PDB Short entry for 1K4S HEADER ISOMERASE/DNA 08-OCT-01 1K4S TITLE HUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA TITLE 2 DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*(5IU)P*(5IU))-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*(SPT)P*GP*AP*AP*AP*AP*AP*(5IU)P*(5IU)P*(5IU)P*(5IU) COMPND 7 P*T)-3'; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*TP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO) COMPND 12 UP*CP*AP*AP*AP*GP*(IDO)UP*CP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*T)-3'; COMPND 13 CHAIN: D; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA TOPOISOMERASE I; COMPND 17 CHAIN: A; COMPND 18 FRAGMENT: CORE DOMAIN AND C-TERMINAL DOMAIN, RESIDUES 174-765; COMPND 19 EC: 5.99.1.2; COMPND 20 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 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 12 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 15 EXPRESSION_SYSTEM_VECTOR: PFACTBAC1 KEYWDS COMPLEX (ISOMERASE-DNA), DNA, TOPOISOMERASE I, ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.L.STAKER,K.HJERRILD,M.D.FEESE,C.A.BEHNKE,A.B.BURGIN JR.,L.J.STEWART REVDAT 4 15-NOV-23 1K4S 1 REMARK REVDAT 3 16-AUG-23 1K4S 1 SEQADV LINK REVDAT 2 24-FEB-09 1K4S 1 VERSN REVDAT 1 04-DEC-02 1K4S 0 JRNL AUTH B.L.STAKER,K.HJERRILD,M.D.FEESE,C.A.BEHNKE,A.B.BURGIN JR., JRNL AUTH 2 L.J.STEWART JRNL TITL THE MECHANISM OF TOPOISOMERASE I POISONING BY A CAMPTOTHECIN JRNL TITL 2 ANALOG JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 15387 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 12426403 JRNL DOI 10.1073/PNAS.242259599 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,ACCELRYS REMARK 3 : SOFTWARE INC.(BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 17874 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RFREE REFLECTIONS SELECTED TO REMARK 3 MAINTAIN TWIN PAIRS IN SAME REMARK 3 SET. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1561 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 17874 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 : 3966 REMARK 3 NUCLEIC ACID ATOMS : 892 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.78 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.46 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) : 0.48 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.361 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.15 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.352 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 1K4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000014560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18471 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.13000 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) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.950 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNX REMARK 200 STARTING MODEL: PDB ENTRY 1A36 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, TRIS-HCL, NA/K