HEADER VIRUS 03-JAN-23 8FOU TITLE STRUCTURE OF AGROBACTERIUM TUMEFACIENS BACTERIOPHAGE MILANO CONTRACTED TITLE 2 TAIL-TUBE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRION-ASSOCIATED PROTEIN; COMPND 3 CHAIN: I; COMPND 4 SYNONYM: TAIL-TUBE, GP21 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM PHAGE MILANO; SOURCE 3 ORGANISM_TAXID: 2557550 KEYWDS MYOPHAGE, REDOX TRIGGER, DISULFIDES, VIRUS EXPDTA ELECTRON MICROSCOPY AUTHOR R.R.SONANI,P.G.LEIMAN,F.WANG,M.A.B.KREUTZBERGER,A.SEBASTIAN, AUTHOR 2 N.C.ESTEVES,R.J.KELLY,B.SCHARF,E.H.EGELMAN REVDAT 2 07-FEB-24 8FOU 1 JRNL REVDAT 1 17-JAN-24 8FOU 0 JRNL AUTH R.R.SONANI,L.K.PALMER,N.C.ESTEVES,A.A.HORTON,A.L.SEBASTIAN, JRNL AUTH 2 R.J.KELLY,F.WANG,M.A.B.KREUTZBERGER,W.K.RUSSELL,P.G.LEIMAN, JRNL AUTH 3 B.E.SCHARF,E.H.EGELMAN JRNL TITL AN EXTENSIVE DISULFIDE BOND NETWORK PREVENTS TAIL JRNL TITL 2 CONTRACTION IN AGROBACTERIUM TUMEFACIENS PHAGE MILANO. JRNL REF NAT COMMUN V. 15 756 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38272938 JRNL DOI 10.1038/S41467-024-44959-Z REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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) : 3.300 REMARK 3 NUMBER OF PARTICLES : 160399 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 8FOU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271130. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : AGROBACTERIUM PHAGE MILANO 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 : 7.40 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2400.00 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) : 4800.00 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) : 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = 28.21 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 34.07 ANGSTROMS REMARK 300 IN ADDITION, THERE IS 6-FOLD CIRCULAR REMARK 300 SYMMETRY AROUND THE HELIX AXIS 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 APPLY THE FOLLOWING TO CHAINS: I 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 0.554438 0.832225 0.000000 -81.16749 REMARK 350 BIOMT2 2 -0.832225 0.554438 0.000000 268.23050 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -68.13600 REMARK 350 BIOMT1 3 0.881600 0.471997 0.000000 -74.22638 REMARK 350 BIOMT2 3 -0.471997 0.881600 0.000000 123.93487 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -34.06800 REMARK 350 BIOMT1 4 0.881600 -0.471997 0.000000 123.93487 REMARK 350 BIOMT2 4 0.471997 0.881600 0.000000 -74.22638 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 34.06800 REMARK 350 BIOMT1 5 0.997947 -0.064045 0.000000 13.87507 REMARK 350 BIOMT2 5 0.064045 0.997947 0.000000 -13.01316 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -68.13600 REMARK 350 BIOMT1 6 0.849561 -0.527490 0.000000 142.30931 REMARK 350 BIOMT2 6 0.527490 0.849561 0.000000 -79.14980 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -34.06800 REMARK 350 BIOMT1 7 0.500000 -0.866025 0.000000 286.75324 REMARK 350 BIOMT2 7 0.866025 0.500000 0.000000 -76.83530 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 0.032039 -0.999487 0.000000 413.00261 REMARK 350 BIOMT2 8 0.999487 0.032039 0.000000 -6.61774 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 34.06800 REMARK 350 BIOMT1 9 0.443509 -0.896270 0.000000 304.96051 REMARK 350 BIOMT2 9 0.896270 0.443509 0.000000 -71.32572 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -68.13600 REMARK 350 BIOMT1 10 -0.032039 -0.999487 0.000000 426.45363 REMARK 350 BIOMT2 10 0.999487 -0.032039 0.000000 6.83328 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -34.06800 REMARK 350 BIOMT1 11 -0.500000 -0.866025 0.000000 496.67118 REMARK 350 BIOMT2 11 0.866025 -0.500000 0.000000 133.08264 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 12 -0.849561 -0.527490 0.000000 498.98568 REMARK 350 BIOMT2 12 0.527490 -0.849561 0.000000 277.52658 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 34.06800 REMARK 350 BIOMT1 13 -0.554438 -0.832225 0.000000 501.00338 REMARK 350 BIOMT2 13 0.832225 -0.554438 0.000000 