PDB Short entry for 1NH3 HEADER ISOMERASE/DNA 18-DEC-02 1NH3 TITLE HUMAN TOPOISOMERASE I ARA-C COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*(GNG)P*GP*AP*AP*AP*AP*AP*UP*UP*UP*UP*T)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*TP*UP*UP*UP*UP*CP*(CAR) COMPND 11 P*AP*AP*GP*UP*CP*UP*UP*UP*UP*T)-3'; COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA TOPOISOMERASE I; COMPND 16 CHAIN: A; COMPND 17 FRAGMENT: CORE SUBDOMAIN, C-TERMINAL DOMAIN; COMPND 18 EC: 5.99.1.2; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: TOP1; SOURCE 12 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 13 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS ARA-C, PROTEIN-DNA COMPLEX, DNA DAMAGE, ISOMERASE, ISOMERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.E.CHRENCIK,A.B.BURGIN,Y.POMMIER,L.STEWART,M.R.REDINBO REVDAT 6 15-NOV-23 1NH3 1 REMARK REVDAT 5 20-SEP-23 1NH3 1 REMARK REVDAT 4 21-DEC-22 1NH3 1 SEQADV LINK REVDAT 3 24-FEB-09 1NH3 1 VERSN REVDAT 2 08-APR-03 1NH3 1 JRNL REVDAT 1 04-MAR-03 1NH3 0 JRNL AUTH J.E.CHRENCIK,A.B.BURGIN,Y.POMMIER,L.STEWART,M.R.REDINBO JRNL TITL STRUCTURAL IMPACT OF THE LEUKEMIA DRUG JRNL TITL 2 1-BETA-D-ARABINOFURANOSYLCYTOSINE (ARA-C) ON THE COVALENT JRNL TITL 3 HUMAN TOPOISOMERASE I-DNA COMPLEX JRNL REF J.BIOL.CHEM. V. 278 12461 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12533542 JRNL DOI 10.1074/JBC.M212930200 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 74.6 REMARK 3 NUMBER OF REFLECTIONS : 13878 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 SET) : 0.235 REMARK 3 FREE R VALUE : 0.311 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1351 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3483 REMARK 3 NUCLEIC ACID ATOMS : 878 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 27.26000 REMARK 3 B22 (A**2) : 27.26000 REMARK 3 B33 (A**2) : -54.52000 REMARK 3 B12 (A**2) : 13.43700 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM SIGMAA (A) : 0.71 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.880 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NH3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000017864. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13878 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 69.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.7 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 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1A31 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, MAGNESIUM CHLORIDE, PEG 400, REMARK 280 DTT, PH 7.