PHOSPHATE, REMARK 280 KCL, DTT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, PH 8 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 124.42133 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 62.21067 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 LYS A 174 REMARK 465 LYS A 175 REMARK 465 PRO A 176 REMARK 465 LYS A 177 REMARK 465 ASN A 178 REMARK 465 LYS A 179 REMARK 465 ASP A 180 REMARK 465 LYS A 181 REMARK 465 ASP A 182 REMARK 465 LYS A 183 REMARK 465 LYS A 184 REMARK 465 VAL A 185 REMARK 465 PRO A 186 REMARK 465 GLU A 187 REMARK 465 PRO A 188 REMARK 465 ASP A 189 REMARK 465 ASN A 190 REMARK 465 LYS A 191 REMARK 465 LYS A 192 REMARK 465 LYS A 193 REMARK 465 LYS A 194 REMARK 465 PRO A 195 REMARK 465 LYS A 196 REMARK 465 LYS A 197 REMARK 465 GLU A 198 REMARK 465 GLU A 199 REMARK 465 GLU A 200 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 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 GLN A 201 CG CD OE1 NE2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 GLU A 289 CG CD OE1 OE2 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 326 CG CD CE NZ REMARK 470 GLU A 332 CG CD OE1 OE2 REMARK 470 LYS A 333 CG CD CE NZ 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 495 CG CD OE1 OE2 REMARK 470 ARG A 546 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 582 CG CD OE1 OE2 REMARK 470 ASP A 609 CG OD1 OD2 REMARK 470 GLU A 610 CG CD OE1 OE2 REMARK 470 ASN A 611 CG OD1 ND2 REMARK 470 LYS A 712 CG CD CE NZ 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 ASP A 760 CG OD1 OD2 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 DC B 8 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DC B 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 PRO A 397 C - N - CA ANGL. DEV. = 11.7 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 LYS A 204 54.13 -119.58 REMARK 500 TRP A 205 -34.70 -38.91 REMARK 500 GLU A 209 155.66 -40.54 REMARK 500 PRO A 212 37.01 -68.73 REMARK 500 GLU A 213 159.43 56.81 REMARK 500 PHE A 240 -154.70 -103.23 REMARK 500 TYR A 241 -105.74 -158.04 REMARK 500 TYR A 242 104.00 80.20 REMARK 500 LYS A 245 73.62 -59.29 REMARK 500 VAL A 246 107.16 -48.56 REMARK 500 MET A 263 13.73 -151.51 REMARK 500 PHE A 278 -77.52 -61.88 REMARK 500 PHE A 279 -71.94 -22.77 REMARK 500 ILE A 294 49.68 -89.95 REMARK 500 THR A 295 -4.02 -59.58 REMARK 500 SER A 298 43.65 -72.57 REMARK 500 LYS A 299 -2.20 -169.65 REMARK 500 GLN A 318 -9.65 -174.98 REMARK 500 ASP A 344 -50.27 37.95 REMARK 500 ASN A 345 3.75 -171.92 REMARK 500 ASN A 352 117.30 -161.72 REMARK 500 LYS A 374 -109.54 -75.08 REMARK 500 ARG A 375 151.85 160.26 REMARK 500 CYS A 386 -101.28 -101.96 REMARK 500 SER A 387 92.34 154.38 REMARK 500 LYS A 388 90.87 -44.42 REMARK 500 ASP A 389 -31.45 157.82 REMARK 500 PRO A 397 124.34 -16.77 REMARK 500 ASN A 408 10.08 -69.76 REMARK 500 THR A 411 -81.43 -83.46 REMARK 500 TRP A 412 136.04 -27.91 REMARK 500 LEU A 429 -170.34 -65.58 REMARK 