HEADER DNA BINDING PROTEIN 06-DEC-21 7QFN TITLE HUMAN TOPOISOMERASE II BETA ATPASE ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE 2-BETA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA TOPOISOMERASE II,BETA ISOZYME; COMPND 5 EC: 5.6.2.2; 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: TOP2B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA TOPOISOMERASE II BETA, HUMAN, ATPASE DOMAIN, TOP2B, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.M.LING,A.BASLE,I.G.COWELL,T.R.BLOWER,C.A.AUSTIN REVDAT 4 19-JUN-24 7QFN 1 REMARK REVDAT 3 01-MAR-23 7QFN 1 CAVEAT SOURCE REMARK HELIX REVDAT 3 2 1 SHEET LINK ATOM REVDAT 2 30-NOV-22 7QFN 1 JRNL REVDAT 1 25-MAY-22 7QFN 0 JRNL AUTH E.M.LING,A.BASLE,I.G.COWELL,B.VAN DEN BERG,T.R.BLOWER, JRNL AUTH 2 C.A.AUSTIN JRNL TITL A COMPREHENSIVE STRUCTURAL ANALYSIS OF THE ATPASE DOMAIN OF JRNL TITL 2 HUMAN DNA TOPOISOMERASE II BETA BOUND TO AMPPNP, ADP, AND JRNL TITL 3 THE BISDIOXOPIPERAZINE, ICRF193. JRNL REF STRUCTURE V. 30 1129 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 35660158 JRNL DOI 10.1016/J.STR.2022.05.009 REMARK 2 REMARK 2 RESOLUTION. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 89.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12583 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.292 REMARK 3 FREE R VALUE TEST SET COUNT : 540 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2886 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.79600 REMARK 3 B22 (A**2) : 1.79600 REMARK 3 B33 (A**2) : -5.82600 REMARK 3 B12 (A**2) : 0.89800 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): 1.673 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.340 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.300 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.249 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2981 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2747 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4024 ; 1.935 ; 1.646 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6419 ; 0.641 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 357 ; 9.256 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 11 ; 9.812 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 549 ;18.251 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 448 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3270 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 579 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 617 ; 0.236 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 76 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1443 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 89 ; 0.167 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.004 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1437 ; 4.398 ; 4.574 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1436 ; 4.396 ; 4.575 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1791 ; 6.242 ; 6.846 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1792 ; 6.243 ; 6.847 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1544 ; 5.215 ; 5.050 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1536 ; 5.179 ; 5.044 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2233 ; 7.576 ; 7.362 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2222 ; 7.557 ; 7.353 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 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 47 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1147 28.7573 15.0194 REMARK 3 T TENSOR REMARK 3 T11: 0.0260 T22: 0.0611 REMARK 3 T33: 0.0424 T12: 0.0169 REMARK 3 T13: 0.0095 T23: 0.0195 REMARK 3 L TENSOR REMARK 3 L11: 1.2156 L22: 1.5242 REMARK 3 L33: 1.3959 L12: 0.6744 REMARK 3 L13: 0.3695 L23: 0.1786 REMARK 3 S TENSOR REMARK 3 S11: 0.0017 S12: 0.0277 S13: 0.1795 REMARK 3 S21: -0.0513 S22: -0.0172 S23: 0.1169 REMARK 3 S31: -0.1433 S32: 0.0543 S33: 0.0155 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7QFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119289. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-21 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 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 : DIALS, XIA2 REMARK 200 DATA SCALING SOFTWARE : POINTLESS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12596 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 REMARK 200 RESOLUTION RANGE LOW (A) : 89.