HEADER SURFACTANT PROTEIN 16-FEB-24 8S2D TITLE NMR STRUCTURE OF ENTOLYSIN A IN MICELLAR DPC SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENTOLYSIN A; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: 1) THE POLYPEPTIDE CHAIN OF ENTOLYSIN A CONSISTS OF 14 COMPND 5 AMINO ACIDS. 2) THE N-TERMINAL AMINO ACID (LEU) IS ACYLATED WITH AN COMPND 6 (R)-3-HYDROXY-DECANOIC ACID (IG8) MOEITY WHICH IS INDICATED AS THE COMPND 7 FIRST RESIDUE. 3) THE DEPSI (ESTER) BOND IS ESTABLISHED BETWEEN THE COMPND 8 ILE15 CARBOXYL AND DSN11 SIDE-CHAIN OH GROUPS. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS ENTOMOPHILA L48; SOURCE 3 ORGANISM_TAXID: 384676; SOURCE 4 STRAIN: L48 KEYWDS NON-RIBOSOMAL POLYPEPTIDE, CYCLIC LIPODEPSIPEPTIDE, ANTIMICROBIAL KEYWDS 2 PEPTIDE, BIOSURFACTANT, SURFACTANT PROTEIN EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR B.KOVACS,N.GEUDENS,J.C.MARTINS REVDAT 2 14-JAN-26 8S2D 1 JRNL REVDAT 1 26-FEB-25 8S2D 0 JRNL AUTH B.KOVACS,D.PRASAD,V.DE ROO,M.VANHEEDE,P.MUANGKAEW,A.MADDER, JRNL AUTH 2 M.HOFTE,R.DE MOT,N.GEUDENS,J.C.MARTINS JRNL TITL HIGHER-LEVEL STRUCTURAL CLASSIFICATION OF PSEUDOMONAS CYCLIC JRNL TITL 2 LIPOPEPTIDES THROUGH THEIR BIOACTIVE CONFORMATION. JRNL REF ADV SCI 20365 2025 JRNL REFN ESSN 2198-3844 JRNL PMID 41391051 JRNL DOI 10.1002/ADVS.202520365 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE LOWEST ENERGY NMR STRUCTURE ISSUED REMARK 3 FROM CNS WAS REFINED USING UNRESTRAINED AMBER MOLECULAR DYNAMICS REMARK 3 SIMULATIONS (AGAINST THE FF14SB FORCE FIELD). HERE, WE MODELLED REMARK 3 THE INTERACTION OF A SINGLE PEPTIDE MOLECULE WITH AN EXPLICIT REMARK 3 DODECYLPHOSPHOCHOLINE (DPC) MICELLE. THE REPRESENTATIVE PEPTIDE REMARK 3 CONFORMATION OF THE TRAJECTORY (=REFINED STRUCTURE) WAS SELECTED REMARK 3 USING CLUSTER ANALYSIS. SOLVENT MODEL: TIP3P. OCCASIONAL TOO- REMARK 3 CLOSE CONTACTS PRESENT IN THE NMR STRUCTURE ENSEMBLE (STRUCTURES REMARK 3 #2-#11) ARE FULLY REMOVED DURING THE AMBER MOLECULARY DYNAMICS REMARK 3 REFINEMENT (STRUCTURE #1). REMARK 4 REMARK 4 8S2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292135862. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 26 (BUFFER ONLY) REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.5 MM ENTOLYSIN A, 150 MM [U REMARK 210 -2H] DPC, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBERTOOLS, TOPSPIN 3.X, CCPNMR REMARK 210 ANALYSIS, CNS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC 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 400 REMARK 400 COMPOUND REMARK 400 HAS INSECTICIDAL PROPERTIES REMARK 400 REMARK 400 THE ENTOLYSIN