HEADER ISOMERASE 18-JUL-03 1Q1D OBSLTE 30-SEP-03 1Q1D 1QZR TITLE CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES TITLE 2 CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE II; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL ATPASE REGION; COMPND 5 EC: 5.99.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 GENE: TOP2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS GHKL ATPASE DOMAIN, ICRF, ICRF-187 DEXRAZOXANE EXPDTA X-RAY DIFFRACTION AUTHOR S.CLASSEN,S.OLLAND,J.M.BERGER REVDAT 3 30-SEP-03 1Q1D 1 OBSLTE REVDAT 2 23-SEP-03 1Q1D 1 JRNL REVDAT 1 26-AUG-03 1Q1D 0 JRNL AUTH S.CLASSEN,S.OLLAND,J.M.BERGER JRNL TITL STRUCTURE OF THE TOPOISOMERASE II ATPASE REGION JRNL TITL 2 AND ITS MECHANISM OF INHIBITION BY THE JRNL TITL 3 CHEMOTHERAPEUTIC AGENT ICRF-187 JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 10629 2003 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 60064 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.400 REMARK 3 FREE R VALUE TEST SET COUNT : 5512 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2760 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 276 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 6959 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.20000 REMARK 3 B22 (A**2) : -0.96000 REMARK 3 B33 (A**2) : -1.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.184 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.511 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6306 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8527 ; 1.040 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 754 ; 5.801 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 966 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4648 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3025 ; 0.191 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 682 ; 0.123 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 38 ; 0.154 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.098 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3782 ; 0.608 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6160 ; 1.184 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2524 ; 1.961 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2367 ; 3.267 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 0 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): 31.7957 45.8669 45.0650 REMARK 3 T TENSOR REMARK 3 T11: 0.0569 T22: 0.0093 REMARK 3 T33: 0.0503 T12: 0.0066 REMARK 3 T13: 0.0021 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.4853 L22: 0.8297 REMARK 3 L33: 0.9658 L12: -0.0108 REMARK 3 L13: -0.2910 L23: 0.0943 REMARK 3 S TENSOR REMARK 3 S11: -0.0199 S12: 0.0083 S13: 0.0485 REMARK 3 S21: 0.1247 S22: 0.0386 S23: -0.0188 REMARK 3 S31: 0.0304 S32: -0.0048 S33: -0.0186 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 