HEADER ISOMERASE/DNA 27-OCT-25 9XD8 TITLE OPEN-SATE CLEAVAGE COMPLEX OF HUMAN TOPOISOMERASE IIA-BETA WITH TITLE 2 OLIGONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE 2-BETA; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: DNA TOPOISOMERASE II,BETA ISOZYME; COMPND 5 EC: 5.6.2.2; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: HUMAN TOPOISOMERASE IIA (BETA ISOFORM), CATALYTIC CORE COMPND 8 757 AMINO ACID CONSTRUCT; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(P*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3'); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: OLIGONUCLEOTIDE; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*AP*GP*CP*CP*GP*AP*GP*C)-3'); COMPND 16 CHAIN: E; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: OLIGONUCLEOTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TOP2B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: NONEA; SOURCE 11 ORGANISM_TAXID: 203745; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: NONEA; SOURCE 15 ORGANISM_TAXID: 203745 KEYWDS TOPOISOMERASE CATALYTIC CORE CLEAVAGE COMPLEX DNA TOPOLOGY, KEYWDS 2 ISOMERASE/DNA, ISOMERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.S.ALI,W.ZHAO,Y.J.TANG REVDAT 1 04-NOV-26 9XD8 0 JRNL AUTH M.S.ALI JRNL TITL OPEN-SATE CLEAVAGE COMPLEX OF HUMAN TOPOISOMERASE IIA-BETA JRNL TITL 2 WITH OLIGONUCLEOTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 20429 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1012 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 20.1100 - 6.1300 0.99 2917 157 0.2102 0.2338 REMARK 3 2 6.1300 - 4.8900 1.00 2808 155 0.2057 0.2520 REMARK 3 3 4.8900 - 4.2800 0.99 2761 154 0.1780 0.2074 REMARK 3 4 4.2800 - 3.8900 0.98 2739 131 0.2131 0.2657 REMARK 3 5 3.8900 - 3.6100 0.99 2762 113 0.2488 0.3329 REMARK 3 6 3.6100 - 3.4000 0.99 2683 161 0.2789 0.3468 REMARK 3 7 3.4000 - 3.2300 1.00 2747 141 0.2925 0.3432 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.416 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.877 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.36 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 5838 REMARK 3 ANGLE : 1.320 7970 REMARK 3 CHIRALITY : 0.062 900 REMARK 3 PLANARITY : 0.010 970 REMARK 3 DIHEDRAL : 16.011 908 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9XD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1300064139. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5-5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20720 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.230 REMARK 200 RESOLUTION RANGE LOW (A) : 20.