A IS LIPOPEPTIDE, A MEMBER OF TOXIN CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ENTOLYSIN A REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE IG8 REMARK 400 DESCRIPTION: D-Ser, L-Val, L-Leu, D-Ser, L-Ile amino acids make REMARK 400 up a macrocycle within the peptide 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 1 DGN A 3 OE1 - CD - NE2 ANGL. DEV. = -14.1 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 5 LEU A 12 31.49 80.13 REMARK 500 6 LEU A 12 31.13 79.54 REMARK 500 7 LEU A 12 30.93 86.34 REMARK 500 9 LEU A 12 30.74 79.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34904 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF ENTOLYSIN A IN MICELLAR DPC SOLUTION DBREF 8S2D A 1 14 PDB 8S2D 8S2D 1 14 SEQRES 1 A 14 LEU DGL DGN DVA DLE DGN DVA DLE DGN DSN VAL LEU SER SEQRES 2 A 14 ILE HET DGL A 2 15 HET DGN A 3 17 HET DVA A 4 16 HET DLE A 5 19 HET DGN A 6 17 HET DVA A 7 16 HET DLE A 8 19 HET DGN A 9 17 HET DSN A 10 10 HET IG8 A 101 31 HETNAM DGL D-GLUTAMIC ACID HETNAM DGN D-GLUTAMINE HETNAM DVA D-VALINE HETNAM DLE D-LEUCINE HETNAM DSN D-SERINE HETNAM IG8 (3~{R})-3-OXIDANYLDECANOIC ACID FORMUL 1 DGL C5 H9 N O4 FORMUL 1 DGN 3(C5 H10 N2 O3) FORMUL 1 DVA 2(C5 H11 N O2) FORMUL 1 DLE 2(C6 H13 N O2) FORMUL 1 DSN C3 H7 N O3 FORMUL 2 IG8 C10 H20 O3 HELIX 1 AA1 LEU A 1 VAL A 11 1 11 HELIX 2 AA2 LEU A 12 ILE A 14 5 3 LINK C LEU A 1 N DGL A 2 1555 1555 1.41 LINK N LEU A 1 C IG8 A 101 1555 1555 1.36 LINK C DGL A 2 N DGN A 3 1555 1555 1.37 LINK C DGN A 3 N DVA A 4 1555 1555 1.38 LINK C DVA A 4 N DLE A 5 1555 1555 1.41 LINK C DLE A 5 N DGN A 6 1555 1555 1.38 LINK C DGN A 6 N DVA A 7 1555 1555 1.36 LINK C DVA A 7 N DLE A 8 1555 1555 1.38 LINK C DLE A 8 N DGN A 9 1555 1555 1.43 LINK C DGN A 9 N DSN A 10 1555 1555 1.42 LINK C DSN A 10 N VAL A 11 1555 1555 1.40 LINK OG DSN A 10 C ILE A 14 1555 1555 1.33 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 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL CONECT 1 233 CONECT 3 20 CONECT 20 3 21 29 CONECT 21 20 22 24 30 CONECT 22 21 23 35 CONECT 23 22 CONECT 24 21 25 31 32 CONECT 25 24 26 33 34 CONECT 26 25 27 28 CONECT 27 26 CONECT 28 26 CONECT 29 20 CONECT 30 21 CONECT 31 24 CONECT 32 24 CONECT 33 25 CONECT 34 25 CONECT 35 22 36 44 CONECT 36 35 37 39 45 CONECT 37 36 38 52 CONECT 38 37 CONECT 39 36 40 46 47 CONECT 40 39 41 48 49 CONECT 41 40 42 43 CONECT 42 41 CONECT 43 41 50 51 CONECT 44 35 CONECT 45 36 CONECT 46 39 CONECT 47 39 CONECT 48 40 CONECT 49 40 CONECT 50 43 CONECT 51 43 CONECT 52 37 53 59 CONECT 53 52 54 57 60 CONECT 54 53 55 56 61 CONECT 55 54 62 63 64 CONECT 