HEADER DNA 11-OCT-22 8BAE TITLE COPPER(II) BOUND TO A NON-CANONICAL QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*AP*TP*GP*CP*T)-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 DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.C.LAMBERT,J.P.HALL REVDAT 2 04-MAR-26 8BAE 1 REMARK REVDAT 1 25-OCT-23 8BAE 0 JRNL AUTH M.C.LAMBERT,J.A.BRAZIER,C.J.CARDIN,J.P.HALL JRNL TITL OXIDATIVE DAMAGE INDUCE COPPER(II)-DNA BINDING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9566 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 20.5700 - 2.1800 1.00 2809 165 0.1156 0.1683 REMARK 3 2 2.1800 - 1.7300 1.00 2822 144 0.1315 0.1733 REMARK 3 3 1.7300 - 1.5100 1.00 2854 133 0.1329 0.1658 REMARK 3 4 1.5100 - 1.3700 1.00 2831 138 0.1529 0.1994 REMARK 3 5 1.3700 - 1.2800 1.00 2821 157 0.1568 0.2120 REMARK 3 6 1.2800 - 1.2000 0.99 2786 142 0.1893 0.2332 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.098 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.29 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 : 0.006 407 REMARK 3 ANGLE : 0.866 654 REMARK 3 CHIRALITY : 0.054 65 REMARK 3 PLANARITY : 0.007 17 REMARK 3 DIHEDRAL : 31.909 161 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 : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and resid 2 through 5) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and resid 2 through 5) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8BAE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292125041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU PHOTONJET-R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 42.60A REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO 42.60A REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9598 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 1MF5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 UL 40 MM SODIUM CACODYLATE, 1 UL 80 REMARK 280 MM HEXAMMINE (III) COBALT, 1 UL 10% MPD, 2 UL 800 MM POTASSIUM REMARK 280 CHLORIDE, UL 30 MM SODIUM CHLORIDE, 2 UL 1 MM DNA, PH 5.7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.80050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.80050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 10.97700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.43350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 10.97700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.43350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.80050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 10.97700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 29.43350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 22.80050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 10.97700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 29.43350 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 22.80100 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 CO NCO B 102 LIES ON A SPECIAL POSITION. REMARK 375 N3 NCO B 102 LIES ON A SPECIAL POSITION. REMARK 375 N5 NCO B 102 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 230 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 232 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 227 LIES ON A SPECIAL POSITION. 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 CU A 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 1 N7 REMARK 620 2 HOH A 225 O 111.1 REMARK 620 3 HOH A 229 O 106.0 93.