HEADER ANTIBIOTIC 19-JAN-18 5Z5R TITLE NUKACIN ISK-1 IN INACTIVE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LANTIBIOTIC NUKACIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BACTERIOCIN ISK-1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS WARNERI; SOURCE 3 ORGANISM_TAXID: 1292 KEYWDS LANTIBIOTICS, ANTIBIOTIC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.KOHDA,D.FUJINAMI REVDAT 3 10-JUL-24 5Z5R 1 SEQRES LINK REVDAT 2 14-JUN-23 5Z5R 1 REMARK LINK REVDAT 1 28-NOV-18 5Z5R 0 JRNL AUTH D.FUJINAMI,A.A.MAHIN,K.M.ELSAYED,M.R.ISLAM,J.I.NAGAO,U.ROY, JRNL AUTH 2 S.MOMIN,T.ZENDO,D.KOHDA,K.SONOMOTO JRNL TITL THE LANTIBIOTIC NUKACIN ISK-1 EXISTS IN AN EQUILIBRIUM JRNL TITL 2 BETWEEN ACTIVE AND INACTIVE LIPID-II BINDING STATES. JRNL REF COMMUN BIOL V. 1 150 2018 JRNL REFN ESSN 2399-3642 JRNL PMID 30272026 JRNL DOI 10.1038/S42003-018-0150-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5Z5R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006017. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 1.1 MM NUKACIN ISK-1, 10 MM REMARK 210 SODIUM PHOSPHATE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: 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 CB DBB A 9 SG CYS A 14 2.12 REMARK 500 CB DAL A 11 SG CYS A 25 2.18 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 LYS A 3 109.13 -52.02 REMARK 500 1 SER A 4 -52.63 -128.66 REMARK 500 1 VAL A 6 -78.16 -62.74 REMARK 500 1 DAL A 11 -168.57 -59.87 REMARK 500 1 HIS A 15 54.44 -140.32 REMARK 500 1 MET A 16 79.60 65.29 REMARK 500 1 ASN A 17 -75.41 -134.74 REMARK 500 1 DAL A 18 71.03 76.41 REMARK 500 1 PHE A 23 31.90 -174.52 REMARK 500 2 LYS A 2 -52.16 -127.19 REMARK 500 2 VAL A 6 -80.47 -80.72 REMARK 500 2 PRO A 8 98.14 -69.76 REMARK 500 2 DAL A 11 -159.13 -61.44 REMARK 500 2 DAL A 18 72.81 126.64 REMARK 500 2 PHE A 23 38.57 -174.83 REMARK 500 3 LYS A 3 -179.42 57.76 REMARK 500 3 SER A 4 -72.74 -134.20 REMARK 500 3 VAL A 6 -71.75 -73.87 REMARK 500 3 PRO A 8 95.49 -69.80 REMARK 500 3 DBB A 9 44.30 131.90 REMARK 500 3 DAL A 11 -160.92 -62.19 REMARK 500 3 CYS A 14 88.65 51.07 REMARK 500 3 HIS A 15 -78.49 -128.73 REMARK 500 3 MET A 16 127.25 176.51 REMARK 500 3 ASN A 17 -79.95 -179.48 REMARK 500 3 PHE A 19 -59.10 -137.95 REMARK 500 3 CYS A 25 -167.82 -64.52 REMARK 500 3 CYS A 26 64.28 -160.98 REMARK 500 4 VAL A 6 -82.69 -50.13 REMARK 500 4 DAL A 11 -167.68 -60.13 REMARK 500 4 ASP A 13 43.33 -177.95 REMARK 500 4 HIS A 15 -68.05 -129.12 REMARK 500 4 MET A 16 115.62 -179.09 REMARK 500 4 ASN A 17 -75.08 -155.11 REMARK 500 4 GLN A 20 133.15 -178.72 REMARK 500 4 PHE A 23 30.53 -172.80 REMARK 500 5 LYS A 3 113.55 -179.31 REMARK 500 5 VAL A 6 -72.71 -141.10 REMARK 500 5 DAL A 11 -160.43 -61.05 REMARK 500 5 ASP A 13 33.94 -179.73 REMARK 500 5 CYS A 14 