500 CYS A 453 69.95 -69.80 REMARK 500 VAL A 454 -48.64 -141.91 REMARK 500 GLU A 494 99.37 -69.54 REMARK 500 GLU A 495 70.74 -48.61 REMARK 500 ASP A 500 98.10 -37.66 REMARK 500 LEU A 518 137.32 172.66 REMARK 500 PHE A 529 158.82 172.95 REMARK 500 ARG A 536 121.62 -39.25 REMARK 500 GLU A 556 121.40 -31.02 REMARK 500 ASN A 557 -2.67 70.59 REMARK 500 LEU A 568 126.82 -177.97 REMARK 500 TYR A 592 -80.84 -60.50 REMARK 500 ALA A 594 -75.60 -52.06 REMARK 500 LEU A 602 4.27 -66.01 REMARK 500 GLU A 604 -73.56 -90.55 REMARK 500 LEU A 605 13.72 -62.82 REMARK 500 GLU A 610 136.03 -25.46 REMARK 500 ASN A 631 -5.87 69.26 REMARK 500 REMARK 500 THIS ENTRY HAS 60 RAMACHANDRAN OUTLIERS. 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 D 111 0.08 SIDE CHAIN REMARK 500 DA D 114 0.07 SIDE CHAIN REMARK 500 DC D 117 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A35 RELATED DB: PDB REMARK 900 HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN NON-COVALENT COMPLEX REMARK 900 WITH A 22 BASE PAIR DNA DUPLEX REMARK 900 RELATED ID: 1A31 RELATED DB: PDB REMARK 900 HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A REMARK 900 22 BASE PAIR DNA DUPLEX REMARK 900 RELATED ID: 1A36 RELATED DB: PDB REMARK 900 HUMAN DNA TOPOISOMERASE I (70 KDA) IN NON-COVALENT COMPLEX WITH A REMARK 900 22 BASE PAIR DNA DUPLEX DBREF 1K4S A 174 765 UNP P11387 TOP1_HUMAN 174 765 DBREF 1K4S B 1 10 PDB 1K4S 1K4S 1 10 DBREF 1K4S C 11 22 PDB 1K4S 1K4S 11 22 DBREF 1K4S D 101 122 PDB 1K4S 1K4S 101 122 SEQADV 1K4S PTR A 723 UNP P11387 TYR 723 MODIFIED RESIDUE SEQRES 1 B 10 DA DA DA DA DA DG DA DC 5IU 5IU SEQRES 1 C 12 SPT DG DA DA DA DA DA 5IU 5IU 5IU 5IU DT SEQRES 1 D 22 DA DA DA DA DA DT 5IU 5IU 5IU 5IU DC DA DA SEQRES 2 D 22 DA DG 5IU DC 5IU 5IU 5IU 5IU DT SEQRES 1 A 592 LYS LYS PRO LYS ASN LYS ASP LYS ASP LYS LYS VAL PRO SEQRES 2 A 592 GLU PRO ASP ASN LYS LYS LYS LYS PRO LYS LYS GLU GLU SEQRES 3 A 592 GLU GLN LYS TRP LYS TRP TRP GLU GLU GLU ARG TYR PRO SEQRES 4 A 592 GLU GLY ILE LYS TRP LYS PHE LEU GLU HIS LYS GLY PRO SEQRES 5 A 592 VAL PHE ALA PRO PRO TYR GLU PRO LEU PRO GLU ASN VAL SEQRES 6 A 592 LYS PHE TYR TYR ASP GLY LYS VAL MET LYS LEU SER PRO SEQRES 7 A 592 LYS ALA GLU GLU VAL ALA THR PHE PHE ALA LYS MET LEU SEQRES 8 A 592 ASP HIS GLU TYR THR THR LYS GLU ILE PHE ARG LYS ASN SEQRES 9 A 592 PHE PHE LYS ASP TRP ARG LYS GLU MET THR ASN GLU GLU SEQRES 10 A 592 LYS ASN ILE ILE THR ASN LEU SER LYS CYS ASP PHE THR SEQRES 11 A 592 GLN MET SER GLN TYR PHE LYS ALA GLN THR GLU ALA ARG SEQRES 12 A 592 LYS GLN MET SER LYS GLU GLU LYS LEU LYS ILE LYS GLU SEQRES 13 A 592 GLU ASN GLU LYS LEU LEU LYS GLU TYR GLY PHE CYS ILE SEQRES 14 A 592 MET ASP ASN HIS LYS GLU ARG ILE ALA ASN PHE LYS ILE SEQRES 15 A 592 GLU PRO PRO GLY LEU PHE ARG GLY ARG GLY ASN HIS PRO SEQRES 16 A 592 LYS MET GLY MET LEU LYS ARG ARG ILE MET PRO GLU ASP SEQRES 17 A 592 ILE ILE ILE ASN CYS SER LYS ASP ALA LYS VAL PRO SER SEQRES 18 A 592 PRO PRO PRO GLY HIS LYS TRP LYS