HEADER DNA 04-JUL-08 2K68 TITLE NMR SOLUTION STRUCTURE OF MODIFIED DNA CONTAINING IMIDAZOLE TITLE 2 NUCLEOSIDES AT NEUTRAL PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*DTP*DTP*DAP*DAP*DTP*DTP*DTP*(D33)P*(D33)P*(D33) COMPND 3 P*DAP*DAP*DAP*DTP*DTP*DAP*DA)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: DID_DNA_17-MER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA 17-MER, HAIRPIN, ARTIFICIAL NUCLEOBASE, IMIDAZOLE NUCLEOSIDE, KEYWDS 2 SHIFTED PKA, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.JOHANNSEN,D.BOEHME,N.DUEPRE,J.MUELLER,R.K.O.SIGEL REVDAT 3 29-MAY-24 2K68 1 REMARK REVDAT 2 16-MAR-22 2K68 1 REMARK LINK REVDAT 1 07-JUL-09 2K68 0 JRNL AUTH S.JOHANNSEN,D.BOEHME,N.DUEPRE,J.MUELLER,R.K.O.SIGEL JRNL TITL SOLUTION STRUCTURE AT DIFFERENT PHS OF A DNA HAIRPIN JRNL TITL 2 CONTAINING ARTIFICIAL NUCLEOTIDES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, 2.0, 2.1, X-PLOR NIH 2.15 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100727. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 7.2; 7.2 REMARK 210 IONIC STRENGTH : 120 MM; 120 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM DID DNA 17-MER, 120 MM REMARK 210 SODIUM PERCHLORATE, 100% D2O; REMARK 210 0.5 MM DID DNA 17-MER, 120 MM REMARK 210 SODIUM PERCHLORATE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC 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 : SPARKY 3.1, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DA A 17 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT A 1 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT A 14 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 17 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DT A 2 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DA A 13 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DT A 14 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DT A 15 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DA A 16 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DA A 17 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 4 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DT A 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 298 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D33 A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D33 A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D33 A 10 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K67 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF MODIFIED DNA CONTAINING IMIDAZOLE REMARK 900 NUCLEOSIDES AT ACIDIC PH REMARK 900 RELATED ID: 2K69 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF MODIFIED DNA CONTAINING IMIDAZOLE REMARK 900 NUCLEOSIDES AT BASIC PH DBREF 2K68 A 1 17 PDB 2K68 2K68 1 17 SEQRES 1 A 17 DT DT DA DA DT DT DT D33 D33 D33 DA DA DA SEQRES 2 A 17 DT DT DA DA HET D33 A 8 26 HET D33 A 9 26 HET D33 A 10 26 HETNAM D33 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 D33 PENTOFURANOSYL)-1H-IMIDAZOLE FORMUL 1 D33 3(C8 H13 N2 O6 P) LINK O3' DT A 7 P D33 A 8 1555 1555 1.61 LINK O3' D33 A 8 P D33 A 9 1555 1555 1.61 LINK O3' D33 A 9 P D33 A 10 1555 1555 1.61 LINK O3' D33 A 10 P DA A 11 1555 1555 1.61 SITE 1 AC1 1 DT A 7 SITE 1 AC2 1 DT A 7 SITE 1 AC3 1 DA A 11 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 199 227 CONECT 223 224 235 245 CONECT 224 223 226 243 CONECT 225 226 235 244 CONECT 226 224 225 234 CONECT 227 199 228 229 230 CONECT 228 227 CONECT 229 227 CONECT 230 227 231 CONECT 231 230 232 239 240 CONECT 232 231 233 237 241 CONECT 233 232 234 CONECT 234 226 233 236 242 CONECT 235 223 225 CONECT 236 234 237 246 247 CONECT 237 232 236 238 248 CONECT 238 237 253 CONECT 239 231 CONECT 240 231 CONECT 241 232 CONECT 242 234 CONECT 243 224 CONECT 244 225 CONECT 245 223 CONECT 246 236 CONECT 247 236 CONECT 248 237 CONECT 249 250 261 271 CONECT 250 249 252 269 CONECT 251 252 261 270 CONECT 252 250 251 260 CONECT 253 238 254 255 256 CONECT 254 253 CONECT 255 253 CONECT 256 253 257 CONECT 257 256 258 265 266 CONECT 258 257 259 263 267 CONECT 259 258 260 CONECT 260 252 259 262 268 CONECT 261 249 251 CONECT 262 260 263 272 273 CONECT 263 258 262 264 274 CONECT 264 263 279 CONECT 265 257 CONECT 266 257 CONECT 267 258 CONECT 268 260 CONECT 269 250 CONECT 270 251 CONECT 271 249 CONECT 272 262 CONECT 273 262 CONECT 274 263 CONECT 275 276 287 297 CONECT 276 275 278 295 CONECT 277 278 287 296 CONECT 278 276 277 286 CONECT 279 264 280 281 282 CONECT 280 279 CONECT 281 279 CONECT 282 279 283 CONECT 283 282 284 291 292 CONECT 284 283 285 289 293 CONECT 285 284 286 CONECT 286 278 285 288 294 CONECT 287 275 277 CONECT 288 286 289 298 299 CONECT 289 284 288 290 300 CONECT 290 289 301 CONECT 291 283 CONECT 292 283 CONECT 293 284 CONECT 294 286 CONECT 295 276 CONECT 296 277 CONECT 297 275 CONECT 298 288 CONECT 299 288 CONECT 300 289 CONECT 301 290 MASTER 162 0 3 0 0 0 3 6 332 1 80 2 END