HEADER LANTIBIOTIC-BINDING PROTEIN 08-MAY-15 2N2E TITLE NMR SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF NISI, A LIPOPROTEIN TITLE 2 FROM LACTOCOCCUS LACTIS WHICH CONFERS IMMUNITY AGAINST NISIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NISIN IMMUNITY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 117-245; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. LACTIS; SOURCE 3 ORGANISM_COMMON: FIRMICUTES; SOURCE 4 ORGANISM_TAXID: 1360; SOURCE 5 GENE: NISI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET11A-SUMO KEYWDS LANTIBIOTIC SELF-IMMUNITY PROTEIN, ANTIBIOTIC, LANTIBIOTIC-BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 MDLTYP MINIMIZED AVERAGE AUTHOR C.HACKER,N.A.CHRIST,S.KORN,E.DUCHARDT-FERNER,U.A.HELLMICH, AUTHOR 2 S.DUESTERHUS,P.KOETTER,K.ENTIAN,J.WOEHNERT REVDAT 4 14-JUN-23 2N2E 1 REMARK REVDAT 3 27-APR-16 2N2E 1 ATOM COMPND DBREF REMARK REVDAT 3 2 1 SEQRES REVDAT 2 09-DEC-15 2N2E 1 JRNL REVDAT 1 21-OCT-15 2N2E 0 JRNL AUTH C.HACKER,N.A.CHRIST,E.DUCHARDT-FERNER,S.KORN,C.GOBL, JRNL AUTH 2 L.BERNINGER,S.DUSTERHUS,U.A.HELLMICH,T.MADL,P.KOTTER, JRNL AUTH 3 K.D.ENTIAN,J.WOHNERT JRNL TITL THE SOLUTION STRUCTURE OF THE LANTIBIOTIC IMMUNITY PROTEIN JRNL TITL 2 NISI AND ITS INTERACTIONS WITH NISIN. JRNL REF J.BIOL.CHEM. V. 290 28869 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 26459561 JRNL DOI 10.1074/JBC.M115.679969 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CCPN_ANALYSIS, CYANA, OPALP REMARK 3 AUTHORS : CCPN (CCPN_ANALYSIS), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA), LUGINBUHL, GUNTERT, BILLETER AND REMARK 3 WUTHRICH (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000104335. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 50 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 30 UM DSS, 400 REMARK 210 UM [U-15N] NISI97, 90 % H2O, 10 % REMARK 210 D2O, 90% H2O/10% D2O; 50 MM REMARK 210 SODIUM PHOSPHATE, 100 MM SODIUM REMARK 210 CHLORIDE, 30 UM DSS, 400 UM [U- REMARK 210 13C; U-15N] NISI97, 90 % H2O, 10 REMARK 210 % D2O, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 H(CCO)NH; 3D C(CO)NH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 3D REMARK 210 HNCACO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 950 REMARK 210 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPN_ANALYSIS, CARA, TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, WATER REMARK 210 REFINEMENT 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 ASP A 98 REMARK 465 LYS A 99 REMARK 465 GLY A 100 REMARK 465 ALA A 101 REMARK 465 VAL A 102 REMARK 465 LYS A 103 REMARK 465 ALA A 104 REMARK 465 LEU A 105 REMARK 465 ARG A 106 REMARK 465 LEU A 107 REMARK 465 GLN A 108 REMARK 465 ASN A 109 REMARK 