276 A 405 REMARK 3 ORIGIN FOR THE GROUP (A): 41.3810 57.1729 20.6665 REMARK 3 T TENSOR REMARK 3 T11: 0.0381 T22: 0.0491 REMARK 3 T33: 0.0915 T12: 0.0108 REMARK 3 T13: 0.0280 T23: 0.0362 REMARK 3 L TENSOR REMARK 3 L11: 1.5163 L22: 0.8848 REMARK 3 L33: 1.4823 L12: 0.2511 REMARK 3 L13: -0.7050 L23: 0.2731 REMARK 3 S TENSOR REMARK 3 S11: 0.0574 S12: 0.1343 S13: 0.2066 REMARK 3 S21: -0.1148 S22: 0.0485 S23: -0.0677 REMARK 3 S31: -0.1643 S32: 0.0183 S33: -0.1059 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 8 B 258 REMARK 3 ORIGIN FOR THE GROUP (A): 26.7680 22.3965 17.1465 REMARK 3 T TENSOR REMARK 3 T11: 0.1042 T22: 0.1092 REMARK 3 T33: 0.0604 T12: -0.0879 REMARK 3 T13: 0.0098 T23: -0.0488 REMARK 3 L TENSOR REMARK 3 L11: 1.1113 L22: 0.6473 REMARK 3 L33: 1.4085 L12: -0.0273 REMARK 3 L13: -0.4312 L23: 0.0163 REMARK 3 S TENSOR REMARK 3 S11: -0.0658 S12: 0.2053 S13: -0.1178 REMARK 3 S21: -0.0213 S22: -0.0141 S23: 0.0594 REMARK 3 S31: 0.3158 S32: -0.2698 S33: 0.0798 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 277 B 405 REMARK 3 ORIGIN FOR THE GROUP (A): 53.2048 33.1637 16.9299 REMARK 3 T TENSOR REMARK 3 T11: 0.0110 T22: 0.1007 REMARK 3 T33: 0.0610 T12: 0.0323 REMARK 3 T13: -0.0107 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.4976 L22: 1.1667 REMARK 3 L33: 1.2270 L12: 0.2373 REMARK 3 L13: -0.7074 L23: 0.1210 REMARK 3 S TENSOR REMARK 3 S11: -0.0359 S12: 0.0231 S13: 0.0537 REMARK 3 S21: 0.0118 S22: 0.0741 S23: -0.1164 REMARK 3 S31: 0.1359 S32: 0.2000 S33: -0.0381 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Q1D COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-2003. REMARK 100 THE RCSB ID CODE IS RCSB019793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUL-2002 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1271 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DCS 3.0 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65576 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 90.8 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.29800 REMARK 200 R SYM FOR SHELL (I) : 0.29800 REMARK 200 FOR SHELL : 3.200 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 1PVG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1500, POTASSIUM CHLORIDE, REMARK 280 GLYCEROL, SODIUM CACODYLATE, PH 6.5, MICROBATCH UNDER OIL, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 29.27650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 107.86200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.72200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 107.86200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.27650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.72200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 VAL A -1 REMARK 465 THR A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 GLU A 4 REMARK 465 PRO A 5 REMARK 