HEADER VIRAL PROTEIN 28-JUN-23 8JVM TITLE AHS-CSF DOMAINS OF PHAGE LAMBDA TAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: TIP ATTACHMENT PROTEIN J; COMPND 3 CHAIN: F, J, Z; COMPND 4 FRAGMENT: AHS-CSF DOMAINS; COMPND 5 SYNONYM: CENTRAL TAIL FIBER,HOST SPECIFICITY PROTEIN J; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA PHAGE LAMBDA; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE LAMBDA; SOURCE 4 ORGANISM_TAXID: 2681611; SOURCE 5 GENE: J, LAMBDAP21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BACTERIOPHAGE, CAUDOVIRALES, SIPHOVIRIDAE, TAIL COMPLEX, DELIVERY KEYWDS 2 DEVICE, PHAGE LAMBDA, CRYO-EM, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.WANG REVDAT 4 24-JAN-24 8JVM 1 JRNL REVDAT 3 15-NOV-23 8JVM 1 JRNL REVDAT 2 08-NOV-23 8JVM 1 JRNL REVDAT 1 18-OCT-23 8JVM 0 JRNL AUTH C.WANG,J.DUAN,Z.GU,X.GE,J.ZENG,J.WANG JRNL TITL ARCHITECTURE OF THE BACTERIOPHAGE LAMBDA TAIL. JRNL REF STRUCTURE V. 32 35 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 37918400 JRNL DOI 10.1016/J.STR.2023.10.006 REMARK 2 REMARK 2 RESOLUTION. 3.86 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) : 3.860 REMARK 3 NUMBER OF PARTICLES : 233877 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8JVM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 05-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039016. 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 : BACTERIOPHAGE LAMBDA TAIL 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 : 7.00 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, J, Z 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: 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 O PRO F 907 NH1 ARG J 901 2.16 REMARK 500 O ALA J 946 OG1 THR J 956 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO Z 945 N PRO Z 945 CA 0.111 REMARK 500 REMARK 500 REMARK: NULL 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 PRO Z 944 CB - CA - C ANGL. DEV. = 16.6 DEGREES REMARK 500 PRO Z 945 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 PRO Z 945 N - CA - C ANGL. DEV. = 20.3 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 VAL F 865 -63.02 -93.77 REMARK 500 LYS F 874 -119.81 46.62 REMARK 500 ARG F 901 115.24 -161.07 REMARK 500 ALA F 908 48.94 32.75 REMARK 500 PHE F 916 60.36 63.19 REMARK 500 PHE F 924 123.48 94.45 REMARK 500 SER F 974 -70.69 -95.01 REMARK 500 LEU J 832 -18.59 -45.05 REMARK 500 ALA J 867 76.10 -100.98 REMARK 500 TYR J 876 12.91 58.90 REMARK 500 ALA J 898 73.96 -113.76 REMARK 500 ALA J 899 116.10 -169.46 REMARK 500 ASN J 900 -70.81 -78.94 REMARK 500 ASN J 921 139.87 70.52 REMARK 500 ILE J 923 -64.90 -126.20 REMARK 500 PHE J 924 154.17 178.77 REMARK 500 ASN J 926 -165.07 -77.58 REMARK 500 SER J 974 -70.28 -86.17 REMARK 500 ALA J 979 -3.50 -152.26 REMARK 500 ASN J 981 119.15 -16.24 REMARK 500 