HEADER SURFACTANT PROTEIN 16-FEB-24 8S2B TITLE NMR STRUCTURE OF PUTISOLVIN I IN MICELLAR DPC SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTISOLVIN I; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: 1) THE POLYPEPTIDE CHAIN OF PUTISOLVIN I CONSISTS OF COMPND 5 12 AMINO ACIDS. 2) THE N-TERMINAL AMINO ACID (LEU) IS ACYLATED WITH A COMPND 6 HEXANOIC ACID MOEITY WHICH IS INDICATED AS THE FIRST RESIDUE. 3) THE COMPND 7 DEPSI (ESTER) BOND IS ESTABLISHED BETWEEN THE SER13 CARBOXYL AND COMPND 8 DSN10 SIDE-CHAIN OH GROUP. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 STRAIN: PCL1445 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 8S2B 1 JRNL REVDAT 1 26-FEB-25 8S2B 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 8S2B 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_1292134364. 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 : 2.7 MM PUTISOLVIN I, 127.8 MM [U REMARK 210 -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: 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 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 10 C SER A 13 1.34 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 6 LEU A 5 18.73 59.84 REMARK 500 7 LEU A 5 18.18 58.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34902 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF XANTHOLYSIN A IN MICELLAR DPC SOLUTION DBREF 8S2B A 2 13 PDB 8S2B 8S2B 2 13 SEQRES 1 A 12 LEU DGL DLE LEU DGN DSN DVA DLE DSN LEU VAL SER HET DGL A 3 15 HET DLE A 4 19 HET DGN A 6 17 HET DSN A 7 11 HET DVA A 8 16 HET DLE A 9 19 HET DSN A 10 10 HET 6NA A 101 18 HETNAM DGL D-GLUTAMIC ACID HETNAM DLE D-LEUCINE HETNAM DGN D-GLUTAMINE HETNAM DSN D-SERINE HETNAM DVA D-VALINE HETNAM 6NA HEXANOIC ACID FORMUL 1 DGL C5 H9 N O4 FORMUL 1 DLE 2(C6 H13 N O2) FORMUL 1 DGN C5 H10 N2 O3 FORMUL 1 DSN 2(C3 H7 N O3) FORMUL 1 DVA C5 H11 N O2 FORMUL 2 6NA C6 H12 O2 HELIX 1 AA1 LEU A 2 DSN A 10 1 9 LINK C LEU A 2 N DGL A 3 1555 1555 1.36 LINK N LEU A 2 C 6NA A 101 1555 1555 1.37 LINK C DGL A 3 N DLE A 4 1555 1555 1.34 LINK C DLE A 4 N LEU A 5 1555 1555 1.34 LINK C LEU A 5 N DGN A 6 1555 1555 1.35 LINK C DGN A 6 N DSN A 7 1555 1555 1.35 LINK C DSN A 7 N DVA A 8 1555 1555 1.35 LINK C DVA A 8 N DLE A 9 1555 1555 1.31 LINK C DLE A 9 N DSN A 10 1555 1555 1.35 LINK C DSN A 10 N LEU A 11 1555 1555 1.30 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 1 194 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 43 CONECT 36 35 37 41 44 CONECT 37 36 38 45 46 CONECT 38 37 39 40 47 CONECT 39 38 48 49 50 CONECT 40 38 51 52 53 CONECT 41 36 42 54 CONECT 42 41 CONECT 43 35 CONECT 44 36 CONECT 45 37 CONECT 46 37 CONECT 47 38 CONECT 48 39 CONECT 49 39 CONECT 50 39 CONECT 51 40 CONECT 52 40 CONECT 53 40 CONECT 54 41 CONECT 56 73 CONECT 73 56 74 82 CONECT 74 73 75 77 83 CONECT 75 74 76 90 CONECT 76 75 CONECT 77 74 78 84 85 CONECT 78 77 79 86 87 CONECT 79 78 80 81 CONECT 80 79 CONECT 81 79 88 89 CONECT 82 73 CONECT 83 74 CONECT 84 77 CONECT 85 77 CONECT 86 78 CONECT 87 78 CONECT 88 81 CONECT 89 81 CONECT 90 75 91 96 CONECT 91 90 92 94 97 CONECT 92 91 93 101 CONECT 93 92 CONECT 94 91 95 98 99 CONECT 95 94 100 CONECT 96 90 CONECT 97 91 CONECT 98 94 CONECT 99 94 CONECT 100 95 CONECT 101 92 102 108 CONECT 102 101 103 106 109 CONECT 103 102 104 105 110 CONECT 104 103 111 112 113 CONECT 105 103 114 115 116 CONECT 106 102 107 117 CONECT 107 106 CONECT 108 101 CONECT 109 102 CONECT 110 103 CONECT 111 104 CONECT 112 104 CONECT 113 104 CONECT 114 105 CONECT 115 105 CONECT 116 105 CONECT 117 106 118 125 CONECT 118 117 119 123 126 CONECT 119 118 120 127 128 CONECT 120 119 121 122 129 CONECT 121 120 130 131 132 CONECT 122 120 133 134 135 CONECT 123 118 124 136 CONECT 124 123 CONECT 125 117 CONECT 126 118 CONECT 127 119 CONECT 128 119 CONECT 129 120 CONECT 130 121 CONECT 131 121 CONECT 132 121 CONECT 133 122 CONECT 134 122 CONECT 135 122 CONECT 136 123 137 142 CONECT 137 136 138 140 143 CONECT 138 137 139 146 CONECT 139 138 CONECT 140 137 141 144 145 CONECT 141 140 CONECT 142 136 CONECT 143 137 CONECT 144 140 CONECT 145 140 CONECT 146 138 CONECT 193 194 196 200 201 CONECT 194 1 193 195 CONECT 195 194 CONECT 196 193 197 202 203 CONECT 197 196 198 204 205 CONECT 198 197 199 206 207 CONECT 199 198 208 209 210 CONECT 200 193 CONECT 201 193 CONECT 202 196 CONECT 203 196 CONECT 204 197 CONECT 205 197 CONECT 206 198 CONECT 207 198 CONECT 208 199 CONECT 209 199 CONECT 210 199 MASTER 112 0 8 1 0 0 0 6 97 1 130 1 END