465 VAL A 6 REMARK 465 GLU A 259 REMARK 465 LYS A 260 REMARK 465 LYS A 261 REMARK 465 ARG A 262 REMARK 465 GLN A 263 REMARK 465 LEU A 264 REMARK 465 ASP A 265 REMARK 465 ASN A 266 REMARK 465 GLY A 267 REMARK 465 GLU A 268 REMARK 465 ASP A 269 REMARK 465 GLY A 270 REMARK 465 ALA A 271 REMARK 465 ALA A 272 REMARK 465 LYS A 273 REMARK 465 SER A 274 REMARK 465 ASP A 275 REMARK 465 LYS A 335 REMARK 465 LYS A 336 REMARK 465 LYS A 337 REMARK 465 LYS A 338 REMARK 465 SER A 339 REMARK 465 ALA A 411 REMARK 465 LEU A 412 REMARK 465 LYS A 413 REMARK 465 GLY B -4 REMARK 465 HIS B -3 REMARK 465 MET B -2 REMARK 465 VAL B -1 REMARK 465 THR B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 GLU B 4 REMARK 465 PRO B 5 REMARK 465 VAL B 6 REMARK 465 SER B 7 REMARK 465 LYS B 261 REMARK 465 ARG B 262 REMARK 465 GLN B 263 REMARK 465 LEU B 264 REMARK 465 ASP B 265 REMARK 465 ASN B 266 REMARK 465 GLY B 267 REMARK 465 GLU B 268 REMARK 465 ASP B 269 REMARK 465 GLY B 270 REMARK 465 ALA B 271 REMARK 465 ALA B 272 REMARK 465 LYS B 273 REMARK 465 SER B 274 REMARK 465 ASP B 275 REMARK 465 LYS B 335 REMARK 465 LYS B 336 REMARK 465 LYS B 337 REMARK 465 LYS B 338 REMARK 465 SER B 339 REMARK 465 ALA B 406 REMARK 465 ASN B 407 REMARK 465 GLU B 408 REMARK 465 GLU B 409 REMARK 465 ASN B 410 REMARK 465 ALA B 411 REMARK 465 LEU B 412 REMARK 465 LYS B 413 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 GLU A 45 CG CD OE1 OE2 REMARK 470 THR A 46 OG1 CG2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 91 CG CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 ILE A 276 CG1 CG2 CD1 REMARK 470 ASP A 296 CG OD1 OD2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 GLU B 45 CG CD OE1 OE2 REMARK 470 THR B 46 OG1 CG2 REMARK 470 ASP B 47 CG OD1 OD2 REMARK 470 LYS B 190 CG CD CE NZ REMARK 470 GLU B 259 CG CD OE1 OE2 REMARK 470 LYS B 260 CG CD CE NZ REMARK 470 LYS B 333 CG CD CE NZ REMARK 470 LYS B 334 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 81 SD MET A 81 CE -0.122 REMARK 500 MET A 219 SD MET A 219 CE -0.110 REMARK 500 MET A 349 SD MET A 349 CE 0.095 REMARK 500 MET B 49 SD MET B 49 CE 0.072 REMARK 500 MET B 349 SD MET B 349 CE 0.063 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN B 142 N - CA - C ANGL. DEV. = 10.3 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 LYS A 243 -39.41 73.16 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PVG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES REMARK 900 CEREVISIAE TOPOISOMERASE II WITHOUT ICRF-187 REMARK 900 RELATED ID: 1BGW RELATED DB: PDB REMARK 900 TOPOISOMERASE RESIDUES 410 - 1202 REMARK 900 RELATED ID: 1BJT RELATED DB: PDB REMARK 900 TOPOISOMERASE II RESIDUES 409 - 1201 DBREF 1Q1D A 1 413 UNP P06786 TOP2_YEAST 1 413 DBREF 1Q1D B 1 413 UNP P06786 TOP2_YEAST 1 413 SEQADV 1Q1D GLY A -4 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D