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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 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: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: LONG, OVAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM MAGNESIUM CHLORIDE, 2-(N REMARK 280 -MORPHOLINO)ETHANESULFONIC ACID PH 5.6, 22% 2-METHYL-2, 4- REMARK 280 PENTANEDIOL (MPD), 277K, PH 5.7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 155.13800 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 77.56900 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.56900 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 155.13800 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, E 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 SER B 445 REMARK 465 VAL B 446 REMARK 465 LYS B 447 REMARK 465 TYR B 448 REMARK 465 SER B 449 REMARK 465 LYS B 450 REMARK 465 ILE B 451 REMARK 465 SER B 597 REMARK 465 LYS B 598 REMARK 465 PHE B 611 REMARK 465 ASP B 612 REMARK 465 GLU B 613 REMARK 465 TRP B 614 REMARK 465 LYS B 615 REMARK 465 LYS B 616 REMARK 465 HIS B 617 REMARK 465 ILE B 618 REMARK 465 GLU B 619 REMARK 465 ASN B 620 REMARK 465 GLN B 621 REMARK 465 LYS B 622 REMARK 465 ALA B 623 REMARK 465 TRP B 624 REMARK 465 LYS B 625 REMARK 465 ILE B 626 REMARK 465 HIS B 694 REMARK 465 GLY B 695 REMARK 465 LEU B 696 REMARK 465 PRO B 697 REMARK 465 ASP B 964 REMARK 465 LYS B 965 REMARK 465 THR B 966 REMARK 465 GLN B 1076 REMARK 465 GLY B 1077 REMARK 465 LYS B 1078 REMARK 465 ILE B 1079 REMARK 465 GLU B 1111 REMARK 465 LYS B 1112 REMARK 465 ALA B 1113 REMARK 465 ALA B 1114 REMARK 465 GLU B 1115 REMARK 465 GLU B 1116 REMARK 465 ASP B 1117 REMARK 465 GLU B 1118 REMARK 465 THR B 1119 REMARK 465 GLN B 1120 REMARK 465 ASN B 1121 REMARK 465 GLN B 1122 REMARK 465 HIS B 1123 REMARK 465 ASP B 1124 REMARK 465 ASP B 1125 REMARK 465 SER B 1126 REMARK 465 SER B 1127 REMARK 465 SER B 1128 REMARK 465 ASP B 1129 REMARK 465 SER B 1130 REMARK 465 GLY B 1131 REMARK 465 THR B 1132 REMARK 465 PRO B 1133 REMARK 465 SER B 1134 REMARK 465 GLY B 1135 REMARK 465 PRO B 1136 REMARK 465 ASP B 1137 REMARK 465 DA E 1 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 LYS B 452 CG CD CE NZ REMARK 470 SER B 513 OG REMARK 470 LYS B 515 CG CD CE NZ REMARK 470 GLU B 542 CG CD OE1 OE2 REMARK 470 LYS B 545 CG CD CE NZ REMARK 470 ILE B 554 CG1 CG2 CD1 REMARK 470 LYS B 600 CG CD CE NZ REMARK 470 LEU B 603 CG CD1 CD2 REMARK 470 PHE B 605 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 627 CG CD CE NZ REMARK 470 ARG B 649 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 671 CG CD CE NZ REMARK 470 ASP B 687 CG OD1 OD2 REMARK 470 ARG B 688 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 690 CG CD OE1 NE2 REMARK 470 ARG B 692 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 693 