HEADER TRANSCRIPTION 12-FEB-03 1NY9 TITLE ANTIBIOTIC BINDING DOMAIN OF A TIPA-CLASS MULTIDRUG RESISTANCE TITLE 2 TRANSCRIPTIONAL REGULATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL ACTIVATOR TIPA-S; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ANTIBIOTIC BINDING DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES LIVIDANS; SOURCE 3 ORGANISM_TAXID: 1916; SOURCE 4 GENE: TIPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL-1 BLUE CELLS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PREP4 AND PDS8 KEYWDS ALL ALPHA, GLOBIN LIKE, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.D.KAHMANN,H.J.SASS,M.G.ALLAN,H.SETO,C.J.THOMPSON,S.GRZESIEK REVDAT 3 23-FEB-22 1NY9 1 REMARK REVDAT 2 24-FEB-09 1NY9 1 VERSN REVDAT 1 15-APR-03 1NY9 0 JRNL AUTH J.D.KAHMANN,H.J.SASS,M.G.ALLAN,H.SETO,C.J.THOMPSON, JRNL AUTH 2 S.GRZESIEK JRNL TITL STRUCTURAL BASIS FOR ANTIBIOTIC RECOGNITION BY THE JRNL TITL 2 TIPA-CLASS OF MULTIDRUG-RESISTANCE TRANSCRIPTIONAL JRNL TITL 3 REGULATORS JRNL REF EMBO J. V. 22 1824 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12682015 JRNL DOI 10.1093/EMBOJ/CDG181 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 WITH MODIFICATIONS, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE MISSING RESIDUES IN REMARK 465 ARE MISSING IN THE STRUCTURE DUE REMARK 3 TO DISORDER, BUT HAD BEEN PRESENT DURING THE EXPERIMENT. REMARK 4 REMARK 4 1NY9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018344. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.9 REMARK 210 IONIC STRENGTH : 6 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM TIPAS U-15N, 5MM REMARK 210 PHOSPHATE BUFFER, 5MM DTT; 1.5 REMARK 210 MM TIPAS U-15N,13C, 5MM REMARK 210 PHOSPHATE BUFFER, 5MM DTT; 1.5 REMARK 210 MM TIPAS U-15N,13C, 5MM REMARK 210 PHOSPHATE BUFFER, 5MM DTT; 0.8 REMARK 210 MM TIPAS U-15N,13C, 10 MR/ML PF1 REMARK 210 PHAGES, 5MM PHOSPHATE BUFFER, REMARK 210 5MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : STANDARD TRIPLE AND DOUBLE REMARK 210 RESONANCE EXPERIMENTS REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, XEASY 1.2, PIPP REMARK 210 4.3.2, XWINNMR 2.6 REMARK 210 METHOD USED : SIMULATED ANNEALING WITH TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 160 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 210 REMARK 210 REMARK: STANDARD TRIPLE AND DOUBLE RESONANCE EXPERIMENTS AS REMARK 210 DESCRIBED IN GRZESIEK ET AL. (1997), PROTEIN SCIENCE 6, 1248- REMARK 210 1263. 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 111 REMARK 465 ILE A 112 REMARK 465 ASN A 113 REMARK 465 LEU A 114 REMARK 465 THR A 115 REMARK 465 PRO A 116 REMARK 465 GLU A 117 REMARK 465 GLU A 118 REMARK 465 LYS A 119 REMARK 465 PHE A 120 REMARK 465 GLU A 121 REMARK 465 VAL A 122 REMARK 465 PHE A 123 REMARK 465 GLY A 124 REMARK 465 ASP A 125 REMARK 465 PHE A 126 REMARK 465 ASP A 127 REMARK 465 PRO A 128 REMARK 465 ASP A 129 REMARK 465 GLN A 130 REMARK 465 TYR A 131 REMARK 465 GLU A 132 REMARK 465 GLU A 133 REMARK 465 GLU A 134 REMARK 465 VAL A 135 REMARK 465 ARG A 136 REMARK 465 GLU A 137 REMARK 465 ARG A 138 REMARK 