HEADER DNA 29-MAY-25 9V89 TITLE CRYSTAL STRUCTURE OF D(CGTTAACG)2 WITH A FIVE-CARBON LINKER CONTAINING TITLE 2 QUINOXALINE-ACRIDINE ASYMMETRIC INTERCALATOR COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS LIGAND-DNA COMPLEX, ASYMMETRIC INTERCALATOR, BIS-INTERCALATION, KEYWDS 2 QUINOXALINE, ACRIDINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.C.WANG,M.H.HOU REVDAT 1 03-JUN-26 9V89 0 JRNL AUTH S.C.WANG,M.H.HOU JRNL TITL CRYSTAL STRUCTURE OF D(CGTTAACG)2 WITH A FIVE-CARBON LINKER JRNL TITL 2 CONTAINING QUINOXALINE-ACRIDINE ASYMMETRIC INTERCALATOR JRNL TITL 3 COMPOUND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 10803 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1081 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.9500 - 2.5400 0.98 1313 147 0.2034 0.2091 REMARK 3 2 2.5400 - 2.0200 0.98 1239 137 0.2339 0.2599 REMARK 3 3 2.0200 - 1.7600 0.98 1212 135 0.2020 0.2334 REMARK 3 4 1.7600 - 1.6000 0.98 1206 134 0.1893 0.1998 REMARK 3 5 1.6000 - 1.4900 0.98 1214 135 0.2144 0.2511 REMARK 3 6 1.4900 - 1.4000 0.97 1193 132 0.2259 0.2511 REMARK 3 7 1.4000 - 1.3300 0.96 1165 130 0.2392 0.2453 REMARK 3 8 1.3300 - 1.2700 0.96 1180 131 0.2519 0.2895 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 410 REMARK 3 ANGLE : 1.430 620 REMARK 3 CHIRALITY : 0.059 65 REMARK 3 PLANARITY : 0.014 19 REMARK 3 DIHEDRAL : 34.419 163 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9V89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1300058310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 07A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97626 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10857 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.20300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX (1.20.1_4487) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6MM OLIGONUCLEOTIDES, 0.6MM QA5, REMARK 280 50MM 2-(N-MORPHOLINO)ETHANESULFONIC ACID HYDRATE (PH 6.5), 200MM REMARK 280 POTASSIUM CHLORIDE, 5MM HEXAMMINE COBALT(III) CHLORIDE, 15% (V/V) REMARK 280 2-METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 11.91750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.95050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.47400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.95050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.91750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.47400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 101 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 216 O REMARK 620 2 HOH A 223 O 91.6 REMARK 620 3 HOH B 222 O 91.8 96.6 REMARK 620 4 HOH B 230 O 87.9 178.9 82.4 REMARK 620 5 HOH B 231 O 176.0 90.1 91.6 90.5 REMARK 620 6 HOH B 232 O 89.4 91.4 171.8 89.5 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 102 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 220 O REMARK 620 2 HOH A 221 O 87.3 REMARK 620 3 HOH A 222 O 90.4 97.1 REMARK 620 4 HOH A 226 O 90.0 176.0 85.8 REMARK 620 5 HOH A 227 O 95.1 84.5 174.3 92.8 REMARK 620 6 HOH A 228 O 179.7 92.4 89.5 90.3 85.0 REMARK 620 N 1 2 3 4 5 DBREF 9V89 A 1 8 PDB 9V89 9V89 1 8 DBREF 9V89 B 1 8 PDB 9V89 9V89 1 8 SEQRES 1 A 8 DC DG DT DT DA DA DC DG SEQRES 1 B 8 DC DG DT DT DA DA DC DG HET CO A 101 1 HET CO A 102 1 HET W1H B 101 33 HET MPD B 102 8 HETNAM CO COBALT (II) ION HETNAM W1H N-[5-(ACRIDIN-9-YLAMINO)PENTYL]QUINOXALINE-2- HETNAM 2 W1H CARBOXAMIDE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 CO 2(CO 2+) FORMUL 5 W1H C27 H25 N5 O FORMUL 6 MPD C6 H14 O2 FORMUL 7 HOH *80(H2 O) LINK CO CO A 101 O HOH A 216 1555 1555 1.84 LINK CO CO A 101 O HOH A 223 1555 1555 2.00 LINK CO CO A 101 O HOH B 222 1555 2554 2.06 LINK CO CO A 101 O HOH B 230 1555 2554 2.08 LINK CO CO A 101 O HOH B 231 1555 3654 1.98 LINK CO CO A 101 O HOH B 232 1555 3654 2.06 LINK CO CO A 102 O HOH A 220 1555 1555 2.20 LINK CO CO A 102 O HOH A 221 1555 3644 1.94 LINK CO CO A 102 O HOH A 222 1555 1555 2.33 LINK CO CO A 102 O HOH A 226 1555 1555 1.95 LINK CO CO A 102 O HOH A 227 1555 3644 2.23 LINK CO CO A 102 O HOH A 228 1555 3644 2.20 CRYST1 23.835 34.948 47.901 90.00 90.00 90.00 P 21 21 21 8 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 0.041955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028614 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020876 0.00000 CONECT 331 389 396 CONECT 332 393 395 399 CONECT 333 334 338 CONECT 334 333 335 CONECT 335 334 336 CONECT 336 335 337 341 CONECT 337 336 338 350 CONECT 338 333 337 CONECT 339 340 345 350 CONECT 340 339 341 342 CONECT 341 336 340 351 CONECT 342 340 343 CONECT 343 342 344 CONECT 344 343 345 CONECT 345 339 344 CONECT 346 347 351 CONECT 347 346 348 CONECT 348 347 349 CONECT 349 348 352 CONECT 350 337 339 CONECT 351 341 346 CONECT 352 349 353 CONECT 353 352 354 CONECT 354 353 355 356 CONECT 355 354 357 361 CONECT 356 354 CONECT 357 355 358 CONECT 358 357 359 365 CONECT 359 358 360 362 CONECT 360 359 361 CONECT 361 355 360 CONECT 362 359 363 CONECT 363 362 364 CONECT 364 363 365 CONECT 365 358 364 CONECT 366 367 CONECT 367 366 368 369 370 CONECT 368 367 CONECT 369 367 CONECT 370 367 371 CONECT 371 370 372 373 CONECT 372 371 CONECT 373 371 CONECT 389 331 CONECT 393 332 CONECT 395 332 CONECT 396 331 CONECT 399 332 MASTER 228 0 4 0 0 0 0 6 451 2 48 2 END