99.38 -67.62 REMARK 500 5 HIS A 15 63.34 -117.74 REMARK 500 5 MET A 16 -77.74 -144.54 REMARK 500 5 ASN A 17 174.72 177.36 REMARK 500 5 DAL A 18 75.34 -68.46 REMARK 500 5 PHE A 23 22.42 -152.51 REMARK 500 6 LYS A 3 -177.50 59.64 REMARK 500 6 DAL A 11 -163.31 -61.35 REMARK 500 6 HIS A 15 -74.95 -138.97 REMARK 500 6 MET A 16 129.47 179.91 REMARK 500 REMARK 500 THIS ENTRY HAS 199 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36158 RELATED DB: BMRB REMARK 900 NUKACIN ISK-1 IN INACTIVE STATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THR39, SER41, AND SER48 ARE DEHYDRATED TO DBB39, DAL41 AND DAL48 BY REMARK 999 POSTTRANSLATIONAL MODIFICATIONS. DBREF 5Z5R A 1 27 UNP Q9KWM4 LANNA_STAWA 31 57 SEQADV 5Z5R DBB A 9 UNP Q9KWM4 THR 39 SEE SEQUENCE DETAILS SEQADV 5Z5R DAL A 11 UNP Q9KWM4 SER 41 SEE SEQUENCE DETAILS SEQADV 5Z5R DAL A 18 UNP Q9KWM4 SER 48 SEE SEQUENCE DETAILS SEQRES 1 A 27 LYS LYS LYS SER GLY VAL ILE PRO DBB VAL DAL HIS ASP SEQRES 2 A 27 CYS HIS MET ASN DAL PHE GLN PHE VAL PHE DBU CYS CYS SEQRES 3 A 27 SER MODRES 5Z5R DBU A 24 THR MODIFIED RESIDUE HET DBB A 9 12 HET DAL A 11 9 HET DAL A 18 9 HET DBU A 24 11 HETNAM DBB D-ALPHA-AMINOBUTYRIC ACID HETNAM DAL D-ALANINE HETNAM DBU (2Z)-2-AMINOBUT-2-ENOIC ACID HETSYN DBU Z-DEHYDROBUTYRINE FORMUL 1 DBB C4 H9 N O2 FORMUL 1 DAL 2(C3 H7 N O2) FORMUL 1 DBU C4 H7 N O2 LINK C PRO A 8 N DBB A 9 1555 1555 1.33 LINK C DBB A 9 N VAL A 10 1555 1555 1.33 LINK C VAL A 10 N DAL A 11 1555 1555 1.33 LINK C DAL A 11 N HIS A 12 1555 1555 1.33 LINK C ASN A 17 N DAL A 18 1555 1555 1.33 LINK C DAL A 18 N PHE A 19 1555 1555 1.33 LINK CB DAL A 18 SG CYS A 26 1555 1555 1.83 LINK C PHE A 23 N DBU A 24 1555 1555 1.33 LINK C DBU A 24 N CYS A 25 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 MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 122 134 CONECT 134 122 135 140 CONECT 135 134 136 138 141 CONECT 136 135 137 146 CONECT 137 136 CONECT 138 135 139 142 CONECT 139 138 143 144 145 CONECT 140 134 CONECT 141 135 CONECT 142 138 CONECT 143 139 CONECT 144 139 CONECT 145 139 CONECT 146 136 CONECT 148 162 CONECT 162 148 163 167 CONECT 163 162 164 165 168 CONECT 164 163 169 170 CONECT 165 163 166 171 CONECT 166 165 CONECT 167 162 CONECT 168 163 CONECT 169 164 CONECT 170 164 CONECT 171 165 CONECT 246 258 CONECT 258 246 259 263 CONECT 259 258 260 261 264 CONECT 260 259 265 266 386 CONECT 261 259 262 267 CONECT 262 261 CONECT 263 258 CONECT 264 259 CONECT 265 260 CONECT 266 260 CONECT 267 261 CONECT 342 360 CONECT 360 342 361 366 CONECT 361 360 362 364 CONECT 362 361 363 367 CONECT 363 362 368 369 370 CONECT 364 361 365 371 CONECT 365 364 CONECT 366 360 CONECT 367 362 CONECT 368 363 CONECT 369 363 CONECT 370 363 CONECT 371 364 CONECT 386 260 MASTER 152 0 4 0 0 0 0 6 205 1 50 3 END