HEADER ISOMERASE 14-MAR-25 9MAT TITLE TOPBP1 BRCT 7-8 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE 2-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA TOPOISOMERASE II-BETA-BINDING PROTEIN 1,TOPBP1,DNA COMPND 5 TOPOISOMERASE II-BINDING PROTEIN 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TOPBP1, KIAA0259; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA TOPOISOMERASE 2-BINDING PROTEIN 1, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.CHEN,L.WANG,K.RUAN REVDAT 1 18-MAR-26 9MAT 0 JRNL AUTH W.CHEN,L.WANG,K.RUAN JRNL TITL SMALL-MOLECULE LIGAND SCREENING AND STRUCTURAL INVESTIGATION JRNL TITL 2 OF THE TOPBP1 BRCT 7-8 DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19_4092: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 29333 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1349 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 47.5900 - 3.5600 1.00 2892 116 0.1420 0.1803 REMARK 3 2 3.5500 - 2.8200 1.00 2805 151 0.1596 0.2016 REMARK 3 3 2.8200 - 2.4600 1.00 2803 138 0.1646 0.2334 REMARK 3 4 2.4600 - 2.2400 1.00 2792 131 0.1576 0.2130 REMARK 3 5 2.2400 - 2.0800 1.00 2796 132 0.1505 0.2044 REMARK 3 6 2.0800 - 1.9600 1.00 2777 137 0.1539 0.1870 REMARK 3 7 1.9600 - 1.8600 1.00 2782 122 0.1683 0.2066 REMARK 3 8 1.8600 - 1.7800 1.00 2807 122 0.1738 0.2289 REMARK 3 9 1.7800 - 1.7100 1.00 2775 137 0.1913 0.2355 REMARK 3 10 1.7100 - 1.6500 1.00 2755 163 0.2130 0.2667 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 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 : 0.009 1910 REMARK 3 ANGLE : 0.995 2586 REMARK 3 CHIRALITY : 0.067 280 REMARK 3 PLANARITY : 0.009 335 REMARK 3 DIHEDRAL : 6.873 259 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1262 THROUGH 1289 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2640 9.8155 -2.0374 REMARK 3 T TENSOR REMARK 3 T11: 0.0692 T22: 0.1017 REMARK 3 T33: 0.0978 T12: -0.0016 REMARK 3 T13: -0.0173 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 1.9506 L22: 1.9145 REMARK 3 L33: 3.2387 L12: -0.9608 REMARK 3 L13: -0.6637 L23: 1.4198 REMARK 3 S TENSOR REMARK 3 S11: 0.0411 S12: 0.0459 S13: -0.1493 REMARK 3 S21: 0.0226 S22: -0.0655 S23: 0.0187 REMARK 3 S31: 0.1120 S32: -0.1649 S33: 0.0467 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1290 THROUGH 1364 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.8577 6.1182 7.0304 REMARK 3 T TENSOR REMARK 3 T11: 0.0797 T22: 0.0718 REMARK 3 T33: 0.0764 T12: -0.0185 REMARK 3 T13: -0.0102 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 2.1468 L22: 1.6778 REMARK 3 L33: 2.4067 L12: 0.0333 REMARK 3 L13: -1.2467 L23: -0.1873 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: 0.0995 S13: 0.0972 REMARK 3 S21: 0.0799 S22: -0.0443 S23: -0.0787 REMARK 3 S31: 0.0249 S32: -0.1179 S33: 0.0156 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1365 THROUGH 1382 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7217 -1.6630 15.7772 REMARK 3 T TENSOR REMARK 3 T11: 0.1137 T22: 0.1493 REMARK 3 T33: 0.0998 T12: -0.0453 REMARK 3 T13: 0.0008 T23: 0.0556 REMARK 3 L TENSOR REMARK 3 L11: 5.3647 L22: 7.1426 REMARK 3 L33: 6.0077 L12: 1.9293 REMARK 3 L13: 1.9176 L23: 3.3779 REMARK 3 S TENSOR REMARK 3 S11: -0.0021 S12: -0.4658 S13: -0.1764 REMARK 3 S21: 0.4126 S22: -0.2280 S23: -0.1042 REMARK 3 S31: 0.0042 S32: 0.1591 S33: 0.1193 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1383 THROUGH 1493 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.7807 -6.6906 20.3000 REMARK 3 T TENSOR REMARK 3 T11: 0.0935 T22: 0.0663 REMARK 3 T33: 0.0845 T12: -0.0067 REMARK 3 T13: 0.0087 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 1.6749 L22: 1.1675 REMARK 3 L33: 1.2380 L12: 0.5905 REMARK 3 L13: 0.0962 L23: -0.5462 REMARK 3 S TENSOR REMARK 3 S11: -0.0444 S12: 0.0722 S13: -0.1186 REMARK 3 S21: -0.0381 S22: -0.0013 S23: -0.0299 REMARK 3 S31: -0.0017 S32: 0.0489 S33: 0.0391 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 9MAT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 18-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97861 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29349 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 47.