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 276K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,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 124.19333 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 62.09667 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 APPLY THE FOLLOWING TO CHAINS: B, C, D, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 627 REMARK 465 ILE A 628 REMARK 465 LEU A 629 REMARK 465 CYS A 630 REMARK 465 ASN A 631 REMARK 465 HIS A 632 REMARK 465 GLN A 633 REMARK 465 ARG A 634 REMARK 465 ALA A 635 REMARK 465 PRO A 636 REMARK 465 PRO A 637 REMARK 465 LYS A 638 REMARK 465 THR A 639 REMARK 465 PHE A 640 REMARK 465 GLU A 641 REMARK 465 LYS A 642 REMARK 465 SER A 643 REMARK 465 MET A 644 REMARK 465 MET A 645 REMARK 465 ASN A 646 REMARK 465 LEU A 647 REMARK 465 GLN A 648 REMARK 465 THR A 649 REMARK 465 LYS A 650 REMARK 465 ILE A 651 REMARK 465 ASP A 652 REMARK 465 ALA A 653 REMARK 465 LYS A 654 REMARK 465 LYS A 655 REMARK 465 GLU A 656 REMARK 465 GLN A 657 REMARK 465 LEU A 658 REMARK 465 ALA A 659 REMARK 465 ASP A 660 REMARK 465 ALA A 661 REMARK 465 ARG A 662 REMARK 465 ARG A 663 REMARK 465 ASP A 664 REMARK 465 LEU A 665 REMARK 465 LYS A 666 REMARK 465 SER A 667 REMARK 465 ALA A 668 REMARK 465 LYS A 669 REMARK 465 ALA A 670 REMARK 465 ASP A 671 REMARK 465 ALA A 672 REMARK 465 LYS A 673 REMARK 465 VAL A 674 REMARK 465 MET A 675 REMARK 465 LYS A 676 REMARK 465 ASP A 677 REMARK 465 ALA A 678 REMARK 465 LYS A 679 REMARK 465 THR A 680 REMARK 465 LYS A 681 REMARK 465 LYS A 682 REMARK 465 VAL A 683 REMARK 465 VAL A 684 REMARK 465 GLU A 685 REMARK 465 SER A 686 REMARK 465 LYS A 687 REMARK 465 LYS A 688 REMARK 465 LYS A 689 REMARK 465 ALA A 690 REMARK 465 VAL A 691 REMARK 465 GLN A 692 REMARK 465 ARG A 693 REMARK 465 LEU A 694 REMARK 465 GLU A 695 REMARK 465 GLU A 696 REMARK 465 GLN A 697 REMARK 465 LEU A 698 REMARK 465 MET A 699 REMARK 465 LYS A 700 REMARK 465 LEU A 701 REMARK 465 GLU A 702 REMARK 465 VAL A 703 REMARK 465 GLN A 704 REMARK 465 ALA A 705 REMARK 465 THR A 706 REMARK 465 ASP A 707 REMARK 465 ARG A 708 REMARK 465 GLU A 709 REMARK 465 GLU A 710 REMARK 465 ASN A 711 REMARK 465 LYS A 712 REMARK 465 GLN A 713 REMARK 465 ILE A 714 REMARK 465 ALA A 715 REMARK 465 LEU A 716 REMARK 465 GLY A 717 REMARK 465 THR A 718 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 210 CB CG CD NE CZ NH1 NH2 REMARK 470 TYR A 211 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 211 OH REMARK 470 GLU A 213 CB CG CD OE1 OE2 REMARK 470 ILE A 215 CB CG1 CG2 CD1 REMARK 470 LYS A 218 CB CG CD CE NZ REMARK 470 GLU A 236 CB CG CD OE1 OE2 REMARK 470 LYS A 239 CB CG CD CE NZ REMARK 