HEADER DNA 17-MAR-21 7EDW TITLE DNA DUPLEX CONTAINING T-T BASE PAIRS IN COMPLEX WITH AU(III) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*AP*CP*CP*TP*TP*GP*GP*TP*CP*C)-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 METAL-MEDIATED BASE PAIR, GOLD, DNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,E.IWASE REVDAT 2 29-MAY-24 7EDW 1 REMARK REVDAT 1 23-MAR-22 7EDW 0 JRNL AUTH J.KONDO,E.IWASE JRNL TITL DNA DUPLEX CONTAINING T-T BASE PAIRS IN COMPLEX WITH AU(III) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 12945 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) : 0.165 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1299 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 28.0200 - 4.1600 0.88 1228 139 0.1288 0.1438 REMARK 3 2 4.1600 - 3.3000 0.89 1242 134 0.1436 0.1280 REMARK 3 3 3.3000 - 2.8800 0.92 1299 140 0.1753 0.2181 REMARK 3 4 2.8800 - 2.6200 0.93 1301 149 0.2098 0.2582 REMARK 3 5 2.6200 - 2.4300 0.94 1284 148 0.1916 0.2340 REMARK 3 6 2.4300 - 2.2900 0.94 1335 148 0.1842 0.2505 REMARK 3 7 2.2900 - 2.1700 0.95 1320 145 0.1874 0.1962 REMARK 3 8 2.1700 - 2.0800 0.95 1350 150 0.2048 0.2345 REMARK 3 9 2.0800 - 2.0000 0.93 1287 146 0.2361 0.2995 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) : 20.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.53 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 7EDW 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_1300021240. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-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 : 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) : 1.03932 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 : 12947 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 2.431 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.32 REMARK 200 R MERGE FOR SHELL (I) : 0.31200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, MPD, SPERMINE REMARK 280 TETRAHYDROCHLORIDE, GOLD CHLORIDE, VAPOR DIFFUSION, HANGING 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 18.53800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.69150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.69150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.53800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.40000 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: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 AU A 101 AU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 6 O4 REMARK 620 2 HOH A 219 O 83.2 REMARK 620 3 DT B 18 O4 108.3 142.0 REMARK 620 4 HOH B 226 O 143.5 108.1 84.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AU A 102 AU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 9 O6 REMARK 620 2 HOH A 208 O 147.4 REMARK 620 3 HOH A 213 O 126.1 57.5 REMARK 620 4 HOH A 218 O 80.2 127.8 122.4 REMARK 620 5 HOH A 225 O 130.1 82.2 65.0 60.6 REMARK 620 6 HOH B 223 O 75.3 97.4 154.8 69.8 113.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AU B 101 AU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 210 O REMARK 620 2 HOH B 205 O 74.7 REMARK 620 3 HOH B 229 O 138.0 131.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 AU B 101 AU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 21 O6 REMARK 620 2 HOH B 221 O 125.8 REMARK 620 N 1 DBREF 7EDW A 1 12 PDB 7EDW 7EDW 1 12 DBREF 7EDW B 13 24 PDB 7EDW 7EDW 13 24 SEQRES 1 A 12 DG DG DA DC DC DT DT DG DG DT DC DC SEQRES 1 B 12 DG DG DA DC DC DT DT DG DG DT DC DC HET AU A 101 1 HET AU A 102 1 HET AU B 101 2 HETNAM AU GOLD ION FORMUL 3 AU 3(AU 1+) FORMUL 6 HOH *55(H2 O) LINK O4 DT A 6 AU AU A 101 1555 1555 2.67 LINK O6 DG A 9 AU AU A 102 1555 1555 2.59 LINK AU AU A 101 O HOH A 219 1555 1555 2.63 LINK AU AU A 101 O4 DT B 18 1555 1555 2.64 LINK AU AU A 101 O HOH B 226 1555 1555 2.73 LINK AU AU A 102 O HOH A 208 1555 1555 2.77 LINK AU AU A 102 O HOH A 213 1555 1555 2.31 LINK AU AU A 102 O HOH A 218 1555 1555 2.37 LINK AU AU A 102 O HOH A 225 1555 1555 2.52 LINK AU AU A 102 O HOH B 223 1555 1555 2.74 LINK O HOH A 210 AU A AU B 101 1555 1555 2.54 LINK O6 DG B 21 AU B AU B 101 1555 