED REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 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 TECNAI ARCTICA REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 1500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: P, X 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 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 P 30 -6.44 75.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15048 RELATED DB: EMDB REMARK 900 BACTERIOPHAGE PHICJT23 MAJOR CAPSID PROTEIN TRIMER TYPE 1 DBREF 8A05 P 1 91 PDB 8A05 8A05 1 91 DBREF 8A05 X 1 5 PDB 8A05 8A05 1 5 SEQRES 1 P 91 MET ASN PHE ILE GLN TYR ILE ASP ASP SER TYR ALA VAL SEQRES 2 P 91 LYS VAL LYS GLU ILE ASN SER SER GLU GLY PHE TYR ILE SEQRES 3 P 91 ASN GLY ILE GLN THR PRO PHE PHE ILE LEU SER VAL PHE SEQRES 4 P 91 ILE GLY ASN LYS ARG VAL THR GLY VAL GLU PHE ASN ASN SEQRES 5 P 91 TYR ASP SER LEU PRO MET LEU SER VAL ILE ASN ASP LEU SEQRES 6 P 91 GLY ASN ILE ASP LEU ASN VAL ILE PRO GLN ASN TYR PHE SEQRES 7 P 91 ALA THR ALA PHE THR GLU ILE TYR PHE ASN ILE PRO PHE SEQRES 1 X 5 UNK UNK UNK UNK UNK HELIX 1 AA1 SER P 55 ASP P 64 1 10 HELIX 2 AA2 PRO P 74 PHE P 78 5 5 SHEET 1 AA1 4 VAL P 13 GLU P 17 0 SHEET 2 AA1 4 PHE P 3 ILE P 7 -1 N ILE P 4 O LYS P 16 SHEET 3 AA1 4 PHE P 34 ILE P 40 -1 O PHE P 39 N PHE P 3 SHEET 4 AA1 4 LYS P 43 ARG P 44 -1 O LYS P 43 N ILE P 40 SHEET 1 AA2 2 PHE P 24 ILE P 26 0 SHEET 2 AA2 2 ILE P 85 PHE P 87 -1 O PHE P 87 N PHE P 24 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