470 ASP A 243 CB CG OD1 OD2 REMARK 470 MET A 247 CB CG SD CE REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 MET A 263 CG SD CE REMARK 470 GLU A 267 CB CG CD OE1 OE2 REMARK 470 THR A 270 CB OG1 CG2 REMARK 470 LYS A 271 CB CG CD CE NZ REMARK 470 GLU A 272 CB CG CD OE1 OE2 REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 LYS A 280 CB CG CD CE NZ REMARK 470 ARG A 283 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 285 CB CG CD OE1 OE2 REMARK 470 ASN A 288 CB CG OD1 ND2 REMARK 470 GLU A 289 CG CD OE1 OE2 REMARK 470 LYS A 291 CB CG CD CE NZ REMARK 470 ASN A 292 CB CG OD1 ND2 REMARK 470 ASN A 296 CB CG OD1 ND2 REMARK 470 GLN A 304 CB CG CD OE1 NE2 REMARK 470 GLN A 307 CB CG CD OE1 NE2 REMARK 470 PHE A 309 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 312 CB CG CD OE1 NE2 REMARK 470 GLU A 314 CG CD OE1 OE2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 317 CG CD CE NZ REMARK 470 GLN A 318 CG CD OE1 NE2 REMARK 470 MET A 319 CG SD CE REMARK 470 LYS A 321 CG CD CE NZ REMARK 470 GLU A 322 CG CD OE1 OE2 REMARK 470 GLU A 323 CG CD OE1 OE2 REMARK 470 LYS A 324 CB CG CD CE NZ REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 ILE A 327 CB CG1 CG2 CD1 REMARK 470 LYS A 328 CB CG CD CE NZ REMARK 470 GLU A 329 CB CG CD OE1 OE2 REMARK 470 GLU A 330 CB CG CD OE1 OE2 REMARK 470 ASN A 331 CB CG OD1 ND2 REMARK 470 GLU A 332 CG CD OE1 OE2 REMARK 470 LYS A 333 CG CD CE NZ REMARK 470 LEU A 335 CB CG CD1 CD2 REMARK 470 GLU A 337 CB CG CD OE1 OE2 REMARK 470 ILE A 342 CB CG1 CG2 CD1 REMARK 470 ASN A 345 CB CG OD1 ND2 REMARK 470 HIS A 346 CB CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 348 CG CD OE1 OE2 REMARK 470 ARG A 362 CB CG CD NE CZ NH1 NH2 REMARK 470 ASN A 366 CB CG OD1 ND2 REMARK 470 LYS A 388 CB CG CD CE NZ REMARK 470 LYS A 452 CB CG CD CE NZ REMARK 470 ASP A 455 CB CG OD1 OD2 REMARK 470 GLN A 460 CB CG CD OE1 NE2 REMARK 470 ARG A 462 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 463 CG CD OE1 OE2 REMARK 470 LYS A 466 CG CD CE NZ REMARK 470 LYS A 468 CG CD CE NZ REMARK 470 LYS A 471 CG CD CE NZ REMARK 470 LYS A 484 CG CD CE NZ REMARK 470 GLU A 492 CB CG CD OE1 OE2 REMARK 470 GLU A 494 CB CG CD OE1 OE2 REMARK 470 GLU A 495 CG CD OE1 OE2 REMARK 470 GLU A 497 CB CG CD OE1 OE2 REMARK 470 GLU A 517 CG CD OE1 OE2 REMARK 470 GLU A 522 CB CG CD OE1 OE2 REMARK 470 LYS A 532 O REMARK 470 ASP A 533 CB CG OD1 OD2 REMARK 470 ARG A 536 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 546 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 556 CB CG CD OE1 OE2 REMARK 470 GLN A 559 CG CD OE1 NE2 REMARK 470 GLU A 561 