HEADER SURFACTANT PROTEIN 16-FEB-24 8S2C TITLE NMR STRUCTURE OF VISCOSIN IN MICELLAR DPC SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: VISCOSIN; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: 1) THE POLYPEPTIDE CHAIN OF VISCOSIN CONSISTS OF 9 COMPND 5 AMINO ACIDS. 2) THE N-TERMINAL AMINO ACID (LEU1) IS ACYLATED WITH AN COMPND 6 (R)-3-HYDROXY-DECANOIC ACID (IG8) MOIETY WHICH IS INDICATED AS THE COMPND 7 FIRST RESIDUE. 3) THE SIDE-CHAIN OF THE D-THR4 RESIDUE IS OF ALLO- COMPND 8 CONFIGURATION (2TL). 4) THE DEPSI (ESTER) BOND IS ESTABLISHED BETWEEN COMPND 9 THE ILE10 CARBOXYL AND ALLO-2TL SIDE-CHAIN OH GROUP. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS FLUORESCENS SBW25; SOURCE 3 ORGANISM_TAXID: 216595 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 8S2C 1 JRNL REVDAT 1 26-FEB-25 8S2C 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). SIDE-CHAIN OUTLIER VALUES FOR THE REMARK 3 2TL4 RESIDUE ARE THE RESULTS OF THE DEPSI BOND. REMARK 4 REMARK 4 8S2C 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_1292132400. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 26 (BUFFER ONLY) REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.8 MM VISCOSIN, 124.3 MM [U-2H] REMARK 210 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 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: 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 LEU A 6 10.96 56.54 REMARK 500 2 DSN A 9 -23.15 143.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 2TL A 4 11.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34903 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF VISCOSIN IN MICELLAR DPC SOLUTION DBREF 8S2C A 2 10 PDB 8S2C 8S2C 2 10 SEQRES 1 A 9 LEU DGL 2TL DVA LEU DSN LEU DSN ILE HET DGL A 3 15 HET 2TL A 4 13 HET DVA A 5 16 HET DSN A 7 11 HET DSN A 9 11 HET IG8 A 101 31 HETNAM DGL D-GLUTAMIC ACID HETNAM 2TL D-ALLOTHREONINE HETNAM DVA D-VALINE HETNAM DSN D-SERINE HETNAM IG8 (3~{R})-3-OXIDANYLDECANOIC ACID FORMUL 1 DGL C5 H9 N O4 FORMUL 1 2TL C4 H9 N O3 FORMUL 1 DVA C5 H11 N O2 FORMUL 1 DSN 2(C3 H7 N O3) FORMUL 2 IG8 C10 H20 O3 HELIX 1 AA1 2TL A 4 LEU A 8 5 5 LINK C LEU A 2 N DGL A 3 1555 1555 1.30 LINK N LEU A 2 C IG8 A 101 1555 1555 1.37 LINK C DGL A 3 N 2TL A 4 1555 1555 1.32 LINK C 2TL A 4 N DVA A 5 1555 1555 1.38 LINK OG1 2TL A 4 C ILE A 10 1555 1555 1.33 LINK C DVA A 5 N LEU A 6 1555 1555 1.32 LINK C LEU A 6 N DSN A 7 1555 1555 1.34 LINK C DSN A 7 N LEU A 8 1555 1555 1.32 LINK C LEU A 8 N DSN A 9 1555 1555 1.33 LINK C DSN A 9 N ILE A 10 1555 1555 1.29 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 1 145 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 42 CONECT 36 35 37 40 43 CONECT 37 36 38 39 44 CONECT 38 37 126 CONECT 39 37 45 46 47 CONECT 40 36 41 48 CONECT 41 40 CONECT 42 35 CONECT 43 36 CONECT 44 37 CONECT 45 39 CONECT 46 39 CONECT 47 39 CONECT 48 40 49 55 CONECT 49 48 50 53 56 CONECT 50 49 51 52 57 CONECT 51 50 58 59 60 CONECT 52 50 61 62 63 CONECT 53 49 54 64 CONECT 54 53 CONECT 55 48 CONECT 56 49 CONECT 57 50 CONECT 58 51 CONECT 59 51 CONECT 60 51 CONECT 61 52 CONECT 62 52 CONECT 63 52 CONECT 64 53 CONECT 66 83 CONECT 83 66 84 89 CONECT 84 83 85 87 90 CONECT 85 84 86 94 CONECT 86 85 CONECT 87 84 88 91 92 CONECT 88 87 93 CONECT 89 83 CONECT 90 84 CONECT 91 87 CONECT 92 87 CONECT 93 88 CONECT 94 85 CONECT 96 113 CONECT 113 96 114 119 CONECT 114 113 115 117 120 CONECT 115 114 116 124 CONECT 116 115 CONECT 117 114 118 121 122 CONECT 118 117 123 CONECT 119 113 CONECT 120 114 CONECT 121 117 CONECT 122 117 CONECT 123 118 CONECT 124 115 CONECT 126 38 CONECT 144 145 147 156 157 CONECT 145 1 144 146 CONECT 146 145 CONECT 147 144 148 149 158 CONECT 148 147 150 159 160 CONECT 149 147 161 CONECT 150 148 151 162 163 CONECT 151 150 152 164 165 CONECT 152 151 153 166 167 CONECT 153 152 155 168 169 CONECT 154 155 170 171 172 CONECT 155 153 154 173 174 CONECT 156 144 CONECT 157 144 CONECT 158 147 CONECT 159 148 CONECT 160 148 CONECT 161 149 CONECT 162 150 CONECT 163 150 CONECT 164 151 CONECT 165 151 CONECT 166 152 CONECT 167 152 CONECT 168 153 CONECT 169 153 CONECT 170 154 CONECT 171 154 CONECT 172 154 CONECT 173 155 CONECT 174 155 MASTER 115 0 6 1 0 0 0 6 79 1 105 1 END