HEADER DNA 11-MAR-20 6M5J TITLE U SHAPED HEAD TO HEAD FOUR-WAY JUNCTION IN TITLE 2 D(TTCTGCTGCTGAA/TTCTGCAGCTGAA) SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*TP*CP*TP*GP*CP*TP*GP*CP*TP*GP*AP*A)-3'); COMPND 3 CHAIN: A, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(P*TP*TP*CP*TP*GP*CP*AP*GP*CP*TP*GP*AP*A)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS T:T MISMATCH, CTG REPEAT, FOUR-WAY JUNCTION, TRIAMINOTRIAZINE- KEYWDS 2 ACRIDINE CONJUGATE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.H.HOU,C.M.CHIEN,R.B.SATANGE REVDAT 2 29-NOV-23 6M5J 1 REMARK LINK REVDAT 1 15-JUL-20 6M5J 0 JRNL AUTH C.M.CHIEN,P.C.WU,R.SATANGE,C.C.CHANG,Z.L.LAI,L.D.HAGLER, JRNL AUTH 2 S.C.ZIMMERMAN,M.H.HOU JRNL TITL STRUCTURAL BASIS FOR TARGETING T:T MISMATCH WITH JRNL TITL 2 TRIAMINOTRIAZINE-ACRIDINE CONJUGATE INDUCES A U-SHAPED JRNL TITL 3 HEAD-TO-HEAD FOUR-WAY JUNCTION IN CTG REPEAT DNA. JRNL REF J.AM.CHEM.SOC. V. 142 11165 2020 JRNL REFN ESSN 1520-5126 JRNL PMID 32478511 JRNL DOI 10.1021/JACS.0C03591 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 50.0 REMARK 3 NUMBER OF REFLECTIONS : 10816 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 522 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 19.2210 - 2.6180 0.48 2591 127 0.1720 0.1824 REMARK 3 2 2.6180 - 2.0788 0.50 2648 119 0.2210 0.2737 REMARK 3 3 2.0788 - 1.8163 0.50 2601 127 0.1933 0.2083 REMARK 3 4 1.8163 - 1.6503 0.47 2454 149 0.1939 0.2276 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.31 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6M5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-18 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) : 0.99984 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 : 11117 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 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: 6M4T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES (PH=6.5) 50 MM, KCL 200 MM, MPD REMARK 280 35%, COCL2 10 MM, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 31.04300 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 DT A 1 P REMARK 480 DT B 1 OP1 REMARK 480 DT C 1 O5' REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 CO CO A 101 O HOH A 216 1.60 REMARK 500 O HOH A 219 O HOH A 228 2.14 REMARK 500 O HOH D 218 O HOH D 235 2.19 REMARK 500 O HOH A 209 O HOH A 220 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O4 DT C 4 OP2 DT D 1 2556 1.93 REMARK 500 O HOH C 229 O HOH C 240 2646 1.96 REMARK 500 REMARK 500 REMARK: NULL 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 DG A 5 N7 REMARK 620 2 DG D 8 N7 172.8 REMARK 620 N 1 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 DG A 8 N7 REMARK 620 2 DG D 5 N7 167.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 101 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 5 N7 REMARK 620 2 DG C 8 N7 153.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 102 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 8 N7 REMARK 620 2 DG C 5 N7 140.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F1R A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F1R B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F1R C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F1R D 101 DBREF 6M5J A 1 13 PDB 6M5J 6M5J 1 13 DBREF 6M5J B 1 13 PDB 6M5J 6M5J 1 13 DBREF 6M5J C 1 13 PDB 6M5J 6M5J 1 13 DBREF 6M5J D 1 13 PDB 6M5J 6M5J 1 13 SEQRES 1 A 13 DT DT DC DT DG DC DT DG DC DT DG DA DA SEQRES 1 B 13 DT DT DC DT DG DC DA DG DC DT DG DA DA SEQRES 1 C 13 DT DT DC DT DG DC DT DG DC DT DG DA DA SEQRES 1 D 13 DT DT DC DT DG DC DT DG DC DT DG DA DA HET CO A 101 1 HET CO A 102 1 HET F1R A 103 31 HET CO B 101 1 HET CO B 102 1 HET F1R B 103 31 HET F1R C 101 31 HET F1R D 101 31 HETNAM CO COBALT (II) ION HETNAM F1R N4-[4-[(6-CHLORANYL-2-METHOXY-ACRIDIN-9-YL) HETNAM 2 F1R AMINO]BUTYL]-1,3,5-TRIAZINE-2,4,6-TRIAMINE FORMUL 5 CO 4(CO 2+) FORMUL 7 F1R 4(C21 H23 CL N8 O) FORMUL 13 HOH *167(H2 O) LINK N7 DG A 5 CO CO A 101 1555 1555 2.34 LINK N7 DG A 8 CO CO A 102 1555 1555 2.15 LINK CO CO A 101 N7 DG D 8 1555 1555 2.28 LINK CO CO A 102 N7 DG D 5 1555 1555 2.14 LINK N7 DG B 5 CO CO B 101 1555 1555 2.37 LINK N7 DG B 8 CO CO B 102 1555 1555 2.28 LINK CO CO B 101 N7 DG C 8 1555 1555 2.17 LINK CO CO B 102 N7 DG C 5 1555 1555 2.34 SITE 1 AC1 6 DG A 5 HOH A 205 HOH A 216 HOH C 224 SITE 2 AC1 6 DG D 8 HOH D 224 SITE 1 AC2 6 DG A 8 HOH A 213 DG D 5 HOH D 205 SITE 2 AC2 6 HOH D 207 HOH D 208 SITE 1 AC3 9 DT A 10 DG A 11 HOH A 209 HOH A 218 SITE 2 AC3 9 HOH A 220 DG B 8 DC C 3 DT C 4 SITE 3 AC3 9 DG C 5 SITE 1 AC4 6 DG B 5 HOH B 204 HOH B 216 DG C 8 SITE 2 AC4 6 HOH C 206 HOH C 208 SITE 1 AC5 6 HOH A 220 DG B 8 HOH B 218 DG C 5 SITE 2 AC5 6 HOH C 202 HOH C 214 SITE 1 AC6 10 DG A 8 DT B 10 DG B 11 HOH B 203 SITE 2 AC6 10 HOH B 211 HOH B 221 DC D 3 DT D 4 SITE 3 AC6 10 DG D 5 HOH D 207 SITE 1 AC7 12 DC A 3 DT A 4 DG A 5 HOH A 215 SITE 2 AC7 12 DT C 10 DG C 11 HOH C 218 HOH C 219 SITE 3 AC7 12 HOH C 221 HOH C 224 HOH C 245 DG D 8 SITE 1 AC8 11 DC B 3 DT B 4 DG B 5 HOH B 206 SITE 2 AC8 11 HOH B 216 DG C 8 DT D 10 DG D 11 SITE 3 AC8 11 HOH D 209 HOH D 215 HOH D 222 CRYST1 57.630 62.086 30.747 90.00 121.84 90.00 P 1 21 1 6 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 0.017352 0.000000 0.010778 0.00000 SCALE2 0.000000 0.016107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.038286 0.00000