HEADER VIRAL PROTEIN 14-JUL-16 5LIJ TITLE POLYALANINE CHAIN BUILT IN BACTERIOPHAGE PHI812K1-420 CEMENT PROTEIN TITLE 2 DENSITY MAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYALANINE CHAIN BUILT IN BACTERIOPHAGE PHI812K1-420 COMPND 3 CEMENT PROTEIN DENSITY MAP; COMPND 4 CHAIN: P; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS PHAGE 812; SOURCE 3 ORGANISM_TAXID: 307898; SOURCE 4 EXPRESSION_SYSTEM: STAPHYLOCOCCACEAE; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 90964 KEYWDS POLYVALENT STAPHYLOCOCCAL BACTORIOPHAGE, MYOVIRIDAE, TAIL SHEATH, KEYWDS 2 TAIL CONTRACTION, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.NOVACEK,M.SIBOROVA,M.BENESIK,R.PANTUCEK,J.DOSKAR,P.PLEVKA REVDAT 4 15-MAY-24 5LIJ 1 REMARK REVDAT 3 11-DEC-19 5LIJ 1 SCALE REVDAT 2 02-AUG-17 5LIJ 1 REVDAT 1 26-JUL-17 5LIJ 0 JRNL AUTH J.NOVACEK,M.SIBOROVA,M.BENESIK,R.PANTUCEK,J.DOSKAR,P.PLEVKA JRNL TITL STRUCTURE AND GENOME RELEASE OF TWORT-LIKE MYOVIRIDAE PHAGE JRNL TITL 2 WITH A DOUBLE-LAYERED BASEPLATE. JRNL REF PROC. NATL. ACAD. SCI. V. 113 9351 2016 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 27469164 JRNL DOI 10.1073/PNAS.1605883113 REMARK 2 REMARK 2 RESOLUTION. 4.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, CTFFIND, JALIGN, JALIGN, RELION, REMARK 3 J3DR 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 : 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) : 4.200 REMARK 3 NUMBER OF PARTICLES : 12018 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 5LIJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000799. 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 : HELICAL REMARK 245 NAME OF SAMPLE : STAPHYLOCOCCUS PHAGE 812 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON II (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 2000.00 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 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: P 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ALA P 1 CB - CA - C ANGL. DEV. = -13.3 DEGREES REMARK 500 ALA P 2 N - CA - CB ANGL. DEV. = -9.7 DEGREES REMARK 500 ALA P 2 N - CA - C ANGL. DEV. = 22.8 DEGREES REMARK 500 ALA P 3 N - CA - CB ANGL. DEV. = 8.8 DEGREES REMARK 500 ALA P 40 N - CA - CB ANGL. DEV. = 8.8 DEGREES REMARK 500 ALA P 66 CB - CA - C ANGL. DEV. = -19.1 DEGREES REMARK 500 ALA P 66 N - CA - C ANGL. DEV. = 38.2 DEGREES REMARK 500 ALA P 67 N - CA - CB ANGL. DEV. = 27.6 DEGREES REMARK 500 ALA P 71 CB - CA - C ANGL. DEV. = -9.2 DEGREES REMARK 500 ALA P 88 N - CA - CB ANGL. DEV. = 9.4 DEGREES REMARK 500 ALA P 124 N - CA - CB ANGL. DEV. = -15.4 DEGREES 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 ALA P 3 -171.56 -179.67 REMARK 500 ALA P 5 -159.66 -156.82 REMARK 500 ALA P 8 -164.12 -172.93 REMARK 500 ALA P 46 -73.46 -56.39 REMARK 500 ALA P 55 -70.38 -46.48 REMARK 500 ALA P 59 -65.56 -134.13 REMARK 500 ALA P 67 -35.40 -145.94 REMARK 500 ALA P 71 -30.85 -141.57 REMARK 500 ALA P 82 19.36 59.24 REMARK 500 ALA P 85 -3.13 -57.14 REMARK 500 ALA P 109 -176.59 -63.21 REMARK 500 ALA P 110 88.70 -65.62 REMARK 500 ALA P 111 -162.74 -171.37 REMARK 500 ALA P 123 -123.03 -140.13 REMARK 500 ALA P 124 -63.68 -90.85 REMARK 500 ALA P 138 -175.64 -179.57 REMARK 500 ALA P 139 -169.78 -127.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA P 32 ALA P 33 -149.86 REMARK 500 ALA P 66 ALA P 67 -125.82 REMARK 500 ALA P 77 ALA P 78 -145.27 REMARK 500 ALA P 78 ALA P 79 -149.41 REMARK 500 ALA P 86 ALA P 87 -149.84 REMARK 500 ALA P 98 ALA P 99 -142.61 REMARK 500 ALA P 125 ALA P 126 -143.53 REMARK 500 ALA P 130 ALA P 131 -134.27 REMARK 500 ALA P 142 ALA P 143 -143.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4054 RELATED DB: EMDB DBREF 5LIJ P 1 152 PDB 5LIJ 5LIJ 1 152 SEQRES 1 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 2 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 3 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 4 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 5 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 6 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 7 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 8 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 9 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 10 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 11 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA SEQRES 12 P 152 ALA ALA ALA ALA ALA ALA ALA ALA ALA HELIX 1 AA1 ALA P 42 ALA P 56 1 15 HELIX 2 AA2 ALA P 142 ALA P 148 5 7 SHEET 1 AA1 2 ALA P 12 ALA P 13 0 SHEET 2 AA1 2 ALA P 95 ALA P 96 1 O ALA P 95 N ALA P 13 SHEET 1 AA2 4 ALA P 21 ALA P 23 0 SHEET 2 AA2 4 ALA P 132 ALA P 135 -1 O ALA P 134 N ALA P 22 SHEET 3 AA2 4 ALA P 114 ALA P 118 -1 N ALA P 115 O ALA P 135 SHEET 4 AA2 4 ALA P 104 ALA P 106 -1 N ALA P 106 O ALA P 114 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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