ALA Z 867 -150.97 56.88 REMARK 500 THR Z 870 -146.50 64.53 REMARK 500 VAL Z 877 40.26 33.37 REMARK 500 ASN Z 900 -166.68 -126.25 REMARK 500 ASN Z 909 40.98 35.53 REMARK 500 GLU Z 912 29.05 -140.39 REMARK 500 ALA Z 918 65.93 38.74 REMARK 500 ASN Z 921 70.54 60.64 REMARK 500 ILE Z 923 -67.08 -93.45 REMARK 500 THR Z 939 -168.97 -127.12 REMARK 500 PRO Z 944 75.54 -5.39 REMARK 500 PRO Z 945 -152.32 -92.80 REMARK 500 ALA Z 946 -110.23 -157.39 REMARK 500 ASP Z 952 49.60 -92.50 REMARK 500 GLU Z 980 -169.86 -120.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-35818 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-35824 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-35825 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-35826 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-36677 RELATED DB: EMDB REMARK 900 AHS-CSF DOMAINS OF PHAGE LAMBDA TAIL DBREF 8JVM F 830 995 UNP P03749 TIPJ_LAMBD 830 995 DBREF 8JVM J 830 995 UNP P03749 TIPJ_LAMBD 830 995 DBREF 8JVM Z 830 995 UNP P03749 TIPJ_LAMBD 830 995 SEQADV 8JVM ALA F 863 UNP P03749 TRP 863 CONFLICT SEQADV 8JVM ALA F 867 UNP P03749 ILE 867 CONFLICT SEQADV 8JVM ALA F 904 UNP P03749 PHE 904 CONFLICT SEQADV 8JVM ALA J 863 UNP P03749 TRP 863 CONFLICT SEQADV 8JVM ALA J 867 UNP P03749 ILE 867 CONFLICT SEQADV 8JVM ALA J 904 UNP P03749 PHE 904 CONFLICT SEQADV 8JVM ALA Z 863 UNP P03749 TRP 863 CONFLICT SEQADV 8JVM ALA Z 867 UNP P03749 ILE 867 CONFLICT SEQADV 8JVM ALA Z 904 UNP P03749 PHE 904 CONFLICT SEQRES 1 F 166 GLU LEU LEU GLU LYS VAL GLU LEU THR GLU ASP ASN ALA SEQRES 2 F 166 SER ARG LEU GLU GLU PHE SER LYS GLU TRP LYS ASP ALA SEQRES 3 F 166 SER ASP LYS TRP ASN ALA MET ALA ALA VAL LYS ALA GLU SEQRES 4 F 166 GLN THR LYS ASP GLY LYS HIS TYR VAL ALA GLY ILE GLY SEQRES 5 F 166 LEU SER MET GLU ASP THR GLU GLU GLY LYS LEU SER GLN SEQRES 6 F 166 PHE LEU VAL ALA ALA ASN ARG ILE ALA ALA ILE ASP PRO SEQRES 7 F 166 ALA ASN GLY ASN GLU THR PRO MET PHE VAL ALA GLN GLY SEQRES 8 F 166 ASN GLN ILE PHE MET ASN ASP VAL PHE LEU LYS ARG LEU SEQRES 9 F 166 THR ALA PRO THR ILE THR SER GLY GLY ASN PRO PRO ALA SEQRES 10 F 166 PHE SER LEU THR PRO ASP GLY LYS LEU THR ALA LYS ASN SEQRES 11 F 166 ALA ASP ILE SER GLY SER VAL ASN ALA ASN SER GLY THR SEQRES 12 F 166 LEU SER ASN VAL THR ILE ALA GLU ASN CYS THR ILE ASN SEQRES 13 F 166 GLY THR LEU ARG ALA GLU LYS ILE VAL GLY SEQRES 1 J 166 GLU LEU LEU GLU LYS VAL GLU LEU THR GLU ASP ASN ALA SEQRES 2 J 166 SER ARG LEU GLU GLU PHE SER LYS GLU TRP LYS ASP ALA SEQRES 3 J 166 SER ASP LYS TRP ASN ALA MET ALA ALA VAL LYS ALA GLU SEQRES 4 J 166 GLN THR LYS ASP GLY LYS HIS TYR VAL ALA GLY ILE GLY SEQRES 5 J 166 LEU SER MET GLU ASP THR GLU GLU GLY LYS LEU SER GLN SEQRES 6 J 166 PHE LEU VAL ALA ALA ASN ARG ILE ALA ALA ILE ASP PRO SEQRES 7 J 166 ALA ASN GLY ASN GLU THR PRO MET PHE VAL ALA GLN GLY