CG CD1 CD2 REMARK 470 GLU B 698 CG CD OE1 OE2 REMARK 470 GLN B 699 CG CD OE1 NE2 REMARK 470 LYS B 707 CG CD CE NZ REMARK 470 SER B 725 OG REMARK 470 LYS B 755 CG CD CE NZ REMARK 470 ARG B 756 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 820 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 849 CG OD1 ND2 REMARK 470 GLU B1051 CG CD OE1 OE2 REMARK 470 LYS B1063 CG CD CE NZ REMARK 470 GLN B1067 CG CD OE1 NE2 REMARK 470 PHE B1070 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE B1071 CG1 CG2 CD1 REMARK 470 LEU B1072 CG CD1 CD2 REMARK 470 GLU B1073 CG CD OE1 OE2 REMARK 470 LYS B1074 CG CD CE NZ REMARK 470 ILE B1081 CG1 CG2 CD1 REMARK 470 ASN B1083 CG OD1 ND2 REMARK 470 ARG B1084 CG CD NE CZ NH1 NH2 REMARK 470 SER B1085 OG REMARK 470 LYS B1086 CG CD CE NZ REMARK 470 LYS B1087 CG CD CE NZ REMARK 470 ASP B1088 CG OD1 OD2 REMARK 470 LEU B1089 CG CD1 CD2 REMARK 470 ILE B1090 CG1 CG2 CD1 REMARK 470 GLN B1091 CG CD OE1 NE2 REMARK 470 MET B1092 CG SD CE REMARK 470 LEU B1093 CG CD1 CD2 REMARK 470 GLN B1095 CG CD OE1 NE2 REMARK 470 ARG B1096 CG CD NE CZ NH1 NH2 REMARK 470 TRP B1106 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B1106 CZ3 CH2 REMARK 470 LYS B1107 CG CD CE NZ REMARK 470 GLU B1108 CG CD OE1 OE2 REMARK 470 PHE B1138 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN B1139 CG OD1 ND2 REMARK 470 ILE B1141 CG1 CG2 CD1 REMARK 470 LEU B1142 CG CD1 CD2 REMARK 470 ASN B1143 CG OD1 ND2 REMARK 470 LYS B1151 CG CD CE NZ REMARK 470 LYS B1153 CG CD CE NZ REMARK 470 VAL B1154 CG1 CG2 REMARK 470 GLU B1155 CG CD OE1 OE2 REMARK 470 GLU B1156 CG CD OE1 OE2 REMARK 470 LYS B1159 CG CD CE NZ REMARK 470 GLN B1160 CG CD OE1 NE2 REMARK 470 ARG B1166 CG CD NE CZ NH1 NH2 REMARK 470 LYS B1172 CG CD CE NZ REMARK 470 GLU B1182 CG CD OE1 OE2 REMARK 470 GLU B1189 CG CD OE1 OE2 REMARK 470 LYS B1193 CG CD CE NZ REMARK 470 GLU B1200 CG CD OE1 OE2 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DG D 13 O3' DG D 13 C3' -0.045 REMARK 500 DG E 5 O3' DG E 5 C3' -0.085 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DC D 16 O5' - P - OP1 ANGL. DEV. = -7.0 DEGREES REMARK 500 DC D 19 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU B 511 75.96 63.02 REMARK 500 ASP B 539 -56.48 -141.46 REMARK 500 GLN B 558 42.91 -83.65 REMARK 500 TRP B 577 88.59 -162.13 REMARK 500 LYS B 600 -118.83 61.85 REMARK 500 GLN B 601 109.89 52.27 REMARK 500 TYR B 629 79.73 -118.74 REMARK 500 TRP B 680 -67.56 -28.56 REMARK 500 ARG B 692 28.20 -66.36 REMARK 500 TYR B 702 -157.74 -123.22 REMARK 500 ALA B 705 36.09 -89.66 REMARK 500 HIS B 774 31.42 -99.00 REMARK 500 PHE B 791 -157.38 -90.22 REMARK 500 SER B 794 -113.07 -106.40 REMARK 500 ALA B 817 170.48 -58.54 REMARK 500 PHE B 834 72.15 -115.05 REMARK 500 VAL B 852 -142.19 -126.97 REMARK 500 GLU B 870 146.16 -173.94 REMARK 500 ASN B 910 20.25 40.38 REMARK 500 ASN B 935 -18.12 64.55 REMARK 500 VAL B 955 -68.55 -130.49 REMARK 500 ALA B 968 152.97 -47.93 REMARK 500 LEU B 969 -15.88 -145.26 REMARK 500 ALA B 998 -75.01 -40.14 REMARK 500 ASN B1014 52.73 -116.11 REMARK 500 SER B1015 42.57 178.53 REMARK 500 ASP B1020 -167.09 -73.48 REMARK 500 LYS B1026 142.97 -170.68 REMARK 500 ASP B1040 -70.16 -54.29 REMARK 500 MET B1056 -67.24 -136.74 REMARK 500 GLN B1067 16.80 -69.97 REMARK 500 ASN B1083 -27.14 59.37 REMARK 500 LYS B1086 -70.44 -62.21 REMARK 500 GLN B1095 21.91 -77.28 REMARK 500 SER B1100 176.51 -58.95 REMARK 500 ASN B1143 6.06 -69.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 557 OD2 REMARK 620 2 ASP B 559 OD2 89.9 REMARK 620 N 1 DBREF 9XD8 B 445 1201 UNP Q02880 TOP2B_HUMAN 450 1206 DBREF 9XD8 D 11 20 PDB 9XD8 9XD8 11 20 DBREF 9XD8 E 1 8 PDB 9XD8 9XD8 1 8 SEQRES 1 B 757 SER VAL LYS TYR SER LYS ILE LYS GLY ILE PRO LYS LEU SEQRES 2 B 757 ASP ASP ALA ASN ASP ALA GLY GLY LYS HIS SER LEU GLU SEQRES 3 B 757 CYS THR LEU ILE LEU THR GLU GLY ASP SER ALA LYS SER SEQRES 4 B 757 LEU ALA VAL SER GLY LEU GLY VAL ILE GLY ARG ASP ARG SEQRES 5 B 757 TYR GLY VAL PHE PRO LEU ARG GLY LYS ILE LEU ASN VAL SEQRES 6 B 757 ARG GLU ALA SER HIS LYS GLN ILE MET GLU ASN ALA GLU SEQRES 7 B 757 ILE ASN ASN ILE ILE LYS ILE VAL GLY LEU GLN TYR LYS SEQRES 8 B 757 LYS SER TYR ASP ASP ALA GLU SER LEU LYS THR LEU ARG SEQRES 9 B 757 TYR GLY LYS ILE MET ILE MET THR ASP GLN ASP GLN ASP SEQRES 10 B 757 GLY SER HIS ILE LYS GLY LEU LEU ILE ASN PHE ILE HIS SEQRES 11 B 757 HIS ASN TRP PRO SER LEU LEU LYS HIS GLY PHE LEU GLU SEQRES 12 B 757 GLU PHE ILE THR PRO ILE VAL LYS ALA SER LYS ASN LYS SEQRES 13 B 757 GLN GLU LEU SER PHE TYR SER ILE PRO GLU PHE ASP GLU SEQRES 14 B 757 TRP LYS LYS HIS ILE GLU ASN GLN LYS ALA TRP LYS ILE SEQRES 15 B 757 LYS TYR TYR LYS GLY LEU GLY THR SER THR ALA LYS GLU SEQRES 16 B 757 ALA LYS GLU TYR PHE ALA ASP MET GLU ARG HIS ARG ILE SEQRES 17 B 757 LEU PHE ARG TYR ALA GLY PRO GLU ASP ASP ALA ALA ILE SEQRES 18 B 757 THR LEU ALA PHE SER LYS LYS LYS ILE ASP ASP ARG LYS SEQRES 19 B 757 GLU TRP LEU THR ASN PHE MET GLU ASP ARG ARG GLN ARG SEQRES 20 B 757 ARG LEU HIS GLY LEU PRO GLU GLN PHE LEU TYR GLY THR SEQRES 21 B 757 ALA THR LYS HIS LEU THR TYR ASN ASP PHE ILE ASN LYS SEQRES 22 B 757 GLU LEU ILE LEU PHE SER ASN SER ASP ASN GLU ARG SER SEQRES 23 B 757 ILE PRO SER LEU VAL ASP GLY PHE LYS PRO GLY GLN ARG SEQRES 24 B 757 LYS VAL LEU PHE THR CYS PHE LYS ARG ASN ASP LYS ARG SEQRES 25 B 757 GLU VAL LYS VAL ALA GLN LEU ALA GLY SER VAL ALA GLU SEQRES 26 B 757 MET SER ALA TYR HIS HIS GLY GLU GLN ALA LEU MET MET SEQRES 