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.53800 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M SODIUM MALONATE PH 7.0, 20% W/V REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.03700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 1261 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 HIS A1426 27.73 -141.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 9MAT A 1264 1493 UNP Q92547 TOPB1_HUMAN 1264 1493 SEQADV 9MAT GLY A 1261 UNP Q92547 EXPRESSION TAG SEQADV 9MAT HIS A 1262 UNP Q92547 EXPRESSION TAG SEQADV 9MAT MET A 1263 UNP Q92547 EXPRESSION TAG SEQRES 1 A 233 GLY HIS MET LEU LYS LYS GLN TYR ILE PHE GLN LEU SER SEQRES 2 A 233 SER LEU ASN PRO GLN GLU ARG ILE ASP TYR CYS HIS LEU SEQRES 3 A 233 ILE GLU LYS LEU GLY GLY LEU VAL ILE GLU LYS GLN CYS SEQRES 4 A 233 PHE ASP PRO THR CYS THR HIS ILE VAL VAL GLY HIS PRO SEQRES 5 A 233 LEU ARG ASN GLU LYS TYR LEU ALA SER VAL ALA ALA GLY SEQRES 6 A 233 LYS TRP VAL LEU HIS ARG SER TYR LEU GLU ALA CYS ARG SEQRES 7 A 233 THR ALA GLY HIS PHE VAL GLN GLU GLU ASP TYR GLU TRP SEQRES 8 A 233 GLY SER SER SER ILE LEU ASP VAL LEU THR GLY ILE ASN SEQRES 9 A 233 VAL GLN GLN ARG ARG LEU ALA LEU ALA ALA MET ARG TRP SEQRES 10 A 233 ARG LYS LYS ILE GLN GLN ARG GLN GLU SER GLY ILE VAL SEQRES 11 A 233 GLU GLY ALA PHE SER GLY TRP LYS VAL ILE LEU HIS VAL SEQRES 12 A 233 ASP GLN SER ARG GLU ALA GLY PHE LYS ARG LEU LEU GLN SEQRES 13 A 233 SER GLY GLY ALA LYS VAL LEU PRO GLY HIS SER VAL PRO SEQRES 14 A 233 LEU PHE LYS GLU ALA THR HIS LEU PHE SER ASP LEU ASN SEQRES 15 A 233 LYS LEU LYS PRO ASP ASP SER GLY VAL ASN ILE ALA GLU SEQRES 16 A 233 ALA ALA ALA GLN ASN VAL TYR CYS LEU ARG THR GLU TYR SEQRES 17 A 233 ILE ALA ASP TYR LEU MET GLN GLU SER PRO PRO HIS VAL SEQRES 18 A 233 GLU ASN TYR CYS LEU PRO GLU ALA ILE SER PHE ILE HET MLA A1501 7 HETNAM MLA MALONIC ACID HETSYN MLA DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; HETSYN 2 MLA METHANEDICARBOXYLIC ACID FORMUL 2 MLA C3 H4 O4 FORMUL 3 HOH *383(H2 O) HELIX 1 AA1 ASN A 1276 LEU A 1290 1 15 HELIX 2 AA2 ASN A 1315 ALA A 1324 1 10 HELIX 3 AA3 ARG A 1331 GLY A 1341 1 11 HELIX 4 AA4 GLU A 1346 GLU A 1350 5 5 HELIX 5 AA5 SER A 1353 ASP A 1358 1 6 HELIX 6 AA6 ASN A 1364 GLN A 1383 1 20 HELIX 7 AA7 ASP A 1404 GLY A 1418 1 15 HELIX 8 AA8 SER A 1427 LYS A 1432 5 6 HELIX 9 AA9 ASN A 1452 GLN A 1459 1 8 HELIX 10 AB1 THR A 1466 GLN A 1475 1 10 HELIX 11 AB2 HIS A 1480 CYS A 1485 5 6 HELIX 12 AB3 LEU A 1486 PHE A 1492 1 7 SHEET 1 AA1 4 LEU A1293 VAL A1294 0 SHEET 2 AA1 4 ILE A1269 SER A1273 1 N PHE A1270 O LEU A1293 SHEET 3 AA1 4 HIS A1306 VAL A1309 1 O VAL A1308 N SER A1273 SHEET 4 AA1 4 TRP A1327 LEU A1329 1 O TRP A1327 N ILE A1307 SHEET 1 AA2 4 LYS A1421 VAL A1422 0 SHEET 2 AA2 4 LYS A1398 LEU A1401 1 N VAL A1399 O LYS A1421 SHEET 3 AA2 4 HIS A1436 SER A1439 1 O HIS A1436 N ILE A1400 SHEET 4 AA2 4 TYR A1462 ARG A1465 1 O LEU A1464 N LEU A1437 CRYST1 48.748 46.074 55.948 90.00 102.53 90.00 P 1 21 1 2 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 0.020514 0.000000 0.004559 0.00000 SCALE2 0.000000 0.021704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018310 0.00000 CONECT 1861 1862 1863 1864 CONECT 1862 1861 CONECT 1863 1861 CONECT 1864 1861 1865 CONECT 1865 1864 1866 1867 CONECT 1866 1865 CONECT 1867 1865 MASTER 279 0 1 12 8 0 0 6 2243 1 7 18 END