HIS A -3 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D MET A -2 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D VAL A -1 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D THR A 0 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D GLY B -4 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D HIS B -3 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D MET B -2 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D VAL B -1 UNP P06786 CLONING ARTIFACT SEQADV 1Q1D THR B 0 UNP P06786 CLONING ARTIFACT SEQRES 1 A 418 GLY HIS MET VAL THR MET SER THR GLU PRO VAL SER ALA SEQRES 2 A 418 SER ASP LYS TYR GLN LYS ILE SER GLN LEU GLU HIS ILE SEQRES 3 A 418 LEU LYS ARG PRO ASP THR TYR ILE GLY SER VAL GLU THR SEQRES 4 A 418 GLN GLU GLN LEU GLN TRP ILE TYR ASP GLU GLU THR ASP SEQRES 5 A 418 CYS MET ILE GLU LYS ASN VAL THR ILE VAL PRO GLY LEU SEQRES 6 A 418 PHE LYS ILE PHE ASP GLU ILE LEU VAL ASN ALA ALA ASP SEQRES 7 A 418 ASN LYS VAL ARG ASP PRO SER MET LYS ARG ILE ASP VAL SEQRES 8 A 418 ASN ILE HIS ALA GLU GLU HIS THR ILE GLU VAL LYS ASN SEQRES 9 A 418 ASP GLY LYS GLY ILE PRO ILE GLU ILE HIS ASN LYS GLU SEQRES 10 A 418 ASN ILE TYR ILE PRO GLU MET ILE PHE GLY HIS LEU LEU SEQRES 11 A 418 THR SER SER ASN TYR ASP ASP ASP GLU LYS LYS VAL THR SEQRES 12 A 418 GLY GLY ARG ASN GLY TYR GLY ALA LYS LEU CYS ASN ILE SEQRES 13 A 418 PHE SER THR GLU PHE ILE LEU GLU THR ALA ASP LEU ASN SEQRES 14 A 418 VAL GLY GLN LYS TYR VAL GLN LYS TRP GLU ASN ASN MET SEQRES 15 A 418 SER ILE CYS HIS PRO PRO LYS ILE THR SER TYR LYS LYS SEQRES 16 A 418 GLY PRO SER TYR THR LYS VAL THR PHE LYS PRO ASP LEU SEQRES 17 A 418 THR ARG PHE GLY MET LYS GLU LEU ASP ASN ASP ILE LEU SEQRES 18 A 418 GLY VAL MET ARG ARG ARG VAL TYR ASP ILE ASN GLY SER SEQRES 19 A 418 VAL ARG ASP ILE ASN VAL TYR LEU ASN GLY LYS SER LEU SEQRES 20 A 418 LYS ILE ARG ASN PHE LYS ASN TYR VAL GLU LEU TYR LEU SEQRES 21 A 418 LYS SER LEU GLU LYS LYS ARG GLN LEU ASP ASN GLY GLU SEQRES 22 A 418 ASP GLY ALA ALA LYS SER ASP ILE PRO THR ILE LEU TYR SEQRES 23 A 418 GLU ARG ILE ASN ASN ARG TRP GLU VAL ALA PHE ALA VAL SEQRES 24 A 418 SER ASP ILE SER PHE GLN GLN ILE SER PHE VAL ASN SER SEQRES 25 A 418 ILE ALA THR THR MET GLY GLY THR HIS VAL ASN TYR ILE SEQRES 26 A 418 THR ASP GLN ILE VAL LYS LYS ILE SER GLU ILE LEU LYS SEQRES 27 A 418 LYS LYS LYS LYS LYS SER VAL LYS SER PHE GLN ILE LYS SEQRES 28 A 418 ASN ASN MET PHE ILE PHE ILE ASN CYS LEU ILE GLU ASN SEQRES 29 A 418 PRO ALA PHE THR SER GLN THR LYS GLU GLN LEU THR THR SEQRES 30 A 418 ARG VAL LYS ASP PHE GLY SER ARG CYS GLU ILE PRO LEU SEQRES 31 A 418 GLU TYR ILE ASN LYS ILE MET LYS THR ASP LEU ALA THR SEQRES 32 A 418 ARG MET PHE GLU ILE ALA ASP ALA ASN GLU GLU ASN ALA SEQRES 33 A 418 LEU LYS SEQRES 1 B 418 GLY HIS MET VAL THR MET SER THR GLU PRO VAL SER ALA SEQRES 2 B 418 SER ASP LYS TYR