27 B 757 THR ILE VAL ASN LEU ALA GLN ASN PHE VAL GLY SER ASN SEQRES 28 B 757 ASN ILE ASN LEU LEU GLN PRO ILE GLY GLN PHE GLY THR SEQRES 29 B 757 ARG LEU HIS GLY GLY LYS ASP ALA ALA SER PRO ARG TYR SEQRES 30 B 757 ILE PHE THR MET LEU SER THR LEU ALA ARG LEU LEU PHE SEQRES 31 B 757 PRO ALA VAL ASP ASP ASN LEU LEU LYS PHE LEU TYR ASP SEQRES 32 B 757 ASP ASN GLN ARG VAL GLU PRO GLU TRP TYR ILE PRO ILE SEQRES 33 B 757 ILE PRO MET VAL LEU ILE ASN GLY ALA GLU GLY ILE GLY SEQRES 34 B 757 THR GLY TRP ALA CYS LYS LEU PRO ASN TYR ASP ALA ARG SEQRES 35 B 757 GLU ILE VAL ASN ASN VAL ARG ARG MET LEU ASP GLY LEU SEQRES 36 B 757 ASP PRO HIS PRO MET LEU PRO ASN TYR LYS ASN PHE LYS SEQRES 37 B 757 GLY THR ILE GLN GLU LEU GLY GLN ASN GLN TYR ALA VAL SEQRES 38 B 757 SER GLY GLU ILE PHE VAL VAL ASP ARG ASN THR VAL GLU SEQRES 39 B 757 ILE THR GLU LEU PRO VAL ARG THR TRP THR GLN VAL TYR SEQRES 40 B 757 LYS GLU GLN VAL LEU GLU PRO MET LEU ASN GLY THR ASP SEQRES 41 B 757 LYS THR PRO ALA LEU ILE SER ASP TYR LYS GLU TYR HIS SEQRES 42 B 757 THR ASP THR THR VAL LYS PHE VAL VAL LYS MET THR GLU SEQRES 43 B 757 GLU LYS LEU ALA GLN ALA GLU ALA ALA GLY LEU HIS LYS SEQRES 44 B 757 VAL PHE LYS LEU GLN THR THR LEU THR CYS ASN SER MET SEQRES 45 B 757 VAL LEU PHE ASP HIS MET GLY CYS LEU LYS LYS TYR GLU SEQRES 46 B 757 THR VAL GLN ASP ILE LEU LYS GLU PHE PHE ASP LEU ARG SEQRES 47 B 757 LEU SER TYR TYR GLY LEU ARG LYS GLU TRP LEU VAL GLY SEQRES 48 B 757 MET LEU GLY ALA GLU SER THR LYS LEU ASN ASN GLN ALA SEQRES 49 B 757 ARG PHE ILE LEU GLU LYS ILE GLN GLY LYS ILE THR ILE SEQRES 50 B 757 GLU ASN ARG SER LYS LYS ASP LEU ILE GLN MET LEU VAL SEQRES 51 B 757 GLN ARG GLY TYR GLU SER ASP PRO VAL LYS ALA TRP LYS SEQRES 52 B 757 GLU ALA GLN GLU LYS ALA ALA GLU GLU ASP GLU THR GLN SEQRES 53 B 757 ASN GLN HIS ASP ASP SER SER SER ASP SER GLY THR PRO SEQRES 54 B 757 SER GLY PRO ASP PHE ASN TYR ILE LEU ASN MET SER LEU SEQRES 55 B 757 TRP SER LEU THR LYS GLU LYS VAL GLU GLU LEU ILE LYS SEQRES 56 B 757 GLN ARG ASP ALA LYS GLY ARG GLU VAL ASN ASP LEU LYS SEQRES 57 B 757 ARG LYS SER PRO SER ASP LEU TRP LYS GLU ASP LEU ALA SEQRES 58 B 757 ALA PHE VAL GLU GLU LEU ASP LYS VAL GLU SER GLN GLU SEQRES 59 B 757 ARG GLU ASP SEQRES 1 D 10 DC DA DG DC DT DC DG DG DC DT SEQRES 1 E 8 DA DG DC DC DG DA DG DC HET MG B1301 1 HET MG B1302 1 HET EDO B1303 4 HET EDO B1304 4 HET MG D 101 1 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 MG 3(MG 2+) FORMUL 6 EDO 2(C2 H6 O2) HELIX 1 AA1 HIS B 467 GLU B 470 5 4 HELIX 2 AA2 GLY B 478 ARG B 494 1 17 HELIX 3 AA3 SER B 513 ASN B 520 1 8 HELIX 4 AA4 ASN B 520 GLY B 531 1 12 HELIX 5 AA5 ASP B 540 THR B 546 1 7 HELIX 6 AA6 ASP B 559 TRP B 577 1 19 HELIX 7 AA7 TRP B 577 LYS B 582 1 6 HELIX 