465 TRP A 139 REMARK 465 GLY A 140 REMARK 465 ASN A 141 REMARK 465 THR A 142 REMARK 465 ASP A 143 REMARK 465 ALA A 144 REMARK 465 TYR A 145 REMARK 465 ARG A 146 REMARK 465 GLN A 147 REMARK 465 SER A 148 REMARK 465 LYS A 149 REMARK 465 GLU A 150 REMARK 465 LYS A 151 REMARK 465 THR A 152 REMARK 465 ALA A 153 REMARK 465 SER A 154 REMARK 465 TYR A 155 REMARK 465 THR A 156 REMARK 465 LYS A 157 REMARK 465 GLU A 158 REMARK 465 ASP A 159 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 O GLU A 217 H SER A 221 1.34 REMARK 500 O SER A 186 H MET A 190 1.37 REMARK 500 O ALA A 248 H THR A 252 1.43 REMARK 500 O ALA A 192 H HIS A 196 1.45 REMARK 500 O LEU A 245 H VAL A 249 1.45 REMARK 500 O GLU A 187 H ASP A 191 1.53 REMARK 500 O LEU A 170 H PHE A 174 1.59 REMARK 500 O THR A 171 H VAL A 175 1.60 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 GLN A 161 -2.53 60.13 REMARK 500 1 TYR A 205 -158.75 58.65 REMARK 500 1 ASP A 206 -138.79 -154.04 REMARK 500 1 TYR A 219 -7.30 -59.98 REMARK 500 1 VAL A 220 -35.73 -149.13 REMARK 500 1 ASP A 222 92.17 42.78 REMARK 500 1 GLU A 223 -14.39 -48.32 REMARK 500 1 LYS A 233 128.10 -179.49 REMARK 500 2 ILE A 163 36.29 -95.16 REMARK 500 2 HIS A 204 -129.40 -153.74 REMARK 500 2 TYR A 205 -113.22 -169.36 REMARK 500 2 ASP A 206 -144.10 49.88 REMARK 500 2 CYS A 207 -159.27 -69.91 REMARK 500 2 VAL A 220 -39.66 -148.41 REMARK 500 2 ASP A 222 92.02 44.98 REMARK 500 2 GLU A 223 -12.45 -48.74 REMARK 500 2 LYS A 233 135.73 -179.33 REMARK 500 2 HIS A 251 -60.48 -96.11 REMARK 500 2 THR A 252 150.48 50.64 REMARK 500 3 ILE A 163 34.50 -80.67 REMARK 500 3 HIS A 204 37.91 -158.12 REMARK 500 3 TYR A 205 -157.15 52.17 REMARK 500 3 ASP A 206 100.26 53.11 REMARK 500 3 TYR A 219 -4.73 -59.71 REMARK 500 3 VAL A 220 -38.20 -150.22 REMARK 500 3 GLU A 223 -15.44 -48.96 REMARK 500 3 LYS A 233 130.21 -179.74 REMARK 500 3 THR A 252 87.85 43.99 REMARK 500 4 GLN A 161 -45.26 -167.05 REMARK 500 4 ARG A 162 126.01 71.98 REMARK 500 4 ILE A 163 63.65 -66.50 REMARK 500 4 HIS A 204 -96.42 -98.28 REMARK 500 4 TYR A 205 -120.94 -152.12 REMARK 500 4 CYS A 207 -110.40 51.37 REMARK 500 4 VAL A 220 -39.24 -149.66 REMARK 500 4 GLU A 223 -16.01 -49.01 REMARK 500 4 LYS A 233 126.98 -179.79 REMARK 500 4 HIS A 251 -61.74 -96.24 REMARK 500 4 THR A 252 152.57 51.43 REMARK 500 5 HIS A 204 -127.52 -169.41 REMARK 500 5 TYR A 205 92.27 -163.91 REMARK 500 5 ASP A 206 -133.68 -156.52 REMARK 500 5 CYS A 207 -158.92 -83.81 REMARK 500 5 VAL A 220 -38.06 -150.33 REMARK 500 5 GLU A 223 -16.80 -48.98 REMARK 500 5 LYS A 233 133.60 -179.15 REMARK 500 6 ARG A 162 -127.40 -74.89 REMARK 500 6 ILE A 163 5.46 56.41 REMARK 500 6 HIS A 204 -102.75 -71.18 REMARK 500 6 TYR A 205 -34.21 -167.24 REMARK 500 REMARK 500 THIS ENTRY HAS 84 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 1 ARG A 162 0.23 SIDE CHAIN REMARK 500 1 ARG A 173 0.18 SIDE CHAIN REMARK 500 1 ARG A 197 0.31 SIDE CHAIN REMARK 500 1 ARG A 202 0.09 SIDE CHAIN REMARK 500 1 ARG A 224 0.28 SIDE CHAIN REMARK 500 1 ARG A 227 0.29 SIDE CHAIN REMARK 500 1 ARG A 241 0.30 SIDE CHAIN REMARK 500 1 ARG A 250 0.21 SIDE CHAIN