GLU VAL ARG HIS ASP SEQRES 19 A 592 ASN LYS VAL THR TRP LEU VAL SER TRP THR GLU ASN ILE SEQRES 20 A 592 GLN GLY SER ILE LYS TYR ILE MET LEU ASN PRO SER SER SEQRES 21 A 592 ARG ILE LYS GLY GLU LYS ASP TRP GLN LYS TYR GLU THR SEQRES 22 A 592 ALA ARG ARG LEU LYS LYS CYS VAL ASP LYS ILE ARG ASN SEQRES 23 A 592 GLN TYR ARG GLU ASP TRP LYS SER LYS GLU MET LYS VAL SEQRES 24 A 592 ARG GLN ARG ALA VAL ALA LEU TYR PHE ILE ASP LYS LEU SEQRES 25 A 592 ALA LEU ARG ALA GLY ASN GLU LYS GLU GLU GLY GLU THR SEQRES 26 A 592 ALA ASP THR VAL GLY CYS CYS SER LEU ARG VAL GLU HIS SEQRES 27 A 592 ILE ASN LEU HIS PRO GLU LEU ASP GLY GLN GLU TYR VAL SEQRES 28 A 592 VAL GLU PHE ASP PHE LEU GLY LYS ASP SER ILE ARG TYR SEQRES 29 A 592 TYR ASN LYS VAL PRO VAL GLU LYS ARG VAL PHE LYS ASN SEQRES 30 A 592 LEU GLN LEU PHE MET GLU ASN LYS GLN PRO GLU ASP ASP SEQRES 31 A 592 LEU PHE ASP ARG LEU ASN THR GLY ILE LEU ASN LYS HIS SEQRES 32 A 592 LEU GLN ASP LEU MET GLU GLY LEU THR ALA LYS VAL PHE SEQRES 33 A 592 ARG THR TYR ASN ALA SER ILE THR LEU GLN GLN GLN LEU SEQRES 34 A 592 LYS GLU LEU THR ALA PRO ASP GLU ASN ILE PRO ALA LYS SEQRES 35 A 592 ILE LEU SER TYR ASN ARG ALA ASN ARG ALA VAL ALA ILE SEQRES 36 A 592 LEU CYS ASN HIS GLN ARG ALA PRO PRO LYS THR PHE GLU SEQRES 37 A 592 LYS SER MET MET ASN LEU GLN THR LYS ILE ASP ALA LYS SEQRES 38 A 592 LYS GLU GLN LEU ALA ASP ALA ARG ARG ASP LEU LYS SER SEQRES 39 A 592 ALA LYS ALA ASP ALA LYS VAL MET LYS ASP ALA LYS THR SEQRES 40 A 592 LYS LYS VAL VAL GLU SER LYS LYS LYS ALA VAL GLN ARG SEQRES 41 A 592 LEU GLU GLU GLN LEU MET LYS LEU GLU VAL GLN ALA THR SEQRES 42 A 592 ASP ARG GLU GLU ASN LYS GLN ILE ALA LEU GLY THR SER SEQRES 43 A 592 LYS LEU ASN PTR LEU ASP PRO ARG ILE THR VAL ALA TRP SEQRES 44 A 592 CYS LYS LYS TRP GLY VAL PRO ILE GLU LYS ILE TYR ASN SEQRES 45 A 592 LYS THR GLN ARG GLU LYS PHE ALA TRP ALA ILE ASP MET SEQRES 46 A 592 ALA ASP GLU ASP TYR GLU PHE MODRES 1K4S 5IU B 9 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU B 10 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S SPT C 11 DT 5'-THIO-THYMIDINE PHOSPHONIC ACID MODRES 1K4S 5IU C 18 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU C 19 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU C 20 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU C 21 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 107 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 108 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 109 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 110 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 116 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 118 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 119 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 120 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S 5IU D 121 DU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE MODRES 1K4S PTR A 723 TYR O-PHOSPHOTYROSINE HET 5IU B 9 20 HET 5IU B 10 