GLN LYS ILE SER GLN LEU GLU HIS ILE SEQRES 3 B 418 LEU LYS ARG PRO ASP THR TYR ILE GLY SER VAL GLU THR SEQRES 4 B 418 GLN GLU GLN LEU GLN TRP ILE TYR ASP GLU GLU THR ASP SEQRES 5 B 418 CYS MET ILE GLU LYS ASN VAL THR ILE VAL PRO GLY LEU SEQRES 6 B 418 PHE LYS ILE PHE ASP GLU ILE LEU VAL ASN ALA ALA ASP SEQRES 7 B 418 ASN LYS VAL ARG ASP PRO SER MET LYS ARG ILE ASP VAL SEQRES 8 B 418 ASN ILE HIS ALA GLU GLU HIS THR ILE GLU VAL LYS ASN SEQRES 9 B 418 ASP GLY LYS GLY ILE PRO ILE GLU ILE HIS ASN LYS GLU SEQRES 10 B 418 ASN ILE TYR ILE PRO GLU MET ILE PHE GLY HIS LEU LEU SEQRES 11 B 418 THR SER SER ASN TYR ASP ASP ASP GLU LYS LYS VAL THR SEQRES 12 B 418 GLY GLY ARG ASN GLY TYR GLY ALA LYS LEU CYS ASN ILE SEQRES 13 B 418 PHE SER THR GLU PHE ILE LEU GLU THR ALA ASP LEU ASN SEQRES 14 B 418 VAL GLY GLN LYS TYR VAL GLN LYS TRP GLU ASN ASN MET SEQRES 15 B 418 SER ILE CYS HIS PRO PRO LYS ILE THR SER TYR LYS LYS SEQRES 16 B 418 GLY PRO SER TYR THR LYS VAL THR PHE LYS PRO ASP LEU SEQRES 17 B 418 THR ARG PHE GLY MET LYS GLU LEU ASP ASN ASP ILE LEU SEQRES 18 B 418 GLY VAL MET ARG ARG ARG VAL TYR ASP ILE ASN GLY SER SEQRES 19 B 418 VAL ARG ASP ILE ASN VAL TYR LEU ASN GLY LYS SER LEU SEQRES 20 B 418 LYS ILE ARG ASN PHE LYS ASN TYR VAL GLU LEU TYR LEU SEQRES 21 B 418 LYS SER LEU GLU LYS LYS ARG GLN LEU ASP ASN GLY GLU SEQRES 22 B 418 ASP GLY ALA ALA LYS SER ASP ILE PRO THR ILE LEU TYR SEQRES 23 B 418 GLU ARG ILE ASN ASN ARG TRP GLU VAL ALA PHE ALA VAL SEQRES 24 B 418 SER ASP ILE SER PHE GLN GLN ILE SER PHE VAL ASN SER SEQRES 25 B 418 ILE ALA THR THR MET GLY GLY THR HIS VAL ASN TYR ILE SEQRES 26 B 418 THR ASP GLN ILE VAL LYS LYS ILE SER GLU ILE LEU LYS SEQRES 27 B 418 LYS LYS LYS LYS LYS SER VAL LYS SER PHE GLN ILE LYS SEQRES 28 B 418 ASN ASN MET PHE ILE PHE ILE ASN CYS LEU ILE GLU ASN SEQRES 29 B 418 PRO ALA PHE THR SER GLN THR LYS GLU GLN LEU THR THR SEQRES 30 B 418 ARG VAL LYS ASP PHE GLY SER ARG CYS GLU ILE PRO LEU SEQRES 31 B 418 GLU TYR ILE ASN LYS ILE MET LYS THR ASP LEU ALA THR SEQRES 32 B 418 ARG MET PHE GLU ILE ALA ASP ALA ASN GLU GLU ASN ALA SEQRES 33 B 418 LEU LYS HET MG 904 1 HET MG 905 1 HET CDX 901 19 HET ANP 902 31 HET ANP 903 31 HETNAM MG MAGNESIUM ION HETNAM CDX (S)-4,4'-(1-METHYL-1,2-ETHANEDIYL)BIS-2,6- HETNAM 2 CDX PIPERAZINEDIONE HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETSYN CDX ICRF-187 FORMUL 3 MG 2(MG 2+) FORMUL 5 CDX C11 H16 N4 O4 FORMUL 6 ANP 2(C10 H17 N6 O12 P3) FORMUL 8 HOH *766(H2 O1) HELIX 1 1 SER A 7 TYR A 12 1 6 HELIX 2 2 SER A 16 ARG A 24 1 9 HELIX 3 3 PRO A 25 GLY A 30 1 6 HELIX 4 4 VAL A 57 ASP A 78 1 22 HELIX 5 5 TYR A 115 HIS A 123 1 9 HELIX 6 6 TYR A 144 PHE A 152 1 9 HELIX 7 7 LEU A 203 GLY A 207 5 5 HELIX 8 8 ASP A 212 VAL A 230 1 19 HELIX 9 9 ASN A 246 LEU A 253 1 8 HELIX 10 10 GLY A 314 LYS A 333 1 20 HELIX 11 11 LYS A 341 ASN A 347 1 7 HELIX 12 