HEADER SURFACTANT PROTEIN 16-FEB-24 8S2A TITLE NMR STRUCTURE OF XANTHOLYSIN A IN MICELLAR DPC SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: XANTHOLYSIN A; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: 1) THE POLYPEPTIDE CHAIN OF XANTHOLYSIN A CONSISTS OF COMPND 5 14 AMINO ACIDS. 2) THE N-TERMINAL AMINO ACID (LEU) IS ACYLATED WITH COMPND 6 AN (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 SER8 SIDE-CHAIN OH GROUP. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 STRAIN: BW11M1 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 8S2A 1 JRNL REVDAT 1 26-FEB-25 8S2A 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 8S2A 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_1292134615. 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 : 3.2 MM XANTHOLYSIN A, 162.9 MM REMARK 210 [U-2H] DPC, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D 1H-1H TOCSY; 2D 1H REMARK 210 -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: OCCASIONAL TOO-CLOSE CONTACTS PRESENT IN THE NMR STRU 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OG DSN A 8 C ILE A 15 1.36 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 1 DVA A 9 CG1 - CB - CG2 ANGL. DEV. = -11.1 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 1 DGN A 11 -4.46 67.65 REMARK 500 1 DGN A 14 -28.45 74.51 REMARK 500 2 DGL A 3 18.10 39.67 REMARK 500 2 DGN A 14 -48.60 94.76 REMARK 500 3 DGL A 3 17.30 39.51 REMARK 500 4 DGL A 3 17.60 33.88 REMARK 500 4 DGN A 14 -63.63 116.06 REMARK 500 5 DGL A 3 17.10 39.61 REMARK 500 5 DGN A 14 -50.31 92.49 REMARK 500 6 DGL A 3 19.02 37.21 REMARK 500 6 DGN A 14 -50.35 93.13 REMARK 500 7 DGL A 3 17.45 39.64 REMARK 500 7 DGN A 14 -64.08 116.24 REMARK 500 8 DGL A 3 17.78 38.00 REMARK 500 8 DGN A 14 -47.69 94.47 REMARK 500 9 DGL A 3 18.15 40.47 REMARK 500 9 DGN A 14 -48.02 94.05 REMARK 500 10 DGL A 3 17.59 39.14 REMARK 500 10 DGN A 14 -47.77 93.66 REMARK 500 11 DGL A 3 19.74 36.64 REMARK 500 11 DGN A 14 -47.39 93.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34901 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF XANTHOLYSIN A IN MICELLAR DPC SOLUTION DBREF 8S2A A 2 15 PDB 8S2A 8S2A 2 15 SEQRES 1 A 14 LEU DGL DGN DVA DLE GLN DSN DVA DLE DGN LEU LEU DGN SEQRES 2 A 14 ILE HET DGL A 3 15 HET DGN A 4 17 HET DVA A 5 16 HET DLE A 6 19 HET DSN A 8 10 HET DVA A 9 16 HET DLE A 10 19 HET DGN A 11 17 HET DGN A 14 17 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 2 DGN A 11 1 10 LINK C LEU A 2 N DGL A 3 1555 1555 1.32 LINK N LEU A 2 C IG8 A 101 1555 1555 1.34 LINK C DGL A 3 N DGN A 4 1555 1555 1.32 LINK C DGN A 4 N DVA A 5 1555 1555 1.37 LINK C DVA A 5 N DLE A 6 1555 1555 1.34 LINK C DLE A 6 N GLN A 7 1555 1555 1.31 LINK C GLN A 7 N DSN A 8 1555 1555 1.37 LINK C DSN A 8 N DVA A 9 1555 1555 1.35 LINK C DVA A 9 N DLE A 10 1555 1555 1.35 LINK C DLE A 10 N DGN A 11 1555 1555 1.34 LINK C DGN A 11 N LEU A 12 1555 1555 1.38 LINK C LEU A 13 N DGN A 14 1555 1555 1.35 LINK C DGN A 14 N ILE A 15 1555 1555 1.34 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 1 242 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 CONECT 89 104 CONECT 104 89 105 110 CONECT 105 104 106 108 111 CONECT 106 105 107 114 CONECT 107 106 CONECT 108 105 109 112 113 CONECT 109 108 CONECT 110 104 CONECT 111 105 CONECT 112 108 CONECT 113 108 CONECT 114 106 115 121 CONECT 115 114 116 119 122 CONECT 116 115 117 118 123 CONECT 117 116 124 125 126 CONECT 118 116 127 128 129 CONECT 119 115 120 130 CONECT 120 119 CONECT 121 114 CONECT 122 115 CONECT 123 116 CONECT 124 117 CONECT 125 117 CONECT 126 117 CONECT 127 118 CONECT 128 118 CONECT 129 118 CONECT 130 119 131 138 CONECT 131 130 132 136 139 CONECT 132 131 133 140 141 CONECT 133 132 134 135 142 CONECT 134 133 143 144 145 CONECT 135 133 146 147 148 CONECT 136 131 137 149 CONECT 137 136 CONECT 138 130 CONECT 139 131 CONECT 140 132 CONECT 141 132 CONECT 142 133 CONECT 143 134 CONECT 144 134 CONECT 145 134 CONECT 146 135 CONECT 147 135 CONECT 148 135 CONECT 149 136 150 158 CONECT 150 149 151 153 159 CONECT 151 150 152 166 CONECT 152 151 CONECT 153 150 154 160 161 CONECT 154 153 155 162 163 CONECT 155 154 156 157 CONECT 156 155 CONECT 157 155 164 165 CONECT 158 149 CONECT 159 150 CONECT 160 153 CONECT 161 153 CONECT 162 154 CONECT 163 154 CONECT 164 157 CONECT 165 157 CONECT 166 151 CONECT 187 204 CONECT 204 187 205 213 CONECT 205 204 206 208 214 CONECT 206 205 207 221 CONECT 207 206 CONECT 208 205 209 215 216 CONECT 209 208 210 217 218 CONECT 210 209 211 212 CONECT 211 210 CONECT 212 210 219 220 CONECT 213 204 CONECT 214 205 CONECT 215 208 CONECT 216 208 CONECT 217 209 CONECT 218 209 CONECT 219 212 CONECT 220 212 CONECT 221 206 CONECT 241 242 244 253 254 CONECT 242 1 241 243 CONECT 243 242 CONECT 244 241 245 246 255 CONECT 245 244 247 256 257 CONECT 246 244 258 CONECT 247 245 248 259 260 CONECT 248 247 249 261 262 CONECT 249 248 250 263 264 CONECT 250 249 252 265 266 CONECT 251 252 267 268 269 CONECT 252 250 251 270 271 CONECT 253 241 CONECT 254 241 CONECT 255 244 CONECT 256 245 CONECT 257 245 CONECT 258 246 CONECT 259 247 CONECT 260 247 CONECT 261 248 CONECT 262 248 CONECT 263 249 CONECT 264 249 CONECT 265 250 CONECT 266 250 CONECT 267 251 CONECT 268 251 CONECT 269 251 CONECT 270 252 CONECT 271 252 MASTER 150 0 10 1 0 0 0 6 125 1 184 2 END