REMARK 500 2 ARG A 162 0.15 SIDE CHAIN REMARK 500 2 ARG A 172 0.18 SIDE CHAIN REMARK 500 2 ARG A 173 0.29 SIDE CHAIN REMARK 500 2 ARG A 197 0.26 SIDE CHAIN REMARK 500 2 ARG A 202 0.11 SIDE CHAIN REMARK 500 2 ARG A 224 0.24 SIDE CHAIN REMARK 500 2 ARG A 227 0.26 SIDE CHAIN REMARK 500 2 ARG A 241 0.19 SIDE CHAIN REMARK 500 2 ARG A 250 0.19 SIDE CHAIN REMARK 500 3 ARG A 162 0.21 SIDE CHAIN REMARK 500 3 ARG A 172 0.25 SIDE CHAIN REMARK 500 3 ARG A 173 0.23 SIDE CHAIN REMARK 500 3 ARG A 197 0.29 SIDE CHAIN REMARK 500 3 ARG A 202 0.13 SIDE CHAIN REMARK 500 3 ARG A 241 0.24 SIDE CHAIN REMARK 500 3 ARG A 250 0.27 SIDE CHAIN REMARK 500 4 ARG A 162 0.31 SIDE CHAIN REMARK 500 4 ARG A 172 0.31 SIDE CHAIN REMARK 500 4 ARG A 173 0.32 SIDE CHAIN REMARK 500 4 ARG A 202 0.29 SIDE CHAIN REMARK 500 4 ARG A 224 0.27 SIDE CHAIN REMARK 500 4 ARG A 241 0.15 SIDE CHAIN REMARK 500 4 ARG A 250 0.20 SIDE CHAIN REMARK 500 5 ARG A 162 0.32 SIDE CHAIN REMARK 500 5 ARG A 172 0.25 SIDE CHAIN REMARK 500 5 ARG A 173 0.28 SIDE CHAIN REMARK 500 5 ARG A 197 0.25 SIDE CHAIN REMARK 500 5 ARG A 202 0.26 SIDE CHAIN REMARK 500 5 ARG A 224 0.31 SIDE CHAIN REMARK 500 5 ARG A 227 0.30 SIDE CHAIN REMARK 500 5 ARG A 241 0.24 SIDE CHAIN REMARK 500 5 ARG A 250 0.31 SIDE CHAIN REMARK 500 6 ARG A 162 0.26 SIDE CHAIN REMARK 500 6 ARG A 172 0.19 SIDE CHAIN REMARK 500 6 ARG A 173 0.29 SIDE CHAIN REMARK 500 6 ARG A 197 0.28 SIDE CHAIN REMARK 500 6 ARG A 241 0.30 SIDE CHAIN REMARK 500 6 ARG A 250 0.16 SIDE CHAIN REMARK 500 7 ARG A 162 0.16 SIDE CHAIN REMARK 500 7 ARG A 172 0.31 SIDE CHAIN REMARK 500 7 ARG A 173 0.30 SIDE CHAIN REMARK 500 7 ARG A 197 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 80 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EXJ RELATED DB: PDB REMARK 900 BACILLUS SUBTILIS MULTIDRUG RESISTANCE REGULATOR BMRR REMARK 900 RELATED ID: 1EXI RELATED DB: PDB REMARK 900 BACILLUS SUBTILIS MULTIDRUG RESISTANCE REGULATOR BMRR REMARK 900 RELATED ID: 1JBG RELATED DB: PDB REMARK 900 BACILLUS SUBTILIS MULTIDRUG TRANSPORTER REGULATOR MTAN DBREF 1NY9 A 111 253 UNP P0A4T9 TIPA_STRLI 111 253 SEQRES 1 A 143 GLY ILE ASN LEU THR PRO GLU GLU LYS PHE GLU VAL PHE SEQRES 2 A 143 GLY ASP PHE ASP PRO ASP GLN TYR GLU GLU GLU VAL ARG SEQRES 3 A 143 GLU ARG TRP GLY ASN THR ASP ALA TYR ARG GLN SER LYS SEQRES 4 A 143 GLU LYS THR ALA SER TYR THR LYS GLU ASP TRP GLN ARG SEQRES 5 A 143 ILE GLN ASP GLU ALA ASP GLU LEU THR ARG ARG PHE VAL SEQRES 6 A 143 ALA LEU MET ASP ALA GLY GLU PRO ALA ASP SER GLU GLY SEQRES 7 A 143 ALA MET ASP ALA ALA GLU ASP HIS ARG GLN GLY ILE ALA SEQRES 8 A 143 ARG ASN HIS TYR ASP CYS GLY TYR GLU MET HIS THR CYS SEQRES 9 A 143 LEU GLY GLU MET TYR VAL SER ASP GLU ARG PHE THR ARG SEQRES 10 A 143 ASN ILE ASP ALA ALA LYS PRO GLY LEU ALA ALA TYR MET SEQRES 11 A 143 ARG ASP ALA ILE LEU ALA ASN ALA VAL ARG HIS THR PRO HELIX 1 1 GLN A 164 GLY A 181 1 18 HELIX 2 2 SER A 186 HIS A 204 1 19 HELIX 3 3 GLY A 208 TYR A 219 1 12 HELIX 4 4 ASP A 222 ASP A 230 1 9 HELIX 5 5 ALA A 231 LYS A 233 5 3 HELIX 6 6 GLY A 235 THR A 252 1 18 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