HEADER DNA 30-AUG-23 8W76 TITLE CRYSTAL STRUCTURE OF D(CGTATACG)2 DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3'); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA, END-TO-END JUNCTION, HELIX-HELIX JUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR R.B.SATANGE,C.L.PENG,M.H.HOU REVDAT 2 11-SEP-24 8W76 1 JRNL REVDAT 1 07-AUG-24 8W76 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. 2.71 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) : 2.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 1698 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 169 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 2.8000 - 2.7000 1.00 0 0 0.2200 0.2600 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.040 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 : 0.004 366 REMARK 3 ANGLE : 0.640 560 REMARK 3 CHIRALITY : 0.030 64 REMARK 3 PLANARITY : 0.002 16 REMARK 3 DIHEDRAL : 34.534 154 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.4932 -1.5525 12.0478 REMARK 3 T TENSOR REMARK 3 T11: 0.2184 T22: 0.3800 REMARK 3 T33: 0.2760 T12: -0.0521 REMARK 3 T13: -0.0260 T23: 0.1118 REMARK 3 L TENSOR REMARK 3 L11: 0.1394 L22: 0.4366 REMARK 3 L33: 0.0787 L12: -0.2011 REMARK 3 L13: 0.0912 L23: -0.1791 REMARK 3 S TENSOR REMARK 3 S11: -0.0592 S12: -0.0909 S13: -0.2566 REMARK 3 S21: -0.3120 S22: -0.0794 S23: 0.1152 REMARK 3 S31: -0.0687 S32: 0.5311 S33: -0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 8 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0410 2.6220 13.1368 REMARK 3 T TENSOR REMARK 3 T11: 0.3506 T22: 0.4992 REMARK 3 T33: 0.3525 T12: 0.0905 REMARK 3 T13: 0.0418 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 0.2695 L22: 0.2830 REMARK 3 L33: 0.0251 L12: 0.2652 REMARK 3 L13: -0.0571 L23: -0.0800 REMARK 3 S TENSOR REMARK 3 S11: 0.1214 S12: 0.3384 S13: 0.0286 REMARK 3 S21: 0.4335 S22: 0.0889 S23: 0.1843 REMARK 3 S31: 0.5336 S32: 0.8045 S33: 0.0253 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 8W76 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300040658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.0 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 : 1753 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03300 REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.12300 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 (%): 56.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0MM OLIGONUCLEOTIDES, 50MM BIS-TRIS REMARK 280 (PH 7.0), 20MM SODIUM CHLORIDE, 10MM CALCIUM CHLORIDE, 80MM REMARK 280 POTASSIUM CHLORIDE, 7MM MANGANESE(II) CHLORIDE TETRAHYDRATE, 10% REMARK 280 PEG 2000, 50% RESERVIOR PEG 2000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.99700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.80700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.80700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.49850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.80700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.80700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.49550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.80700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.80700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.49850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.80700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.80700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 58.49550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 38.99700 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: 760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 MN C 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 8 OP2 REMARK 620 2 DG C 8 N7 112.1 REMARK 620 3 DG C 8 OP2 0.0 112.1 REMARK 620 4 HOH C 201 O 154.9 92.1 154.9 REMARK 620 5 HOH C 201 O 99.9 108.6 99.9 64.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 102 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 8 OP1 REMARK 620 2 DG C 8 O3' 57.9 REMARK 620 3 DG D 8 OP1 65.9 110.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 8 N7 REMARK 620 2 HOH D 201 O 88.0 REMARK 620 3 HOH D 202 O 83.5 124.1 REMARK 620 4 HOH D 203 O 86.6 58.7 65.6 REMARK 620 5 HOH D 204 O 154.0 74.9 89.8 67.8 REMARK 620 N 1 2 3 4 DBREF 8W76 C 1 8 PDB 8W76 8W76 1 8 DBREF 8W76 D 1 8 PDB 8W76 8W76 1 8 SEQRES 1 C 8 DC DG DT DA DT DA DC DG SEQRES 1 D 8 DC DG DT DA DT DA DC DG HET MN C 101 1 HET MN D 101 1 HET MN D 102 1 HET MN D 103 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 4(MN 2+) FORMUL 7 HOH *6(H2 O) LINK OP2 DG C 8 MN MN C 101 1555 1555 2.01 LINK N7 DG C 8 MN MN C 101 1555 1555 1.84 LINK OP2 DG C 8 MN MN C 101 1555 7555 2.18 LINK OP1 DG C 8 MN MN D 102 1555 4554 2.46 LINK O3' DG C 8 MN MN D 102 1555 5555 2.53 LINK MN MN C 101 O HOH C 201 1555 1555 2.12 LINK MN MN C 101 O HOH C 201 1555 7555 2.10 LINK N7 DG D 8 MN MN D 101 1555 1555 2.28 LINK OP1 DG D 8 MN MN D 102 1555 1555 2.07 LINK O3' DG D 8 MN MN D 103 1555 1555 2.76 LINK MN MN D 101 O HOH D 201 1555 1555 2.30 LINK MN MN D 101 O HOH D 202 1555 1555 2.14 LINK MN MN D 101 O HOH D 203 1555 1555 2.63 LINK MN MN D 101 O HOH D 204 1555 1555 2.18 CRYST1 37.614 37.614 77.994 90.00 90.00 90.00 P 41 21 2 16 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 0.026586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026586 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012821 0.00000