HEADER DNA 17-MAR-21 7EDV TITLE DNA DUPLEX CONTAINING C-G-AU-C BASE TRIPLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*AP*CP*CP*CP*CP*GP*GP*TP*CP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS METAL-MEDIATED BASE PAIR, GOLD, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,E.IWASE REVDAT 3 26-NOV-25 7EDV 1 JRNL REVDAT 2 29-MAY-24 7EDV 1 REMARK REVDAT 1 23-MAR-22 7EDV 0 JRNL AUTH K.KOSUGI,A.SUGAWARA,E.IWASE,H.PARK,S.FUJIWARA,H.KANAZAWA, JRNL AUTH 2 A.ONO,J.KONDO JRNL TITL GOLD-MEDIATED BASE PAIRS IN NUCLEIC ACIDS: SELECTIVE JRNL TITL 2 COORDINATION TO NATURAL AND THIOCARBONYL-MODIFIED CYTOSINES JRNL TITL 3 DEPENDENT UPON THE OXIDATION STATE OF GOLD JRNL REF CHEMBIOCHEM V. 26 2025 JRNL REFN ESSN 1439-7633 JRNL DOI 10.1002/CBIC.202500565 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.450 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 5183 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.380 REMARK 3 FREE R VALUE TEST SET COUNT : 538 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 27.1800 - 3.1900 1.00 1166 138 0.1370 0.1496 REMARK 3 2 3.1800 - 2.5300 1.00 1166 138 0.1845 0.2373 REMARK 3 3 2.5300 - 2.2100 1.00 1159 130 0.1895 0.2195 REMARK 3 4 2.2100 - 2.0100 0.99 1154 132 0.2183 0.2561 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.41 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 7EDV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-17 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5183 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 27.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.16 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, MPD, SPERMINE REMARK 280 TETRAHYDROCHLORIDE, LITHIUM CHLORIDE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.56267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.12533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.12533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 15.56267 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: 1430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -77.81333 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 229 LIES ON A SPECIAL POSITION. 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 N7 DG A 8 AU AU A 101 1.76 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 AU A 101 AU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 6 O2 REMARK 620 2 DC A 6 N3 54.3 REMARK 620 N 1 DBREF 7EDV A 1 12 PDB 7EDV 7EDV 1 12 SEQRES 1 A 12 DG DG DA DC DC DC DC DG DG DT DC DC HET AU A 101 1 HETNAM AU GOLD ION FORMUL 2 AU AU 1+ FORMUL 3 HOH *37(H2 O) LINK O2 DC A 6 AU AU A 101 1555 1555 2.75 LINK N3 DC A 6 AU AU A 101 1555 1555 1.92 CRYST1 38.595 38.595 46.688 90.00 90.00 120.00 P 31 2 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 0.025910 0.014959 0.000000 0.00000 SCALE2 0.000000 0.029918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021419 0.00000 TER 241 DC A 12 HETATM 242 AU AU A 101 9.551 -12.020 -38.558 0.56 24.96 AU HETATM 243 O HOH A 201 9.620 -8.839 -29.175 1.00 36.90 O HETATM 244 O HOH A 202 -0.876 -26.086 -45.744 1.00 30.35 O HETATM 245 O HOH A 203 14.762 -21.919 -40.334 1.00 36.85 O HETATM 246 O HOH A 204 16.989 -10.865 -36.407 1.00 32.49 O HETATM 247 O HOH A 205 3.038 -12.175 -34.557 1.00 28.79 O HETATM 248 O HOH A 206 13.980 -21.527 -48.831 1.00 30.39 O HETATM 249 O HOH A 207 10.061 -5.421 -32.748 1.00 33.14 O HETATM 250 O HOH A 208 10.000 -9.814 -32.235 1.00 31.80 O HETATM 251 O HOH A 209 8.187 -20.102 -27.667 1.00 32.82 O HETATM 252 O HOH A 210 14.249 -19.311 -20.810 1.00 34.79 O HETATM 253 O HOH A 211 8.876 -8.775 -39.686 1.00 26.19 O HETATM 254 O HOH A 212 10.627 -26.872 -48.952 1.00 27.98 O HETATM 255 O HOH A 213 21.633 -13.910 -41.452 1.00 36.40 O HETATM 256 O HOH A 214 19.294 -7.623 -36.092 1.00 36.46 O HETATM 257 O HOH A 215 14.672 -15.026 -35.948 1.00 30.41 O HETATM 258 O HOH A 216 14.799 -16.422 -47.751 1.00 28.67 O HETATM 259 O HOH A 217 3.613 -27.970 -38.981 1.00 33.74 O HETATM 260 O HOH A 218 2.269 -24.383 -42.040 1.00 36.92 O HETATM 261 O HOH A 219 3.967 -22.466 -45.501 1.00 34.63 O HETATM 262 O HOH A 220 19.756 -22.311 -25.269 1.00 36.15 O HETATM 263 O HOH A 221 -0.453 -24.096 -43.047 1.00 29.99 O HETATM 264 O HOH A 222 16.301 -13.308 -37.270 1.00 27.37 O HETATM 265 O HOH A 223 13.341 -16.773 -38.040 1.00 30.07 O HETATM 266 O HOH A 224 6.087 -23.947 -41.679 1.00 36.37 O HETATM 267 O HOH A 225 8.009 -27.698 -40.115 1.00 36.00 O HETATM 268 O HOH A 226 6.986 -22.298 -43.320 1.00 31.52 O HETATM 269 O HOH A 227 14.490 -8.885 -33.897 1.00 39.88 O HETATM 270 O HOH A 228 9.722 -21.826 -41.098 1.00 28.27 O HETATM 271 O HOH A 229 10.984 -19.025 -38.907 0.50 32.60 O HETATM 272 O HOH A 230 9.427 -30.142 -47.903 1.00 38.05 O HETATM 273 O HOH A 231 12.261 -10.271 -32.707 1.00 28.11 O HETATM 274 O HOH A 232 15.510 -25.646 -48.287 1.00 40.15 O HETATM 275 O HOH A 233 -2.372 -25.830 -42.500 1.00 38.93 O HETATM 276 O HOH A 234 -1.266 -28.141 -41.400 1.00 36.65 O HETATM 277 O HOH A 235 19.584 -10.263 -37.006 1.00 38.13 O HETATM 278 O HOH A 236 4.333 -3.780 -34.974 1.00 49.79 O HETATM 279 O HOH A 237 16.538 -10.902 -33.337 1.00 43.59 O CONECT 114 242 CONECT 115 242 CONECT 242 114 115 MASTER 236 0 1 0 0 0 0 6 278 1 3 1 END