SEQRES 8 J 166 ASN GLN ILE PHE MET ASN ASP VAL PHE LEU LYS ARG LEU SEQRES 9 J 166 THR ALA PRO THR ILE THR SER GLY GLY ASN PRO PRO ALA SEQRES 10 J 166 PHE SER LEU THR PRO ASP GLY LYS LEU THR ALA LYS ASN SEQRES 11 J 166 ALA ASP ILE SER GLY SER VAL ASN ALA ASN SER GLY THR SEQRES 12 J 166 LEU SER ASN VAL THR ILE ALA GLU ASN CYS THR ILE ASN SEQRES 13 J 166 GLY THR LEU ARG ALA GLU LYS ILE VAL GLY SEQRES 1 Z 166 GLU LEU LEU GLU LYS VAL GLU LEU THR GLU ASP ASN ALA SEQRES 2 Z 166 SER ARG LEU GLU GLU PHE SER LYS GLU TRP LYS ASP ALA SEQRES 3 Z 166 SER ASP LYS TRP ASN ALA MET ALA ALA VAL LYS ALA GLU SEQRES 4 Z 166 GLN THR LYS ASP GLY LYS HIS TYR VAL ALA GLY ILE GLY SEQRES 5 Z 166 LEU SER MET GLU ASP THR GLU GLU GLY LYS LEU SER GLN SEQRES 6 Z 166 PHE LEU VAL ALA ALA ASN ARG ILE ALA ALA ILE ASP PRO SEQRES 7 Z 166 ALA ASN GLY ASN GLU THR PRO MET PHE VAL ALA GLN GLY SEQRES 8 Z 166 ASN GLN ILE PHE MET ASN ASP VAL PHE LEU LYS ARG LEU SEQRES 9 Z 166 THR ALA PRO THR ILE THR SER GLY GLY ASN PRO PRO ALA SEQRES 10 Z 166 PHE SER LEU THR PRO ASP GLY LYS LEU THR ALA LYS ASN SEQRES 11 Z 166 ALA ASP ILE SER GLY SER VAL ASN ALA ASN SER GLY THR SEQRES 12 Z 166 LEU SER ASN VAL THR ILE ALA GLU ASN CYS THR ILE ASN SEQRES 13 Z 166 GLY THR LEU ARG ALA GLU LYS ILE VAL GLY HELIX 1 AA1 LEU F 831 LYS F 866 1 36 HELIX 2 AA2 ALA F 918 GLN F 922 5 5 HELIX 3 AA3 LEU J 831 LYS J 866 1 36 HELIX 4 AA4 PRO J 907 ASN J 911 5 5 HELIX 5 AA5 LEU Z 832 LYS Z 866 1 35 SHEET 1 AA1 2 LEU F 882 THR F 887 0 SHEET 2 AA1 2 GLY F 890 PHE F 895 -1 O GLY F 890 N THR F 887 SHEET 1 AA2 2 ARG F 932 THR F 934 0 SHEET 2 AA2 2 THR Z 937 THR Z 939 1 O THR Z 939 N LEU F 933 SHEET 1 AA3 2 LEU F 955 ALA F 957 0 SHEET 2 AA3 2 ALA Z 960 ILE Z 962 1 O ASP Z 961 N LEU F 955 SHEET 1 AA4 2 ASN F 959 ILE F 962 0 SHEET 2 AA4 2 LYS J 954 ALA J 957 1 O ALA J 957 N ASP F 961 SHEET 1 AA5 6 LEU F 988 ARG F 989 0 SHEET 2 AA5 6 CYS J 982 ILE J 984 1 O CYS J 982 N ARG F 989 SHEET 3 AA5 6 THR Z 972 ILE Z 978 1 O VAL Z 976 N THR J 983 SHEET 4 AA5 6 VAL F 966 ILE F 978 1 N LEU F 973 O THR Z 977 SHEET 5 AA5 6 ASN J 967 LEU J 973 1 O ASN J 969 N ASN F 975 SHEET 6 AA5 6 ASN Z 967 ALA Z 968 1 O ALA Z 968 N THR J 972 SHEET 1 AA6 3 ALA J 960 ILE J 962 0 SHEET 2 AA6 3 VAL F 966 ILE F 978 1 N ASN F 967 O ILE J 962 SHEET 3 AA6 3 THR Z 983 ILE Z 984 1 O THR Z 983 N VAL F 976 SHEET 1 AA7 3 VAL J 976 ILE J 978 0 SHEET 2 AA7 3 CYS F 982 ILE F 984 1 N THR F 983 O ILE J 978 SHEET 3 AA7 3 ARG Z 989 ALA Z 990 1 O ARG Z 989 N ILE F 984 SHEET 1 AA8 2 GLY J 881 ASP J 886 0 SHEET 2 AA8 2 LYS J 891 LEU J 896 -1 O LEU J 896 N GLY J 881 SHEET 1 AA9 2 ILE J 905 ASP J 906 0 SHEET 2 AA9 2 THR J 913 PRO J 914 -1 O THR J 913 N ASP J 906 SHEET 1 AB1 2 GLY Z 881 MET Z 884 0 SHEET 2 AB1 2 SER Z 893 LEU Z 896 -1 O GLN Z 894 N SER Z 883 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