151.60539 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 -68.13600 REMARK 350 BIOMT1 14 -0.881600 -0.471997 0.000000 494.06226 REMARK 350 BIOMT2 14 0.471997 -0.881600 0.000000 295.90102 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 -34.06800 REMARK 350 BIOMT1 15 -1.000000 0.000000 0.000000 419.83588 REMARK 350 BIOMT2 15 0.000000 -1.000000 0.000000 419.83588 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 16 -0.881600 0.471997 0.000000 295.90101 REMARK 350 BIOMT2 16 -0.471997 -0.881600 0.000000 494.06226 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 34.06800 REMARK 350 BIOMT1 17 -0.997947 0.064045 0.000000 405.96081 REMARK 350 BIOMT2 17 -0.064045 -0.997947 0.000000 432.84905 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 -68.13600 REMARK 350 BIOMT1 18 -0.849561 0.527490 0.000000 277.52658 REMARK 350 BIOMT2 18 -0.527490 -0.849561 0.000000 498.98568 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 -34.06800 REMARK 350 BIOMT1 19 -0.500000 0.866025 0.000000 133.08264 REMARK 350 BIOMT2 19 -0.866025 -0.500000 0.000000 496.67118 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 20 -0.032039 0.999487 0.000000 6.83328 REMARK 350 BIOMT2 20 -0.999487 -0.032039 0.000000 426.45363 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 34.06800 REMARK 350 BIOMT1 21 -0.443509 0.896270 0.000000 114.87538 REMARK 350 BIOMT2 21 -0.896270 -0.443509 0.000000 491.16160 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 -68.13600 REMARK 350 BIOMT1 22 0.032039 0.999487 0.000000 -6.61774 REMARK 350 BIOMT2 22 -0.999487 0.032039 0.000000 413.00261 REMARK 350 BIOMT3 22 0.000000 0.000000 1.000000 -34.06800 REMARK 350 BIOMT1 23 0.500000 0.866025 0.000000 -76.83530 REMARK 350 BIOMT2 23 -0.866025 0.500000 0.000000 286.75324 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 24 0.849561 0.527490 0.000000 -79.14980 REMARK 350 BIOMT2 24 -0.527490 0.849561 0.000000 142.30931 REMARK 350 BIOMT3 24 0.000000 0.000000 1.000000 34.06800 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 I 1 REMARK 465 ALA I 2 REMARK 465 PRO I 130 REMARK 465 GLY I 131 REMARK 465 SER I 132 REMARK 465 LEU I 133 REMARK 465 ALA I 134 REMARK 465 ALA I 135 REMARK 465 ALA I 136 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 ASN I 4 -11.36 -140.51 REMARK 500 ASN I 52 55.80 32.28 REMARK 500 LEU I 128 74.38 52.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8FOP RELATED DB: PDB REMARK 900 RELATED ID: EMD-29354 RELATED DB: EMDB REMARK 900 STRUCTURE OF AGROBACTERIUM TUMEFACIENS BACTERIOPHAGE MILANO CURVED REMARK 900 TAIL DBREF1 8FOU I 1 136 UNP A0A482MHE7_9CAUD DBREF2 8FOU I A0A482MHE7 1 136 SEQRES 1 I 136 MET ALA CYS ASN LYS GLN ASN GLY VAL LYS ASN ILE LEU SEQRES 2 I 136 ILE THR PHE THR ASP CYS ASP THR GLN GLU VAL ILE GLY SEQRES 3 I 136 PRO ILE SER HIS GLU GLN PRO ASP ASP THR LEU PRO THR SEQRES 4 I 136 TYR LYS ASN CYS ALA TRP THR ASN THR ALA LEU THR ASN SEQRES 5 I 136 GLY TYR VAL GLN ARG SER ALA SER ASN ALA THR MET THR SEQRES 6 I 136 LEU PRO VAL VAL ARG ASP LEU ARG VAL PRO LEU ALA PHE SEQRES 7 I 136 TYR GLN GLY CYS ALA GLN VAL ASP VAL GLN VAL GLU LYS SEQRES 8 I 136 PHE ASP GLY THR VAL MET THR LEU THR GLU GLY ALA VAL SEQRES 9 I 136 VAL GLU PRO GLU GLU SER ASP GLY ARG SER VAL THR MET SEQRES 10 I 136 ASN ILE VAL ALA SER GLU ILE ASP GLU LEU LEU PRO PRO SEQRES 11 I 136 GLY SER LEU ALA ALA ALA HELIX 1 AA1 LEU I 50 TYR I 54 5 5 HELIX 2 AA2 PRO I 75 GLN I 80 5 6 SHEET 1 AA1 4 VAL I 24 HIS I 30 0 SHEET 2 AA1 4 VAL I 9 ASP I 18 -1 N PHE I 16 O ILE I 25 SHEET 3 AA1 4 ALA I 83 LYS I 91 -1 O GLU I 90 N LYS I 10 SHEET 4 AA1 4 VAL I 96 THR I 98 -1 O MET I 97 N VAL I 89 SHEET 1 AA2 4 THR I 39 TYR I 40 0 SHEET 2 AA2 4 ALA I 62 VAL I 69 -1 O THR I 65 N THR I 39 SHEET 3 AA2 4 SER I 114 ALA I 121 -1 O ILE I 119 N MET I 64 SHEET 4 AA2 4 ALA I 103 VAL I 104 -1 N ALA I 103 O VAL I 120 SHEET 1 AA3 2 TRP I 45 THR I 46 0 SHEET 2 AA3 2 SER I 58 ALA I 59 -1 O SER I 58 N THR I 46 CISPEP 1 GLY I 26 PRO I 27 0 -0.34 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