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,
KEYWDS 2 ISOMERASE/DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.E.CHRENCIK,A.B.BURGIN,Y.POMMIER,L.STEWART,M.R.REDINBO
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,
JRNL AUTH 2 M.R.REDINBO
JRNL TITL STRUCTURAL IMPACT OF THE LEUKEMIA DRUG
JRNL TITL 2 1-BETA-D-ARABINOFURANOSYLCYTOSINE (ARA-C) ON THE
JRNL TITL 3 COVALENT 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 1
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) : 3.88
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. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-03.
REMARK 100 THE RCSB ID CODE IS RCSB017864.
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 UBB B 10 O3P
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: 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 MET A 555 CA - C - O ANGL. DEV. = -14.2 DEGREES
REMARK 500 GLU A 556 CA - C - O ANGL. DEV. = -14.9 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 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 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
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 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, 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 -41.09
REMARK 500 GLU A 556 55.55
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 22 DISTANCE = 8.10 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1A31 RELATED DB: PDB
REMARK 900 HUMAN RECONSTITUTED TOPOISOMERASE I IN COVALENT COMPLEX
REMARK 900 WITH 22 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
REMARK 900 PAIR 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
REMARK 900 POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR
REMARK 900 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 MET
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 O3P PTR A 723 C3' UBB B 10 1555 1555 1.65
LINK O3' GNG C 11 P DG C 12 1555 1555 1.61
LINK O3' DU B 9 P UBB B 10 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
(ATOM LINES ARE NOT SHOWN.)
END