CB CG CD OE1 OE2 REMARK 470 ASP A 566 CG OD1 OD2 REMARK 470 ARG A 567 CB CG CD NE CZ NH1 NH2 REMARK 470 ASP A 579 CB CG OD1 OD2 REMARK 470 GLU A 582 CG CD OE1 OE2 REMARK 470 GLN A 600 CB CG CD OE1 NE2 REMARK 470 LEU A 602 CB CG CD1 CD2 REMARK 470 ASP A 609 CB CG OD1 OD2 REMARK 470 GLU A 610 CG CD OE1 OE2 REMARK 470 ASN A 611 CG OD1 ND2 REMARK 470 ILE A 612 CB CG1 CG2 CD1 REMARK 470 LYS A 615 CB CG CD CE NZ REMARK 470 LEU A 617 CB CG CD1 CD2 REMARK 470 ARG A 621 CB CG CD NE CZ NH1 NH2 REMARK 470 ASN A 623 CB CG OD1 ND2 REMARK 470 ARG A 624 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS A 735 CG CD CE NZ REMARK 470 GLU A 741 CG CD OE1 OE2 REMARK 470 LYS A 742 CG CD CE NZ REMARK 470 LYS A 746 CB CG CD CE NZ REMARK 470 THR A 747 CB OG1 CG2 REMARK 470 ARG A 749 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 750 CB CG CD OE1 OE2 REMARK 470 PHE A 752 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 760 CG OD1 OD2 REMARK 470 GLU A 761 CB CG CD OE1 OE2 REMARK 470 ASP A 762 CG OD1 OD2 REMARK 470 GLU A 764 CG CD OE1 OE2 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 O GLU A 556 N ASN A 557 1.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CAR D 112 C3' - O3' - P ANGL. DEV. = -26.9 DEGREES REMARK 500 DA D 113 O3' - P - O5' ANGL. DEV. = -17.9 DEGREES REMARK 500 MET A 555 CA - C - O ANGL. DEV. = -14.2 DEGREES REMARK 500 MET A 555 O - C - N ANGL. DEV. = -23.8 DEGREES REMARK 500 GLU A 556 C - N - CA ANGL. DEV. = 36.8 DEGREES REMARK 500 GLU A 556 CA - C - O ANGL. DEV. = -14.9 DEGREES REMARK 500 GLU A 556 CA - C - N ANGL. DEV. = 42.8 DEGREES REMARK 500 GLU A 556 O - C - N ANGL. DEV. = -39.5 DEGREES REMARK 500 ASN A 557 C - N - CA ANGL. DEV. = 16.3 DEGREES REMARK 500 ASN A 557 N - CA - CB ANGL. DEV. = -45.0 DEGREES REMARK 500 ASN A 557 N - CA - C ANGL. DEV. = -16.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 212 175.30 -58.83 REMARK 500 PRO A 230 116.52 -27.32 REMARK 500 TYR A 231 119.12 -27.57 REMARK 500 LYS A 239 -164.98 -123.55 REMARK 500 PHE A 240 96.23 179.79 REMARK 500 ASP A 243 49.33 32.44 REMARK 500 PRO A 251 -9.49 -50.50 REMARK 500 MET A 263 64.33 -151.59 REMARK 500 ASP A 265 45.92 -91.07 REMARK 500 GLU A 267 -6.00 -58.37 REMARK 500 GLU A 285 22.92 -79.42 REMARK 500 SER A 320 171.79 -59.78 REMARK 500 LYS A 321 34.18 -78.65 REMARK 500 GLU A 322 -30.88 -156.71 REMARK 500 MET A 343 -158.75 -154.83 REMARK 500 ASP A 344 -74.37 -52.35 REMARK 500 ASN A 345 -100.45 -78.52 REMARK 500 PRO A 368 -9.29 -57.92 REMARK 500 ARG A 375 160.57 -47.97 REMARK 500 PRO A 397 98.06 -16.98 REMARK 500 HIS A 406 50.45 -108.11 REMARK 500 ILE