HEADER DNA 31-AUG-23 8W7W TITLE CRYSTAL STRUCTURE OF D(CGTATACG)2 WITH ACRIDINE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3'); COMPND 3 CHAIN: A, B, D, E; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DRUG-DNA COMPLEX, BIS-INTERCALATOR, ACRIDINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR S.C.HUANG,R.B.SATANGE,M.H.HOU REVDAT 2 11-SEP-24 8W7W 1 JRNL REVDAT 1 07-AUG-24 8W7W 0 JRNL AUTH S.C.HUANG,C.W.CHEN,R.SATANGE,C.C.HSIEH,C.C.CHANG,S.C.WANG, JRNL AUTH 2 C.L.PENG,T.L.CHEN,M.H.CHIANG,Y.C.HORNG,M.H.HOU JRNL TITL TARGETING DNA JUNCTION SITES BY BIS-INTERCALATORS INDUCES JRNL TITL 2 TOPOLOGICAL CHANGES WITH POTENT ANTITUMOR EFFECTS. JRNL REF NUCLEIC ACIDS RES. V. 52 9303 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 39036959 JRNL DOI 10.1093/NAR/GKAE643 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.17.1_3660: ???) 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 11047 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1113 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 24.1200 - 3.1500 0.88 1143 131 0.1616 0.1521 REMARK 3 2 3.1500 - 2.5000 0.95 1234 128 0.2653 0.2810 REMARK 3 3 2.5000 - 2.1900 0.98 1243 140 0.2497 0.2494 REMARK 3 4 2.1900 - 1.9900 0.99 1274 150 0.2676 0.3085 REMARK 3 5 1.9900 - 1.8400 0.99 1232 145 0.2466 0.2782 REMARK 3 6 1.8400 - 1.7400 0.99 1281 132 0.2364 0.2731 REMARK 3 7 1.7400 - 1.6500 1.00 1285 146 0.2324 0.2603 REMARK 3 8 1.6500 - 1.5800 0.97 1242 141 0.2617 0.3298 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.350 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 : 0.009 810 REMARK 3 ANGLE : 1.263 1226 REMARK 3 CHIRALITY : 0.051 128 REMARK 3 PLANARITY : 0.009 36 REMARK 3 DIHEDRAL : 32.979 314 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.4340 11.3488 0.2452 REMARK 3 T TENSOR REMARK 3 T11: 0.2406 T22: 0.2795 REMARK 3 T33: 0.2145 T12: -0.0146 REMARK 3 T13: -0.0137 T23: -0.0124 REMARK 3 L TENSOR REMARK 3 L11: 0.7772 L22: 1.4676 REMARK 3 L33: 7.3440 L12: 0.2534 REMARK 3 L13: -1.0594 L23: -0.2113 REMARK 3 S TENSOR REMARK 3 S11: 0.3031 S12: -0.2883 S13: 0.0642 REMARK 3 S21: -0.0169 S22: 0.2043 S23: 0.0234 REMARK 3 S31: -0.1669 S32: 0.4094 S33: -0.4827 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.9358 6.5795 -0.4189 REMARK 3 T TENSOR REMARK 3 T11: 0.2247 T22: 0.2283 REMARK 3 T33: 0.2337 T12: 0.0139 REMARK 3 T13: -0.0082 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.2842 L22: 0.8555 REMARK 3 L33: 6.7817 L12: -0.2048 REMARK 3 L13: -0.3702 L23: -0.6144 REMARK 3 S TENSOR REMARK 3 S11: 0.2558 S12: 0.0263 S13: 0.1518 REMARK 3 S21: -0.1003 S22: 0.1793 S23: -0.2216 REMARK 3 S31: 0.2869 S32: -0.2630 S33: -0.3377 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.7182 24.9850 3.6212 REMARK 3 T TENSOR REMARK 3 T11: 0.1823 T22: 0.2227 REMARK 3 T33: 0.1684 T12: -0.0081 REMARK 3 T13: 0.0043 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 6.4226 L22: 1.0848 REMARK 3 L33: 0.8488 L12: -0.8513 REMARK 3 L13: -0.5235 L23: 0.1774 REMARK 3 S TENSOR REMARK 3 S11: -0.4641 S12: 0.3963 S13: -0.3062 REMARK 3 S21: -0.0293 S22: 0.1464 S23: 0.0386 REMARK 3 S31: 0.0114 S32: -0.2043 