465 PHE A 110 REMARK 465 ASP A 111 REMARK 465 VAL A 112 REMARK 465 THR A 113 REMARK 465 SER A 114 REMARK 465 ASP A 115 REMARK 465 ILE A 116 REMARK 465 SER A 117 REMARK 465 ASP A 118 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 ASN A 226 C ASN A 226 O 0.771 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 ARG A 178 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 ASN A 226 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 7 TYR A 195 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 9 GLY A 196 C - N - CA ANGL. DEV. = 13.1 DEGREES REMARK 500 16 ARG A 173 NE - CZ - NH2 ANGL. DEV. = -3.2 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 SER A 141 -107.75 -89.04 REMARK 500 1 ASP A 142 99.48 -160.23 REMARK 500 1 ALA A 158 65.81 -168.58 REMARK 500 1 ILE A 179 -82.79 -63.30 REMARK 500 1 ASP A 180 144.81 -170.75 REMARK 500 1 ASP A 182 -21.09 -145.47 REMARK 500 1 SER A 184 75.94 49.39 REMARK 500 1 ASN A 185 21.06 -67.38 REMARK 500 2 SER A 141 -90.23 -92.74 REMARK 500 2 ASP A 142 93.63 -169.86 REMARK 500 2 GLN A 154 -51.94 -125.43 REMARK 500 2 ALA A 158 70.77 -167.67 REMARK 500 2 ASP A 180 115.98 -177.48 REMARK 500 2 ASN A 185 51.71 -105.67 REMARK 500 2 SER A 189 65.55 -168.92 REMARK 500 2 GLU A 208 -51.56 -122.65 REMARK 500 3 SER A 141 -111.01 -86.63 REMARK 500 3 ASP A 142 101.26 -162.46 REMARK 500 3 ALA A 158 54.89 -168.15 REMARK 500 3 ASP A 180 106.21 -51.62 REMARK 500 3 ASP A 182 21.70 -141.21 REMARK 500 3 SER A 184 -80.15 -74.71 REMARK 500 3 ASN A 185 10.68 56.24 REMARK 500 4 SER A 141 -116.51 -106.76 REMARK 500 4 ALA A 158 33.17 -162.11 REMARK 500 4 ILE A 179 -77.07 -91.29 REMARK 500 4 SER A 184 4.76 -68.11 REMARK 500 4 SER A 189 49.08 -156.95 REMARK 500 5 SER A 141 -130.56 -104.76 REMARK 500 5 ALA A 158 38.98 -161.00 REMARK 500 5 TRP A 176 6.04 -62.96 REMARK 500 5 ARG A 178 40.54 -98.29 REMARK 500 5 LYS A 181 -44.99 -140.84 REMARK 500 5 ASP A 182 29.33 -146.60 REMARK 500 5 LYS A 187 13.67 -149.41 REMARK 500 5 ASP A 216 -4.83 69.25 REMARK 500 6 SER A 141 -143.61 -93.36 REMARK 500 6 ALA A 158 68.66 -172.25 REMARK 500 6 SER A 184 104.97 -169.24 REMARK 500 6 LYS A 187 24.24 45.65 REMARK 500 7 SER A 141 -110.16 -100.54 REMARK 500 7 ASP A 142 99.03 -162.40 REMARK 500 7 GLN A 154 -52.33 -126.00 REMARK 500 7 ALA A 158 66.29 -169.57 REMARK 500 7 ILE A 179 -51.15 -128.40 REMARK 500 7 LYS A 181 -23.40 62.70 REMARK 500 7 ASN A 185 78.66 21.86 REMARK 500 7 SER A 186 -38.03 -135.19 REMARK 500 8 SER A 141 -125.77 -88.78 REMARK 500 8 GLN A 154 -52.58 -126.10 REMARK 500 REMARK 500 THIS ENTRY HAS 129 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 5 ARG A 173 0.10 SIDE CHAIN REMARK 500 5 ARG A 202 0.12 SIDE CHAIN REMARK 500 6 ARG A 161 0.08 SIDE