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG B 1 N7 REMARK 620 2 DG B 1 N7 5.7 REMARK 620 3 HOH B 201 O 99.3 103.6 REMARK 620 4 HOH B 210 O 95.0 90.2 164.5 REMARK 620 N 1 2 3 DBREF 8BAE A 1 7 PDB 8BAE 8BAE 1 7 DBREF 8BAE B 1 7 PDB 8BAE 8BAE 1 7 SEQRES 1 A 7 DG DC DA DT DG DC DT SEQRES 1 B 7 DG DC DA DT DG DC DT HET CU A 101 1 HET NCO A 102 25 HET NCO A 103 25 HET NCO A 104 25 HET CU B 101 1 HET NCO B 102 50 HETNAM CU COPPER (II) ION HETNAM NCO COBALT HEXAMMINE(III) FORMUL 3 CU 2(CU 2+) FORMUL 4 NCO 4(CO H18 N6 3+) FORMUL 9 HOH *68(H2 O) LINK N7 DG A 1 CU CU A 101 1555 1555 2.40 LINK CU CU A 101 O HOH A 225 1555 1555 2.02 LINK CU CU A 101 O HOH A 229 1555 1555 2.08 LINK N7 A DG B 1 CU CU B 101 1555 1555 2.02 LINK N7 B DG B 1 CU CU B 101 1555 1555 1.87 LINK CU CU B 101 O HOH B 201 1555 1555 1.86 LINK CU CU B 101 O HOH B 210 1555 1555 1.94 CRYST1 21.954 58.867 45.601 90.00 90.00 90.00 C 2 2 21 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 0.045550 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016987 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021929 0.00000 MTRIX1 1 0.999184 -0.036500 0.017316 0.28041 1 MTRIX2 1 -0.036485 -0.999334 -0.001160 8.70813 1 MTRIX3 1 0.017347 0.000528 -0.999849 22.81902 1 CONECT 11 539 CONECT 243 615 CONECT 244 615 CONECT 539 11 690 694 CONECT 540 541 542 543 544 CONECT 540 545 546 CONECT 541 540 547 548 549 CONECT 542 540 550 551 552 CONECT 543 540 553 554 555 CONECT 544 540 556 557 558 CONECT 545 540 559 560 561 CONECT 546 540 562 563 564 CONECT 547 541 CONECT 548 541 CONECT 549 541 CONECT 550 542 CONECT 551 542 CONECT 552 542 CONECT 553 543 CONECT 554 543 CONECT 555 543 CONECT 556 544 CONECT 557 544 CONECT 558 544 CONECT 559 545 CONECT 560 545 CONECT 561 545 CONECT 562 546 CONECT 563 546 CONECT 564 546 CONECT 565 566 567 568 569 CONECT 565 570 571 CONECT 566 565 572 573 574 CONECT 567 565 575 576 577 CONECT 568 565 578 579 580 CONECT 569 565 581 582 583 CONECT 570 565 584 585 586 CONECT 571 565 587 588 589 CONECT 572 566 CONECT 573 566 CONECT 574 566 CONECT 575 567 CONECT 576 567 CONECT 577 567 CONECT 578 568 CONECT 579 568 CONECT 580 568 CONECT 581 569 CONECT 582 569 CONECT 583 569 CONECT 584 570 CONECT 585 570 CONECT 586 570 CONECT 587 571 CONECT 588 571 CONECT 589 571 CONECT 590 591 592 593 594 CONECT 590 595 596 CONECT 591 590 597 598 599 CONECT 592 590 600 601 602 CONECT 593 590 603 604 605 CONECT 594 590 606 607 608 CONECT 595 590 609 610 611 CONECT 596 590 612 613 614 CONECT 597 591 CONECT 598 591 CONECT 599 591 CONECT 600 592 CONECT 601 592 CONECT 602 592 CONECT 603 593 CONECT 604 593 CONECT 605 593 CONECT 606 594 CONECT 607 594 CONECT 608 594 CONECT 609 595 CONECT 610 595 CONECT 611 595 CONECT 612 596 CONECT 613 596 CONECT 614 596 CONECT 615 243 244 699 708 CONECT 616 618 620 622 624 CONECT 616 626 628 CONECT 617 619 621 623 625 CONECT 617 627 629 CONECT 618 616 630 632 634 CONECT 619 617 631 633 635 CONECT 620 616 636 638 640 CONECT 621 617 637 639 641 CONECT 622 616 642 644 646 CONECT 623 617 643 645 647 CONECT 624 616 648 650 652 CONECT 625 617 649 651 653 CONECT 626 616 654 656 658 CONECT 627 617 655 657 659 CONECT 628 616 660 662 664 CONECT 629 617 661 663 665 CONECT 630 618 CONECT 631 619 CONECT 632 618 CONECT 633 619 CONECT 634 618 CONECT 635 619 CONECT 636 620 CONECT 637 621 CONECT 638 620 CONECT 639 621 CONECT 640 620 CONECT 641 621 CONECT 642 622 CONECT 643 623 CONECT 644 622 CONECT 645 623 CONECT 646 622 CONECT 647 623 CONECT 648 624 CONECT 649 625 CONECT 650 624 CONECT 651 625 CONECT 652 624 CONECT 653 625 CONECT 654 626 CONECT 655 627 CONECT 656 626 CONECT 657 627 CONECT 658 626 CONECT 659 627 CONECT 660 628 CONECT 661 629 CONECT 662 628 CONECT 663 629 CONECT 664 628 CONECT 665 629 CONECT 690 539 CONECT 694 539 CONECT 699 615 CONECT 708 615 MASTER 259 0 6 0 0 0 0 9 378 2 139 2 END