A 420 -71.56 -73.70 REMARK 500 PRO A 431 -3.92 -58.37 REMARK 500 LYS A 451 -49.02 -26.78 REMARK 500 LYS A 466 37.44 -98.15 REMARK 500 MET A 470 -83.00 -43.10 REMARK 500 LYS A 484 -72.29 -70.92 REMARK 500 TYR A 523 76.00 56.26 REMARK 500 MET A 555 17.46 -66.34 REMARK 500 ARG A 567 70.36 -103.62 REMARK 500 LEU A 568 135.27 -171.53 REMARK 500 ASP A 609 37.07 -86.17 REMARK 500 ASN A 611 -152.00 -106.87 REMARK 500 ILE A 612 -99.35 -59.27 REMARK 500 PRO A 613 0.47 -62.99 REMARK 500 PTR A 723 -38.94 63.98 REMARK 500 ILE A 743 -65.92 -94.12 REMARK 500 ASN A 745 -168.52 -73.07 REMARK 500 ASP A 760 -163.36 -104.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 556 ASN A 557 -81.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC B 8 0.07 SIDE CHAIN REMARK 500 DU C 18 0.07 SIDE CHAIN REMARK 500 DG D 115 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 MET A 555 -41.10 REMARK 500 GLU A 556 55.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A31 RELATED DB: PDB REMARK 900 HUMAN RECONSTITUTED TOPOISOMERASE I IN COVALENT COMPLEX WITH 22 REMARK 900 BASE PAIR DNA OLIGONUCLEOTIDE REMARK 900 RELATED ID: 1EJ9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX REMARK 900 RELATED ID: 1LPQ RELATED DB: PDB REMARK 900 HUMAN TOPOISOMERASE I IN NONCOVALENT COMPLEX WITH A 22 BASE PAIR REMARK 900 DNA DUPLEX CONTAINING AN 8-OXO-G LESION REMARK 900 RELATED ID: 1K4T RELATED DB: PDB REMARK 900 HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON REMARK 900 TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE DNA (DUPLEX OLIGO) WAS ADDED TO THE REMARK 999 PROTEIN DURING CRYSTALLIZATION. AT THIS REMARK 999 TIME, THE PROTEIN INITIATES A TRANSESTERIFICATION REMARK 999 REACTION IN WHICH ONE STRAND OF DNA IS BROKEN INTO REMARK 999 CHAINS B AND C, AND THE PROTEIN CHAIN A IS COVALENTLY REMARK 999 LINKED TO THE DNA THROUGH RESIDUE 723. DBREF 1NH3 A 203 765 UNP P11387 TOP1_HUMAN 203 764 DBREF 1NH3 B 1 10 PDB 1NH3 1NH3 1 10 DBREF 1NH3 C 11 22 PDB 1NH3 1NH3 11 22 DBREF 1NH3 D 101 122 PDB 1NH3 1NH3 101 122 SEQADV 1NH3 MET A 699 UNP P11387 INITIATING METHIONINE SEQADV 1NH3 PTR A 723 UNP P11387 TYR 722 MODIFIED RESIDUE SEQRES 1 B 10 DA DA DA DA DA DG DA DC DU UBB SEQRES 1 C 12 GNG DG DA DA DA DA DA DU DU DU DU DT SEQRES 1 D 22 DA DA DA DA DA DT DU DU DU DU DC CAR DA SEQRES 2 D 22 DA DG DU DC DU DU DU DU DT SEQRES 1 A 563 TRP LYS TRP TRP GLU GLU GLU ARG TYR PRO GLU GLY ILE SEQRES 2 A 563 LYS TRP LYS PHE LEU GLU HIS LYS GLY PRO VAL PHE ALA SEQRES 3 A 563 PRO PRO TYR GLU PRO LEU PRO GLU ASN VAL LYS PHE TYR SEQRES 4 A 563 TYR ASP GLY LYS VAL MET LYS LEU SER PRO LYS ALA