56 54 65 66 67 CONECT 57 53 58 68 CONECT 58 57 CONECT 59 52 CONECT 60 53 CONECT 61 54 CONECT 62 55 CONECT 63 55 CONECT 64 55 CONECT 65 56 CONECT 66 56 CONECT 67 56 CONECT 68 57 69 76 CONECT 69 68 70 74 77 CONECT 70 69 71 78 79 CONECT 71 70 72 73 80 CONECT 72 71 81 82 83 CONECT 73 71 84 85 86 CONECT 74 69 75 87 CONECT 75 74 CONECT 76 68 CONECT 77 69 CONECT 78 70 CONECT 79 70 CONECT 80 71 CONECT 81 72 CONECT 82 72 CONECT 83 72 CONECT 84 73 CONECT 85 73 CONECT 86 73 CONECT 87 74 88 96 CONECT 88 87 89 91 97 CONECT 89 88 90 104 CONECT 90 89 CONECT 91 88 92 98 99 CONECT 92 91 93 100 101 CONECT 93 92 94 95 CONECT 94 93 CONECT 95 93 102 103 CONECT 96 87 CONECT 97 88 CONECT 98 91 CONECT 99 91 CONECT 100 92 CONECT 101 92 CONECT 102 95 CONECT 103 95 CONECT 104 89 105 111 CONECT 105 104 106 109 112 CONECT 106 105 107 108 113 CONECT 107 106 114 115 116 CONECT 108 106 117 118 119 CONECT 109 105 110 120 CONECT 110 109 CONECT 111 104 CONECT 112 105 CONECT 113 106 CONECT 114 107 CONECT 115 107 CONECT 116 107 CONECT 117 108 CONECT 118 108 CONECT 119 108 CONECT 120 109 121 128 CONECT 121 120 122 126 129 CONECT 122 121 123 130 131 CONECT 123 122 124 125 132 CONECT 124 123 133 134 135 CONECT 125 123 136 137 138 CONECT 126 121 127 139 CONECT 127 126 CONECT 128 120 CONECT 129 121 CONECT 130 122 CONECT 131 122 CONECT 132 123 CONECT 133 124 CONECT 134 124 CONECT 135 124 CONECT 136 125 CONECT 137 125 CONECT 138 125 CONECT 139 126 140 148 CONECT 140 139 141 143 149 CONECT 141 140 142 156 CONECT 142 141 CONECT 143 140 144 150 151 CONECT 144 143 145 152 153 CONECT 145 144 146 147 CONECT 146 145 CONECT 147 145 154 155 CONECT 148 139 CONECT 149 140 CONECT 150 143 CONECT 151 143 CONECT 152 144 CONECT 153 144 CONECT 154 147 CONECT 155 147 CONECT 156 141 157 162 CONECT 157 156 158 160 163 CONECT 158 157 159 166 CONECT 159 158 CONECT 160 157 161 164 165 CONECT 161 160 214 CONECT 162 156 CONECT 163 157 CONECT 164 160 CONECT 165 160 CONECT 166 158 CONECT 214 161 CONECT 232 233 235 244 245 CONECT 233 1 232 234 CONECT 234 233 CONECT 235 232 236 237 246 CONECT 236 235 238 247 248 CONECT 237 235 249 CONECT 238 236 239 250 251 CONECT 239 238 240 252 253 CONECT 240 239 241 254 255 CONECT 241 240 243 256 257 CONECT 242 243 258 259 260 CONECT 243 241 242 261 262 CONECT 244 232 CONECT 245 232 CONECT 246 235 CONECT 247 236 CONECT 248 236 CONECT 249 237 CONECT 250 238 CONECT 251 238 CONECT 252 239 CONECT 253 239 CONECT 254 240 CONECT 255 240 CONECT 256 241 CONECT 257 241 CONECT 258 242 CONECT 259 242 CONECT 260 242 CONECT 261 243 CONECT 262 243 MASTER 136 0 10 2 0 0 0 6 121 1 181 2 END