1555 2.53 LINK AU A AU B 101 O HOH B 205 1555 1555 2.67 LINK AU B AU B 101 O HOH B 221 1555 1555 2.62 LINK AU A AU B 101 O HOH B 229 1555 1555 2.75 CRYST1 37.076 42.800 67.383 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 0.026972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014841 0.00000 TER 243 DC A 12 TER 486 DC B 24 HETATM 487 AU AU A 101 3.159 29.310 58.271 0.78 34.21 AU HETATM 488 AU AU A 102 -0.790 28.277 52.031 0.64 36.97 AU HETATM 489 AU A AU B 101 6.805 34.175 63.832 0.28 33.06 AU HETATM 490 AU B AU B 101 5.184 34.490 63.442 0.52 64.04 AU HETATM 491 O HOH A 201 5.919 15.009 40.986 1.00 38.19 O HETATM 492 O HOH A 202 -1.022 27.249 49.326 1.00 32.62 O HETATM 493 O HOH A 203 5.697 18.003 46.463 1.00 40.10 O HETATM 494 O HOH A 204 2.466 26.218 61.621 1.00 37.83 O HETATM 495 O HOH A 205 7.081 26.134 62.594 1.00 43.63 O HETATM 496 O HOH A 206 0.901 29.378 56.526 1.00 26.79 O HETATM 497 O HOH A 207 4.252 33.463 47.481 1.00 36.09 O HETATM 498 O HOH A 208 -2.600 29.706 53.561 1.00 35.74 O HETATM 499 O HOH A 209 -5.008 30.810 54.563 1.00 41.81 O HETATM 500 O HOH A 210 8.085 32.569 65.324 1.00 36.40 O HETATM 501 O HOH A 211 3.543 28.707 61.073 1.00 26.07 O HETATM 502 O HOH A 212 -5.117 31.097 51.445 1.00 42.42 O HETATM 503 O HOH A 213 -2.663 29.278 51.126 1.00 40.10 O HETATM 504 O HOH A 214 11.500 36.639 67.418 1.00 41.28 O HETATM 505 O HOH A 215 -3.990 28.026 57.983 1.00 40.32 O HETATM 506 O HOH A 216 6.384 28.874 61.609 1.00 41.21 O HETATM 507 O HOH A 217 10.604 36.565 69.875 1.00 45.32 O HETATM 508 O HOH A 218 -0.457 25.932 51.989 1.00 39.79 O HETATM 509 O HOH A 219 2.096 26.915 58.459 1.00 30.70 O HETATM 510 O HOH A 220 -3.313 28.966 47.984 1.00 44.57 O HETATM 511 O HOH A 221 -1.285 27.862 56.722 1.00 34.53 O HETATM 512 O HOH A 222 12.909 26.185 59.004 1.00 37.65 O HETATM 513 O HOH A 223 -5.145 28.862 52.748 1.00 33.38 O HETATM 514 O HOH A 224 8.191 20.515 60.726 1.00 52.45 O HETATM 515 O HOH A 225 -2.774 26.751 51.730 1.00 49.50 O HETATM 516 O HOH B 201 5.468 38.263 59.749 1.00 42.59 O HETATM 517 O HOH B 202 -3.552 36.769 64.244 1.00 34.87 O HETATM 518 O HOH B 203 1.212 28.962 71.657 1.00 41.89 O HETATM 519 O HOH B 204 4.299 39.825 62.297 1.00 49.07 O HETATM 520 O HOH B 205 6.293 34.974 66.330 1.00 38.15 O HETATM 521 O HOH B 206 6.019 34.733 49.624 1.00 39.27 O HETATM 522 O HOH B 207 3.663 31.765 59.675 1.00 27.98 O HETATM 523 O HOH B 208 6.573 36.334 71.139 1.00 42.28 O HETATM 524 O HOH B 209 4.334 36.584 61.132 1.00 38.73 O HETATM 525 O HOH B 210 -3.304 36.124 60.288 1.00 33.14 O HETATM 526 O HOH B 211 8.794 23.452 47.852 1.00 41.50 O HETATM 527 O HOH B 212 7.433 35.511 57.093 1.00 43.29 O HETATM 528 O HOH B 213 -2.188 21.655 51.370 1.00 45.70 O HETATM 529 O HOH B 214 -2.392 22.631 49.245 1.00 44.74 O HETATM 530 O HOH B 215 1.412 44.788 57.731 1.00 40.91 O HETATM 531 O HOH B 216 4.037 27.766 56.026 1.00 27.80 O HETATM 532 O HOH B 217 7.002 27.713 56.307 1.00 40.67 O HETATM 533 O HOH B 218 7.778 35.386 73.868 1.00 41.61 O HETATM 534 O HOH B 219 11.003 25.150 78.252 1.00 42.30 O HETATM 535 O HOH B 220 5.645 18.176 49.217 1.00 40.82 O HETATM 536 O HOH B 221 5.134 37.076 63.860 1.00 40.59 O HETATM 537 O HOH B 222 2.625 25.433 55.374 1.00 37.32 O HETATM 538 O HOH B 223 0.877 27.522 54.071 1.00 35.10 O HETATM 539 O HOH B 224 3.992 37.084 72.452 1.00 41.17 O HETATM 540 O HOH B 225 12.875 31.622 57.833 1.00 47.51 O HETATM 541 O HOH B 226 5.857 29.064 58.564 1.00 29.17 O HETATM 542 O HOH B 227 7.134 32.903 80.393 1.00 47.06 O HETATM 543 O HOH B 228 6.507 37.905 66.539 1.00 42.44 O HETATM 544 O HOH B 229 7.238 35.610 61.530 1.00 46.04 O HETATM 545 O HOH B 230 6.533 39.216 64.263 1.00 37.21 O CONECT 117 487 CONECT 179 488 CONECT 360 487 CONECT 422 490 CONECT 487 117 360 509 541 CONECT 488 179 498 503 508 CONECT 488 515 538 CONECT 489 500 520 544 CONECT 490 422 536 CONECT 498 488 CONECT 500 489 CONECT 503 488 CONECT 508 488 CONECT 509 487 CONECT 515 488 CONECT 520 489 CONECT 536 490 CONECT 538 488 CONECT 541 487 CONECT 544 489 MASTER 240 0 3 0 0 0 0 6 542 2 20 2 END