CHAIN REMARK 500 6 ARG A 202 0.09 SIDE CHAIN REMARK 500 9 ARG A 161 0.08 SIDE CHAIN REMARK 500 9 ARG A 190 0.09 SIDE CHAIN REMARK 500 10 ARG A 190 0.10 SIDE CHAIN REMARK 500 10 ARG A 202 0.10 SIDE CHAIN REMARK 500 11 TYR A 138 0.10 SIDE CHAIN REMARK 500 12 ARG A 161 0.08 SIDE CHAIN REMARK 500 13 TYR A 133 0.07 SIDE CHAIN REMARK 500 13 ARG A 161 0.11 SIDE CHAIN REMARK 500 14 TYR A 133 0.07 SIDE CHAIN REMARK 500 15 PHE A 121 0.13 SIDE CHAIN REMARK 500 15 ARG A 190 0.08 SIDE CHAIN REMARK 500 15 ARG A 202 0.08 SIDE CHAIN REMARK 500 16 PHE A 121 0.09 SIDE CHAIN REMARK 500 16 TYR A 138 0.09 SIDE CHAIN REMARK 500 17 ARG A 129 0.10 SIDE CHAIN REMARK 500 17 TYR A 138 0.10 SIDE CHAIN REMARK 500 17 ARG A 161 0.11 SIDE CHAIN REMARK 500 18 PHE A 121 0.11 SIDE CHAIN REMARK 500 18 ARG A 129 0.14 SIDE CHAIN REMARK 500 18 ARG A 190 0.10 SIDE CHAIN REMARK 500 20 PHE A 121 0.13 SIDE CHAIN REMARK 500 20 TYR A 138 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25175 RELATED DB: BMRB REMARK 900 N-TERMINAL DOMAIN OF THE LANTIBIOTIC IMMUNITY PROTEIN NISI REMARK 900 RELATED ID: 25193 RELATED DB: BMRB REMARK 900 NISI REMARK 900 RELATED ID: 25194 RELATED DB: BMRB DBREF 2N2E A 98 226 UNP P42708 NISI_LACLL 117 245 SEQRES 1 A 129 ASP LYS GLY ALA VAL LYS ALA LEU ARG LEU GLN ASN PHE SEQRES 2 A 129 ASP VAL THR SER ASP ILE SER ASP ASP ASN PHE VAL ILE SEQRES 3 A 129 ASP LYS ASN ASP SER ARG LYS ILE ASP TYR MET GLY ASN SEQRES 4 A 129 ILE TYR SER ILE SER ASP THR THR VAL SER ASP GLU GLU SEQRES 5 A 129 LEU GLY GLU TYR GLN ASP VAL LEU ALA GLU VAL ARG VAL SEQRES 6 A 129 PHE ASP SER VAL SER GLY LYS SER ILE PRO ARG SER GLU SEQRES 7 A 129 TRP GLY ARG ILE ASP LYS ASP GLY SER ASN SER LYS GLN SEQRES 8 A 129 SER ARG THR GLU TRP ASP TYR GLY GLU ILE HIS SER ILE SEQRES 9 A 129 ARG GLY LYS SER LEU THR GLU ALA PHE ALA VAL GLU ILE SEQRES 10 A 129 ASN ASP ASP PHE LYS LEU ALA THR LYS VAL GLY ASN SHEET 1 A 7 VAL A 122 ASP A 124 0 SHEET 2 A 7 ASP A 127 TYR A 133 -1 O ASP A 132 N VAL A 122 SHEET 3 A 7 ASN A 136 THR A 144 -1 O TYR A 138 N ILE A 131 SHEET 4 A 7 ASP A 217 LYS A 223 -1 O THR A 222 N SER A 139 SHEET 5 A 7 ALA A 209 ILE A 214 -1 N VAL A 212 O LYS A 219 SHEET 6 A 7 ARG A 190 ILE A 201 -1 N HIS A 199 O ALA A 211 SHEET 7 A 7 LEU A 150 ASP A 155 -1 N ASP A 155 O ILE A 198 SHEET 1 B 7 VAL A 122 ASP A 124 0 SHEET 2 B 7 ASP A 127 TYR A 133 -1 O ASP A 132 N VAL A 122 SHEET 3 B 7 ASN A 136 THR A 144 -1 O TYR A 138 N ILE A 131 SHEET 4 B 7 ASP A 217 LYS A 223 -1 O THR A 222 N SER A 139 SHEET 5 B 7 ALA A 209 ILE A 214 -1 N VAL A 212 O LYS A 219 SHEET 6 B 7 ARG A 190 ILE A 201 -1 N HIS A 199 O ALA A 211 SHEET 7 B 7 VAL A 160 ASP A 164 -1 N ARG A 161 O TRP A 193 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