HEADER ISOMERASE/DNA 08-OCT-01 1K4S
TITLE HUMAN DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22
TITLE 2 BASE PAIR DNA 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)
COMPND 7 P*(5IU)P*(5IU)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)
COMPND 12 UP*(IDO)UP*CP*AP*AP*AP*GP*(IDO)UP*CP*(IDO)UP*(IDO)UP*(IDO)
COMPND 13 UP*(IDO)UP*T)-3';
COMPND 14 CHAIN: D;
COMPND 15 ENGINEERED: YES;
COMPND 16 MOL_ID: 4;
COMPND 17 MOLECULE: DNA TOPOISOMERASE I;
COMPND 18 CHAIN: A;
COMPND 19 FRAGMENT: CORE DOMAIN AND C-TERMINAL DOMAIN, RESIDUES 174-
COMPND 20 765;
COMPND 21 EC: 5.99.1.2;
COMPND 22 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
EXPDTA X-RAY DIFFRACTION
AUTHOR B.L.STAKER,K.HJERRILD,M.D.FEESE,C.A.BEHNKE,A.B.BURGIN JR.,
AUTHOR 2 L.J.STEWART
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,
JRNL AUTH 2 A.B.BURGIN JR.,L.J.STEWART
JRNL TITL THE MECHANISM OF TOPOISOMERASE I POISONING BY A
JRNL TITL 2 CAMPTOTHECIN 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 1
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
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
REMARK 3 TO MAINTAIN TWIN PAIRS IN
REMARK 3 SAME SET.
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
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 : 877
REMARK 3 HETEROGEN ATOMS : 15
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) : 1.36
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.16
REMARK 3 IMPROPER ANGLES (DEGREES) : 3.35
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
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1K4S COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-01.
REMARK 100 THE RCSB ID CODE IS RCSB014560.
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
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 5IU B 10 O3' OP1
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
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 LYS A 712 20.19 -164.70
REMARK 500 GLN A 713 -32.08 -142.52
REMARK 500 LEU A 716 -131.65 -69.31
REMARK 500 THR A 718 -74.85 36.19
REMARK 500 LEU A 721 -37.48 -36.17
REMARK 500 PRO A 739 101.17 -54.11
REMARK 500 TRP A 754 -63.81 171.22
REMARK 500 ILE A 756 -81.56 -59.45
REMARK 500 ALA A 759 149.64 -179.53
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
REMARK 900 COMPLEX 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
REMARK 900 WITH A 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
REMARK 900 WITH A 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 C3' 5IU B 10 O3P PTR A 723 1555 1555 1.44
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 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
(ATOM LINES ARE NOT SHOWN.)
END