GLU SEQRES 5 A 563 GLU VAL ALA THR PHE PHE ALA LYS MET LEU ASP HIS GLU SEQRES 6 A 563 TYR THR THR LYS GLU ILE PHE ARG LYS ASN PHE PHE LYS SEQRES 7 A 563 ASP TRP ARG LYS GLU MET THR ASN GLU GLU LYS ASN ILE SEQRES 8 A 563 ILE THR ASN LEU SER LYS CYS ASP PHE THR GLN MET SER SEQRES 9 A 563 GLN TYR PHE LYS ALA GLN THR GLU ALA ARG LYS GLN MET SEQRES 10 A 563 SER LYS GLU GLU LYS LEU LYS ILE LYS GLU GLU ASN GLU SEQRES 11 A 563 LYS LEU LEU LYS GLU TYR GLY PHE CYS ILE MET ASP ASN SEQRES 12 A 563 HIS LYS GLU ARG ILE ALA ASN PHE LYS ILE GLU PRO PRO SEQRES 13 A 563 GLY LEU PHE ARG GLY ARG GLY ASN HIS PRO LYS MET GLY SEQRES 14 A 563 MET LEU LYS ARG ARG ILE MET PRO GLU ASP ILE ILE ILE SEQRES 15 A 563 ASN CYS SER LYS ASP ALA LYS VAL PRO SER PRO PRO PRO SEQRES 16 A 563 GLY HIS LYS TRP LYS GLU VAL ARG HIS ASP ASN LYS VAL SEQRES 17 A 563 THR TRP LEU VAL SER TRP THR GLU ASN ILE GLN GLY SER SEQRES 18 A 563 ILE LYS TYR ILE MET LEU ASN PRO SER SER ARG ILE LYS SEQRES 19 A 563 GLY GLU LYS ASP TRP GLN LYS TYR GLU THR ALA ARG ARG SEQRES 20 A 563 LEU LYS LYS CYS VAL ASP LYS ILE ARG ASN GLN TYR ARG SEQRES 21 A 563 GLU ASP TRP LYS SER LYS GLU MET LYS VAL ARG GLN ARG SEQRES 22 A 563 ALA VAL ALA LEU TYR PHE ILE ASP LYS LEU ALA LEU ARG SEQRES 23 A 563 ALA GLY ASN GLU LYS GLU GLU GLY GLU THR ALA ASP THR SEQRES 24 A 563 VAL GLY CYS CYS SER LEU ARG VAL GLU HIS ILE ASN LEU SEQRES 25 A 563 HIS PRO GLU LEU ASP GLY GLN GLU TYR VAL VAL GLU PHE SEQRES 26 A 563 ASP PHE LEU GLY LYS ASP SER ILE ARG TYR TYR ASN LYS SEQRES 27 A 563 VAL PRO VAL GLU LYS ARG VAL PHE LYS ASN LEU GLN LEU SEQRES 28 A 563 PHE MET GLU ASN LYS GLN PRO GLU ASP ASP LEU PHE ASP SEQRES 29 A 563 ARG LEU ASN THR GLY ILE LEU ASN LYS HIS LEU GLN ASP SEQRES 30 A 563 LEU MET GLU GLY LEU THR ALA LYS VAL PHE ARG THR TYR SEQRES 31 A 563 ASN ALA SER ILE THR LEU GLN GLN GLN LEU LYS GLU LEU SEQRES 32 A 563 THR ALA PRO ASP GLU ASN ILE PRO ALA LYS ILE LEU SER SEQRES 33 A 563 TYR ASN ARG ALA ASN ARG ALA VAL ALA ILE LEU CYS ASN SEQRES 34 A 563 HIS GLN ARG ALA PRO PRO LYS THR PHE GLU LYS SER MET SEQRES 35 A 563 MET ASN LEU GLN THR LYS ILE ASP ALA LYS LYS GLU GLN SEQRES 36 A 563 LEU ALA ASP ALA ARG ARG ASP LEU LYS SER ALA LYS ALA SEQRES 37 A 563 ASP ALA LYS VAL MET LYS ASP ALA LYS THR LYS LYS VAL SEQRES 38 A 563 VAL GLU SER LYS LYS LYS ALA VAL GLN ARG LEU GLU GLU SEQRES 39 A 563 GLN LEU MET LYS LEU GLU VAL GLN ALA THR ASP ARG GLU SEQRES 40 A 563 GLU ASN LYS GLN ILE ALA LEU GLY THR SER LYS LEU ASN SEQRES 41 A 563 PTR LEU ASP PRO ARG ILE THR VAL ALA TRP CYS LYS LYS SEQRES 42 A 563 TRP GLY VAL PRO ILE GLU LYS ILE TYR ASN LYS THR GLN SEQRES 