S33: 0.2710 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3435 29.7380 3.1448 REMARK 3 T TENSOR REMARK 3 T11: 0.2489 T22: 0.2084 REMARK 3 T33: 0.2181 T12: 0.0015 REMARK 3 T13: -0.0204 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 5.7647 L22: 0.7088 REMARK 3 L33: 0.1319 L12: -0.5508 REMARK 3 L13: -0.3184 L23: -0.0214 REMARK 3 S TENSOR REMARK 3 S11: -0.4484 S12: -0.0675 S13: 0.3402 REMARK 3 S21: -0.2003 S22: 0.2131 S23: -0.1341 REMARK 3 S31: 0.0328 S32: 0.0312 S33: 0.1304 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 8W7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300040730. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11068 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02200 REMARK 200 FOR THE DATA SET : 29.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.16900 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3MM OLIGONUCLEOTIDES, 0.3MM LIGAND, REMARK 280 25MM BIS-TRIS (PH 7.0), 50MM SODIUM CHLORIDE, 10MM MAGNESIUM REMARK 280 CHLORIDE HEXAHYDRATE, 15% (V/V) 2-METHYL-2,4-PENTANEDIOL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.04750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 MG E 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 202 O REMARK 620 2 HOH A 204 O 168.8 REMARK 620 3 HOH A 207 O 85.5 83.7 REMARK 620 4 HOH A 213 O 94.4 81.2 82.4 REMARK 620 5 DT E 5 OP2 82.5 104.0 110.2 166.6 REMARK 620 6 HOH E 205 O 90.6 97.8 154.0 72.3 94.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT B 5 OP2 REMARK 620 2 HOH B 203 O 81.3 REMARK 620 3 HOH B 205 O 103.6 90.6 REMARK 620 4 HOH D 202 O 102.4 165.4 102.1 REMARK 620 5 HOH D 208 O 105.4 81.0 148.0 84.4 REMARK 620 6 HOH D 211 O 171.9 95.8 68.8 82.4 81.4 REMARK 620 N 1 2 3 4 5 DBREF 8W7W A 1 8 PDB 8W7W 8W7W 1 8 DBREF 8W7W B 1 8 PDB 8W7W 8W7W 1 8 DBREF 8W7W D 1 8 PDB 8W7W 8W7W 1 8 DBREF 8W7W E 1 8 PDB 8W7W 8W7W 1 8 SEQRES 1 A 8 DC DG DT DA DT DA DC DG SEQRES 1 B 8 DC DG DT DA DT DA DC DG SEQRES 1 D 8 DC DG DT DA DT DA DC DG SEQRES 1 E 8 DC DG DT DA DT DA DC DG HET VZX A 101 17 HET VZX B 101 18 HET MG B 102 1 HET VZX D 101 17 HET VZX E 101 18 HET MG E 102 1 HETNAM VZX ~{N},~{N}'-DI(ACRIDIN-9-YL)PENTANE-1,5-DIAMINE HETNAM MG MAGNESIUM ION FORMUL 5 VZX 4(C31 H28 N4) FORMUL 7 MG 2(MG 2+) FORMUL 11 HOH *39(H2 O) LINK CBC VZX A 101 C1 VZX B 101 1555 1555 1.49 LINK CBC VZX D 101 C1 VZX E 101 1555 1555 1.49 LINK O HOH A 202 MG MG E 102 2655 1555 2.36 LINK O HOH A 204 MG MG E 102 2655 1555 2.04 LINK O HOH A 207 MG MG E 102 2655 1555 2.27 LINK O HOH A 213 MG MG E 102 2655 1555 2.02 LINK OP2 DT B 5 MG MG B 102 1555 1555 2.12 LINK MG MG B 102 O HOH B 203 1555 1555 2.23 LINK MG MG B 102 O HOH B 205 1555 1555 2.35 LINK MG MG B 102 O HOH D 202 1555 2645 2.14 LINK MG MG B 102 O HOH D 208 1555 2645 2.21 LINK MG MG B 102 O HOH D 211 1555 2645 2.17 LINK OP2 DT E 5 MG MG E 102 1555 1555 2.17 LINK MG MG E 102 O HOH E 205 1555 1555 2.06 CRYST1 24.146 72.095 24.127 90.00 92.67 90.00 P 1 21 1 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 0.041415 0.000000 0.001928 0.00000 SCALE2 0.000000 0.013871 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041492 0.00000