HEADER DNA 16-FEB-26 11BJ TITLE CRYSTAL STRUCTURE OF TRABECTEDIN-DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*AP*TP*AP*GP*CP*TP*AP*GP*CP*TP*AP*T)-3'); COMPND 3 CHAIN: E, F; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE DNA CONTAINS AN INOSINE BASE. EACH STRAND IS COMPND 6 CROSSLINKED TO A TRABECTEDIN ADDUCT BY THE N2 OF A GUANINE. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DNA, ANTICANCER, DRUG, TC-NER, XPG INHIBITOR, DNA REPAIR EXPDTA X-RAY DIFFRACTION AUTHOR C.HOU,O.V.TSODIKOV REVDAT 1 27-MAY-26 11BJ 0 JRNL AUTH C.HOU,N.T.CHANDRIKA,M.LEGGAS,S.GARNEAU-TSODIKOVA, JRNL AUTH 2 O.V.TSODIKOV JRNL TITL CRYSTAL STRUCTURE OF TRABECTEDIN-DNA COMPLEX. JRNL REF J.MOL.BIOL. 69866 2026 JRNL REFN ESSN 1089-8638 JRNL PMID 42155620 JRNL DOI 10.1016/J.JMB.2026.169866 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 4264 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 223 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 283 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.4410 REMARK 3 BIN FREE R VALUE SET COUNT : 12 REMARK 3 BIN FREE R VALUE : 0.5240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 488 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.43000 REMARK 3 B22 (A**2) : -2.72000 REMARK 3 B33 (A**2) : 6.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.313 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.226 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.222 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.874 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 670 ; 0.005 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 348 ; 0.019 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1029 ; 1.011 ; 1.323 REMARK 3 BOND ANGLES OTHERS (DEGREES): 824 ; 1.655 ; 2.683 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 88 ; 0.057 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 360 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 110 ; 0.012 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 670 ; 2.350 ; 6.887 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 671 ; 2.349 ; 6.886 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1030 ; 3.637 ;10.322 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 975 ; 5.334 ;65.728 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 976 ; 5.332 ;65.750 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 11BJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-26. REMARK 100 THE DEPOSITION ID IS D_1000305226. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4597 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 46.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM TRIS PH 7.5, 5 MM MGCL2, AND 2 REMARK 280 MM SPERMINE HYDROCHLORIDE IN THE DROP, INCUBATED AGAINST 19% V/V REMARK 280 2-METHYL-2,4-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K 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 19.61850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.16550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.51600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.16550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.61850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.51600 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: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 DBREF 11BJ E -2 9 PDB 11BJ 11BJ -2 9 DBREF 11BJ F 8 19 PDB 11BJ 11BJ 8 19 SEQRES 1 E 12 DA DT DA DG DC DT DA DI DC DT DA DT SEQRES 1 F 12 DA DT DA DG DC DT DA DI DC DT DA DT HET ECT E 101 53 HET ECT F 101 53 HETNAM ECT ECTEINASCIDIN 743 HETSYN ECT TRABECTEDIN FORMUL 3 ECT 2(C39 H43 N3 O11 S) FORMUL 5 HOH *3(H2 O) LINK N2 DG E 1 C40 ECT E 101 1555 1555 1.30 LINK N2 DG F 11 C40 ECT F 101 1555 1555 1.31 CRYST1 39.237 47.032 50.331 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 0.025486 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019868 0.00000 CONECT 80 528 CONECT 326 581 CONECT 491 492 515 CONECT 492 491 493 509 CONECT 493 492 494 506 CONECT 494 493 495 498 CONECT 495 494 496 CONECT 496 495 497 CONECT 497 496 498 CONECT 498 494 497 499 CONECT 499 498 500 501 CONECT 500 499 CONECT 501 499 502 506 CONECT 502 501 503 CONECT 503 502 504 505 CONECT 504 503 CONECT 505 503 CONECT 506 493 501 507 CONECT 507 506 508 510 CONECT 508 507 509 532 CONECT 509 492 508 528 CONECT 510 507 511 CONECT 511 510 512 CONECT 512 511 513 516 527 CONECT 513 512 514 515 CONECT 514 513 CONECT 515 491 513 CONECT 516 512 517 524 CONECT 517 516 518 CONECT 518 517 519 521 CONECT 519 518 520 CONECT 520 519 CONECT 521 518 522 523 CONECT 522 521 CONECT 523 521 524 CONECT 524 516 523 525 CONECT 525 524 526 CONECT 526 525 527 CONECT 527 512 526 CONECT 528 80 509 529 CONECT 529 528 530 543 CONECT 530 529 531 532 CONECT 531 530 CONECT 532 508 530 533 CONECT 533 532 534 542 CONECT 534 533 535 536 CONECT 535 534 CONECT 536 534 537 539 CONECT 537 536 538 CONECT 538 537 CONECT 539 536 540 541 CONECT 540 539 CONECT 541 539 542 CONECT 542 533 541 543 CONECT 543 529 542 CONECT 544 545 568 CONECT 545 544 546 562 CONECT 546 545 547 559 CONECT 547 546 548 551 CONECT 548 547 549 CONECT 549 548 550 CONECT 550 549 551 CONECT 551 547 550 552 CONECT 552 551 553 554 CONECT 553 552 CONECT 554 552 555 559 CONECT 555 554 556 CONECT 556 555 557 558 CONECT 557 556 CONECT 558 556 CONECT 559 546 554 560 CONECT 560 559 561 563 CONECT 561 560 562 585 CONECT 562 545 561 581 CONECT 563 560 564 CONECT 564 563 565 CONECT 565 564 566 569 580 CONECT 566 565 567 568 CONECT 567 566 CONECT 568 544 566 CONECT 569 565 570 577 CONECT 570 569 571 CONECT 571 570 572 574 CONECT 572 571 573 CONECT 573 572 CONECT 574 571 575 576 CONECT 575 574 CONECT 576 574 577 CONECT 577 569 576 578 CONECT 578 577 579 CONECT 579 578 580 CONECT 580 565 579 CONECT 581 326 562 582 CONECT 582 581 583 596 CONECT 583 582 584 585 CONECT 584 583 CONECT 585 561 583 586 CONECT 586 585 587 595 CONECT 587 586 588 589 CONECT 588 587 CONECT 589 587 590 592 CONECT 590 589 591 CONECT 591 590 CONECT 592 589 593 594 CONECT 593 592 CONECT 594 592 595 CONECT 595 586 594 596 CONECT 596 582 595 MASTER 241 0 2 0 0 0 0 6 597 2 108 2 END