8 AA8 LEU B 603 ILE B 608 1 6 HELIX 9 AA9 GLY B 631 SER B 635 5 5 HELIX 10 AB1 THR B 636 ASP B 646 1 11 HELIX 11 AB2 ASP B 646 HIS B 650 1 5 HELIX 12 AB3 GLY B 658 SER B 670 1 13 HELIX 13 AB4 LYS B 673 ARG B 692 1 20 HELIX 14 AB5 TYR B 711 GLU B 718 1 8 HELIX 15 AB6 GLU B 718 ILE B 731 1 14 HELIX 16 AB7 LYS B 739 ASN B 753 1 15 HELIX 17 AB8 VAL B 760 SER B 771 1 12 HELIX 18 AB9 GLY B 776 GLN B 789 1 14 HELIX 19 AC1 SER B 818 TYR B 821 5 4 HELIX 20 AC2 LEU B 829 PHE B 834 1 6 HELIX 21 AC3 PRO B 835 LEU B 842 5 8 HELIX 22 AC4 PRO B 862 ASN B 867 1 6 HELIX 23 AC5 ASP B 884 ASP B 897 1 14 HELIX 24 AC6 TRP B 947 VAL B 955 1 9 HELIX 25 AC7 VAL B 955 GLY B 962 1 8 HELIX 26 AC8 THR B 989 ALA B 999 1 11 HELIX 27 AC9 GLY B 1000 PHE B 1005 1 6 HELIX 28 AD1 THR B 1030 ILE B 1075 1 46 HELIX 29 AD2 SER B 1085 GLN B 1095 1 11 HELIX 30 AD3 ASP B 1101 GLN B 1110 1 10 HELIX 31 AD4 ASN B 1139 ASN B 1143 1 5 HELIX 32 AD5 SER B 1145 LEU B 1149 5 5 HELIX 33 AD6 THR B 1150 ARG B 1173 1 24 HELIX 34 AD7 SER B 1175 GLU B 1200 1 26 SHEET 1 AA1 6 TYR B 497 LEU B 502 0 SHEET 2 AA1 6 THR B 472 GLU B 477 1 N THR B 472 O GLY B 498 SHEET 3 AA1 6 LYS B 551 MET B 555 1 O MET B 555 N LEU B 475 SHEET 4 AA1 6 LEU B 586 PHE B 589 1 O GLU B 587 N ILE B 552 SHEET 5 AA1 6 ARG B 651 ARG B 655 -1 O ILE B 652 N GLU B 588 SHEET 6 AA1 6 HIS B 708 THR B 710 1 O LEU B 709 N ARG B 655 SHEET 1 AA2 2 VAL B 758 LYS B 759 0 SHEET 2 AA2 2 PHE B 823 THR B 824 -1 O THR B 824 N VAL B 758 SHEET 1 AA3 2 PHE B 844 TYR B 846 0 SHEET 2 AA3 2 ARG B 851 PRO B 854 -1 O VAL B 852 N LEU B 845 SHEET 1 AA4 2 GLU B 870 ILE B 872 0 SHEET 2 AA4 2 ALA B 877 LYS B 879 -1 O CYS B 878 N GLY B 871 SHEET 1 AA5 3 THR B 914 GLY B 919 0 SHEET 2 AA5 3 GLN B 922 SER B 926 -1 O SER B 926 N THR B 914 SHEET 3 AA5 3 GLN B1008 THR B1012 -1 O THR B1009 N VAL B 925 SHEET 1 AA6 4 GLU B 928 ASP B 933 0 SHEET 2 AA6 4 THR B 936 GLU B 941 -1 O THR B 936 N VAL B 932 SHEET 3 AA6 4 PHE B 984 LYS B 987 -1 O PHE B 984 N ILE B 939 SHEET 4 AA6 4 ASP B 972 GLU B 975 -1 N ASP B 972 O LYS B 987 SHEET 1 AA7 2 MET B1016 PHE B1019 0 SHEET 2 AA7 2 LEU B1025 TYR B1028 -1 O TYR B1028 N MET B1016 LINK OD2 ASP B 557 MG MG B1301 1555 1555 2.18 LINK OD2 ASP B 559 MG MG B1301 1555 1555 2.10 CRYST1 96.151 96.151 232.707 90.00 90.00 120.00 P 32 2 1 6 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 0.010400 0.006005 0.000000 0.00000 SCALE2 0.000000 0.012009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004297 0.00000 CONECT 793 5694 CONECT 810 5694 CONECT 5694 793 810 CONECT 5696 5697 5698 CONECT 5697 5696 CONECT 5698 5696 5699 CONECT 5699 5698 CONECT 5700 5701 5702 CONECT 5701 5700 CONECT 5702 5700 5703 CONECT 5703 5702 MASTER 458 0 5 34 21 0 0 6 5693 3 11 61 END