12 ARG A 373 PHE A 377 5 5 HELIX 13 13 PRO A 384 MET A 392 1 9 HELIX 14 14 THR A 394 ASN A 410 1 17 HELIX 15 15 SER B 16 ARG B 24 1 9 HELIX 16 16 PRO B 25 GLY B 30 1 6 HELIX 17 17 VAL B 57 ASP B 78 1 22 HELIX 18 18 TYR B 115 HIS B 123 1 9 HELIX 19 19 TYR B 144 PHE B 152 1 9 HELIX 20 20 LEU B 203 GLY B 207 5 5 HELIX 21 21 ASP B 212 VAL B 230 1 19 HELIX 22 22 ASN B 246 LEU B 253 1 8 HELIX 23 23 TYR B 254 LYS B 260 1 7 HELIX 24 24 GLY B 314 LYS B 334 1 21 HELIX 25 25 LYS B 341 ASN B 347 1 7 HELIX 26 26 ARG B 373 PHE B 377 5 5 HELIX 27 27 PRO B 384 MET B 392 1 9 HELIX 28 28 THR B 394 ASP B 405 1 12 SHEET 1 A 2 GLN A 13 LYS A 14 0 SHEET 2 A 2 THR B 126 SER B 127 -1 O SER B 127 N GLN A 13 SHEET 1 B 2 GLN A 35 ASP A 43 0 SHEET 2 B 2 CYS A 48 ILE A 56 -1 O LYS A 52 N GLN A 39 SHEET 1 C 3 ILE A 179 CYS A 180 0 SHEET 2 C 3 GLN A 167 GLU A 174 -1 N GLU A 174 O ILE A 179 SHEET 3 C 3 LYS A 184 SER A 187 -1 O LYS A 184 N VAL A 170 SHEET 1 D 8 ILE A 179 CYS A 180 0 SHEET 2 D 8 GLN A 167 GLU A 174 -1 N GLU A 174 O ILE A 179 SHEET 3 D 8 SER A 153 ASP A 162 -1 N PHE A 156 O TRP A 173 SHEET 4 D 8 TYR A 194 PRO A 201 -1 O THR A 198 N ILE A 157 SHEET 5 D 8 THR A 94 ASP A 100 -1 N VAL A 97 O VAL A 197 SHEET 6 D 8 ARG A 83 HIS A 89 -1 N HIS A 89 O THR A 94 SHEET 7 D 8 ASN A 234 LEU A 237 1 O TYR A 236 N VAL A 86 SHEET 8 D 8 LYS A 240 SER A 241 -1 O LYS A 240 N LEU A 237 SHEET 1 E 2 THR A 126 SER A 127 0 SHEET 2 E 2 GLN B 13 LYS B 14 -1 O GLN B 13 N SER A 127 SHEET 1 F 5 LEU A 280 ASN A 285 0 SHEET 2 F 5 TRP A 288 VAL A 294 -1 O VAL A 290 N GLU A 282 SHEET 3 F 5 MET A 349 CYS A 355 -1 O PHE A 352 N ALA A 291 SHEET 4 F 5 GLN A 300 VAL A 305 1 N GLN A 300 O ILE A 351 SHEET 5 F 5 ILE A 308 ALA A 309 -1 O ILE A 308 N VAL A 305 SHEET 1 G 2 GLN B 35 ASP B 43 0 SHEET 2 G 2 CYS B 48 ILE B 56 -1 O CYS B 48 N ASP B 43 SHEET 1 H 3 ILE B 179 CYS B 180 0 SHEET 2 H 3 GLN B 167 GLU B 174 -1 N GLU B 174 O ILE B 179 SHEET 3 H 3 LYS B 184 SER B 187 -1 O LYS B 184 N VAL B 170 SHEET 1 I 8 ILE B 179 CYS B 180 0 SHEET 2 I 8 GLN B 167 GLU B 174 -1 N GLU B 174 O ILE B 179 SHEET 3 I 8 SER B 153 ASP B 162 -1 N PHE B 156 O TRP B 173 SHEET 4 I 8 TYR B 194 PRO B 201 -1 O THR B 198 N ILE B 157 SHEET 5 I 8 THR B 94 ASP B 100 -1 N VAL B 97 O VAL B 197 SHEET 6 I 8 ARG B 83 HIS B 89 -1 N HIS B 89 O THR B 94 SHEET 7 I 8 ASN B 234 LEU B 237 1 O TYR B 236 N VAL B 86 SHEET 8 I 8 LYS B 240 SER B 241 -1 O LYS B 240 N LEU B 237 SHEET 1 J 5 LEU B 280 ASN B 285 0 SHEET 2 J 5 TRP B 288 VAL B 294 -1 O VAL B 290 N GLU B 282 SHEET 3 J 5 MET B 349 CYS B 355 -1 O PHE B 352 N ALA B 291 SHEET 4 J 5 GLN B 300 VAL B 305 1 N GLN B 300 O ILE B 351 SHEET 5 J 5 ILE B 308 ALA B 309 -1 O ILE B 308 N VAL B 305 CRYST1 58.553 71.444 215.724 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017079 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004636 0.00000