43 A 563 ARG GLU LYS PHE ALA TRP ALA ILE ASP MET ALA ASP GLU SEQRES 44 A 563 ASP TYR GLU PHE MODRES 1NH3 UBB B 10 U 2',3'-DIDEOXY-URIDINE-5'-MONOPHOSPHATE MODRES 1NH3 GNG C 11 G 2'-DEOXY-GUANOSINE MODRES 1NH3 CAR D 112 DC CYTOSINE ARABINOSE-5'-PHOSPHATE MODRES 1NH3 PTR A 723 TYR O-PHOSPHOTYROSINE HET UBB B 10 18 HET GNG C 11 19 HET CAR D 112 20 HET PTR A 723 16 HETNAM UBB 2',3'-DIDEOXY-URIDINE-5'-MONOPHOSPHATE HETNAM GNG 2'-DEOXY-GUANOSINE HETNAM CAR CYTOSINE ARABINOSE-5'-PHOSPHATE HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 UBB C9 H13 N2 O7 P FORMUL 2 GNG C10 H13 N5 O4 FORMUL 3 CAR C9 H14 N3 O8 P FORMUL 4 PTR C9 H12 N O6 P FORMUL 5 HOH *33(H2 O) HELIX 1 1 LYS A 252 LYS A 262 1 11 HELIX 2 2 LYS A 271 ASP A 281 1 11 HELIX 3 3 GLU A 289 ILE A 294 1 6 HELIX 4 4 ASN A 296 SER A 298 5 3 HELIX 5 5 PHE A 302 ALA A 315 1 14 HELIX 6 6 GLU A 322 ILE A 327 1 6 HELIX 7 7 GLU A 332 TYR A 338 1 7 HELIX 8 8 SER A 433 ARG A 449 1 17 HELIX 9 9 CYS A 453 ASP A 464 1 12 HELIX 10 10 TRP A 465 SER A 467 5 3 HELIX 11 11 GLU A 469 LEU A 485 1 17 HELIX 12 12 ARG A 508 GLU A 510 5 3 HELIX 13 13 GLU A 544 GLU A 556 1 13 HELIX 14 14 ASN A 569 MET A 581 1 13 HELIX 15 15 LYS A 587 LEU A 605 1 19 HELIX 16 16 LYS A 615 ASN A 623 1 9 HELIX 17 17 ASP A 725 TRP A 736 1 12 HELIX 18 18 PRO A 739 ILE A 743 5 5 HELIX 19 19 THR A 747 PHE A 752 1 6 HELIX 20 20 PHE A 752 ASP A 757 1 6 SHEET 1 A 3 GLU A 221 HIS A 222 0 SHEET 2 A 3 PHE A 340 ILE A 342 -1 O ILE A 342 N GLU A 221 SHEET 3 A 3 GLU A 348 ARG A 349 -1 O GLU A 348 N CYS A 341 SHEET 1 B 3 LYS A 245 VAL A 246 0 SHEET 2 B 3 TYR A 241 TYR A 242 -1 N TYR A 242 O LYS A 245 SHEET 3 B 3 CYS A 300 ASP A 301 -1 O ASP A 301 N TYR A 241 SHEET 1 C 4 GLU A 403 ARG A 405 0 SHEET 2 C 4 ILE A 383 ASN A 385 1 N ILE A 384 O ARG A 405 SHEET 3 C 4 VAL A 414 THR A 417 -1 O SER A 415 N ILE A 383 SHEET 4 C 4 ILE A 424 ILE A 427 -1 O LYS A 425 N TRP A 416 SHEET 1 D 3 ILE A 512 LEU A 518 0 SHEET 2 D 3 GLN A 521 LEU A 530 -1 O GLN A 521 N LEU A 518 SHEET 3 D 3 ARG A 536 PRO A 542 -1 O TYR A 537 N PHE A 529 LINK O3' DU B 9 P UBB B 10 1555 1555 1.61 LINK C3' UBB B 10 O3P PTR A 723 1555 1555 1.65 LINK O3' GNG C 11 P DG C 12 1555 1555 1.61 LINK O3' DC D 111 P CAR D 112 1555 1555 1.61 LINK O3' CAR D 112 P DA D 113 1555 1555 1.66 LINK C ASN A 722 N PTR A 723 1555 1555 1.34 LINK C PTR A 723 N LEU A 724 1555 1555 1.33 CRYST1 72.970 72.970 186.290 90.00 90.00 120.00 P 32 3 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 0.013704 0.007912 0.000000 0.00000 SCALE2 0.000000 0.015824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005368 0.00000