19 HET SPT C 11 17 HET 5IU C 18 20 HET 5IU C 19 20 HET 5IU C 20 20 HET 5IU C 21 20 HET 5IU D 107 20 HET 5IU D 108 20 HET 5IU D 109 20 HET 5IU D 110 20 HET 5IU D 116 20 HET 5IU D 118 20 HET 5IU D 119 20 HET 5IU D 120 20 HET 5IU D 121 20 HET PTR A 723 16 HETNAM 5IU 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE HETNAM SPT 5'-THIO-THYMIDINE PHOSPHONIC ACID HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 5IU 15(C9 H12 I N2 O8 P) FORMUL 2 SPT C10 H15 N2 O7 P S FORMUL 4 PTR C9 H12 N O6 P HELIX 1 1 LYS A 204 GLU A 208 5 5 HELIX 2 2 SER A 250 LYS A 262 1 13 HELIX 3 3 HIS A 266 LYS A 271 1 6 HELIX 4 4 LYS A 271 GLU A 285 1 15 HELIX 5 5 THR A 287 ILE A 294 1 8 HELIX 6 6 PHE A 302 LYS A 317 1 16 HELIX 7 7 SER A 320 GLY A 339 1 20 HELIX 8 8 MET A 378 ASP A 381 5 4 HELIX 9 9 SER A 433 LYS A 451 1 19 HELIX 10 10 VAL A 454 TRP A 465 1 12 HELIX 11 11 GLU A 469 ALA A 486 1 18 HELIX 12 12 ARG A 508 GLU A 510 5 3 HELIX 13 13 GLY A 531 ILE A 535 5 5 HELIX 14 14 GLU A 544 GLU A 556 1 13 HELIX 15 15 ASN A 569 MET A 581 1 13 HELIX 16 16 THR A 585 LEU A 605 1 21 HELIX 17 17 ASN A 611 ASN A 631 1 21 HELIX 18 18 THR A 718 PTR A 723 1 6 HELIX 19 19 ASP A 725 GLY A 737 1 13 HELIX 20 20 PRO A 739 ILE A 743 5 5 HELIX 21 21 ASN A 745 PHE A 752 1 8 SHEET 1 A 2 LEU A 220 GLU A 221 0 SHEET 2 A 2 ILE A 342 MET A 343 -1 O ILE A 342 N GLU A 221 SHEET 1 B 4 GLU A 403 ARG A 405 0 SHEET 2 B 4 ILE A 383 ASN A 385 1 N ILE A 384 O ARG A 405 SHEET 3 B 4 VAL A 414 THR A 417 -1 O SER A 415 N ILE A 383 SHEET 4 B 4 ILE A 424 ILE A 427 -1 O LYS A 425 N TRP A 416 SHEET 1 C 3 ILE A 512 LEU A 518 0 SHEET 2 C 3 GLN A 521 PHE A 527 -1 O VAL A 524 N HIS A 515 SHEET 3 C 3 ASN A 539 PRO A 542 -1 O ASN A 539 N PHE A 527 LINK O3' DC B 8 P 5IU B 9 1555 1555 1.62 LINK O3' 5IU B 9 P 5IU B 10 1555 1555 1.61 LINK C3' 5IU B 10 O3P PTR A 723 1555 1555 1.44 LINK O3' SPT C 11 P DG C 12 1555 1555 1.60 LINK O3' DA C 17 P 5IU C 18 1555 1555 1.60 LINK O3' 5IU C 18 P 5IU C 19 1555 1555 1.61 LINK O3' 5IU C 19 P 5IU C 20 1555 1555 1.61 LINK O3' 5IU C 20 P 5IU C 21 1555 1555 1.60 LINK O3' 5IU C 21 P DT C 22 1555 1555 1.60 LINK O3' DT D 106 P 5IU D 107 1555 1555 1.61 LINK O3' 5IU D 107 P 5IU D 108 1555 1555 1.61 LINK O3' 5IU D 108 P 5IU D 109 1555 1555 1.61 LINK O3' 5IU D 109 P 5IU D 110 1555 1555 1.61 LINK O3' 5IU D 110 P DC D 111 1555 1555 1.62 LINK O3' DG D 115 P 5IU D 116 1555 1555 1.60 LINK O3' 5IU D 116 P DC D 117 1555 1555 1.61 LINK O3' DC D 117 P 5IU D 118 1555 1555 1.60 LINK O3' 5IU D 118 P 5IU D 119 1555 1555 1.60 LINK O3' 5IU D 119 P 5IU D 120 1555 1555 1.61 LINK O3' 5IU D 120 P 5IU D 121 1555 1555 1.61 LINK O3' 5IU D 121 P DT D 122 1555 1555 1.60 LINK C ASN A 722 N PTR A 723 1555 1555 1.34 LINK C PTR A 723 N LEU A 724 1555 1555 1.32 CRYST1 73.235 73.235 186.632 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 0.013655 0.007884 0.000000 0.00000 SCALE2 0.000000 0.015767 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005358 0.00000