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, MOLREP REMARK 200 STARTING MODEL: D_1292119290 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULPHATE, 0.1 M BIS REMARK 280 TRIS (PH 5.5), 25 % W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+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 -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 0.00000 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 0.00000 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 0.00000 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -112.0 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A 42 REMARK 465 ASN A 43 REMARK 465 ALA A 44 REMARK 465 SER A 45 REMARK 465 VAL A 46 REMARK 465 ASP A 169 REMARK 465 ASP A 170 REMARK 465 GLU A 171 REMARK 465 LYS A 172 REMARK 465 LYS A 173 REMARK 465 VAL A 356 REMARK 465 VAL A 357 REMARK 465 LYS A 358 REMARK 465 LYS A 359 REMARK 465 LYS A 360 REMARK 465 ASN A 361 REMARK 465 LYS A 362 REMARK 465 ALA A 363 REMARK 465 GLY A 364 REMARK 465 VAL A 365 REMARK 465 SER A 366 REMARK 465 ILE A 423 REMARK 465 VAL A 424 REMARK 465 GLU A 425 REMARK 465 SER A 426 REMARK 465 ILE A 427 REMARK 465 LEU A 428 REMARK 465 ASN A 429 REMARK 465 TRP A 430 REMARK 465 VAL A 431 REMARK 465 LYS A 432 REMARK 465 PHE A 433 REMARK 465 LYS A 434 REMARK 465 ALA A 435 REMARK 465 GLN A 436 REMARK 465 THR A 437 REMARK 465 GLN A 438 REMARK 465 LEU A 439 REMARK 465 ASN A 440 REMARK 465 LYS A 441 REMARK 465 LYS A 442 REMARK 465 CYS A 443 REMARK 465 SER A 444 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H THR A 194 O THR A 234 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 47 CD GLU A 47 OE1 0.103 REMARK 500 GLU A 196 CD GLU A 196 OE2 0.087 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 ARG A 267 CG - CD - NE ANGL. DEV. = -12.7 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 ASP A 64 -60.60 -9.80 REMARK 500 ASN A 137 -157.66 -114.23 REMARK 500 ARG A 178 -43.81 -168.29 REMARK 500 ASN A 310 -165.16 -167.10 REMARK 500 LYS A 322 47.60 -143.61 REMARK 500 PHE A 324 123.48 -37.43 REMARK 500 LYS A 394 14.92 58.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 419 ASN A 420 -148.64 REMARK 500 ASN A 420 CYS A 421 149.89 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 ARG A 267 0.13 SIDE CHAIN 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 A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 103 OE2 REMARK 620 2 ASN A 107 OD1 125.3 REMARK 620 3 ADP A 501 O3B 150.1 81.5 REMARK 620 4 ADP A 501 O2A 105.1 80.7 62.6 REMARK 620 N 1 2 3 DBREF 7QFN A 45 444 UNP Q02880 TOP2B_HUMAN 50 449 SEQADV 7QFN SER A 42 UNP Q02880 EXPRESSION TAG SEQADV 7QFN ASN A 43 UNP Q02880 EXPRESSION TAG SEQADV 7QFN ALA A 44 UNP Q02880 EXPRESSION TAG SEQRES 1 A 403 SER ASN ALA SER VAL GLU ARG VAL TYR GLN LYS LYS THR SEQRES 2 A 403 GLN LEU GLU HIS ILE LEU LEU ARG PRO ASP THR TYR ILE SEQRES 3 A 403 GLY SER VAL GLU PRO LEU THR GLN PHE MET TRP VAL TYR SEQRES 4 A 403 ASP GLU ASP VAL GLY MET ASN CYS ARG GLU VAL THR PHE SEQRES 5 A 403 VAL PRO GLY LEU TYR LYS ILE PHE ASP GLU ILE LEU VAL SEQRES 6 A 403 ASN ALA ALA ASP ASN LYS GLN ARG ASP LYS ASN MET THR SEQRES 7 A 403 CYS ILE LYS VAL SER ILE ASP PRO GLU SER ASN ILE ILE SEQRES 8 A 403 SER ILE TRP ASN ASN GLY LYS GLY ILE PRO VAL VAL GLU SEQRES 9 A 403 HIS LYS VAL GLU LYS VAL TYR VAL PRO ALA LEU ILE PHE SEQRES 10 A 403 GLY GLN LEU LEU THR SER SER ASN TYR ASP ASP ASP GLU SEQRES 11 A 403 LYS LYS VAL THR GLY GLY ARG ASN GLY TYR GLY ALA LYS SEQRES 12 A 403 LEU CYS ASN ILE PHE SER THR LYS PHE THR VAL GLU THR SEQRES 13 A 403 ALA CYS LYS GLU TYR LYS HIS SER PHE LYS GLN THR TRP SEQRES 14 A 403 MET ASN ASN MET MET LYS THR SER GLU ALA LYS ILE LYS SEQRES 15 A 403 HIS PHE ASP GLY GLU ASP TYR THR CYS ILE THR PHE GLN SEQRES 16 A 403 PRO ASP LEU SER LYS PHE LYS MET GLU LYS LEU ASP LYS SEQRES 17 A 403 ASP ILE VAL ALA LEU MET THR ARG ARG ALA TYR ASP LEU SEQRES 18 A 403 ALA GLY SER CYS ARG GLY VAL LYS VAL MET PHE ASN GLY SEQRES 19 A 403 LYS LYS LEU PRO VAL ASN GLY PHE ARG SER TYR VAL ASP SEQRES 20 A 403 LEU TYR VAL LYS ASP LYS LEU ASP GLU THR GLY VAL ALA SEQRES 21 A 403 LEU LYS VAL ILE HIS GLU LEU ALA ASN GLU ARG TRP ASP SEQRES 22 A 403 VAL CYS LEU THR LEU SER GLU LYS GLY PHE GLN GLN ILE SEQRES 23 A 403 SER PHE VAL ASN SER ILE ALA THR THR LYS GLY GLY ARG SEQRES 24 A 403 HIS VAL ASP TYR VAL VAL ASP GLN VAL VAL GLY LYS LEU SEQRES 25 A 403 ILE GLU VAL VAL LYS LYS LYS ASN LYS ALA GLY VAL SER SEQRES 26 A 403 VAL LYS PRO PHE GLN VAL LYS ASN HIS ILE TRP VAL PHE SEQRES 27 A 403 ILE ASN CYS LEU ILE GLU ASN PRO THR PHE ASP SER GLN SEQRES 28 A 403 THR LYS GLU ASN MET THR LEU GLN PRO LYS SER PHE GLY SEQRES 29 A 403 SER LYS CYS GLN LEU SER GLU LYS PHE PHE LYS ALA ALA SEQRES 30 A 403 SER ASN CYS GLY ILE VAL GLU SER ILE LEU ASN TRP VAL SEQRES 31 A 403 LYS PHE LYS ALA GLN THR GLN LEU ASN LYS LYS CYS SER HET ADP A 501 37 HET SO4 A 502 5 HET SO4 A 503 5 HET MG A 504 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 MG MG 2+ FORMUL 6 HOH *13(H2 O) HELIX 1 AA1 THR A 54 ARG A 62 1 9 HELIX 2 AA2 ARG A 62 GLY A 68 1 7 HELIX 3 AA3 VAL A 94 ASP A 115 1 22 HELIX 4 AA4 VAL A 153 GLN A 160 1 8 HELIX 5 AA5 GLY A 182 PHE A 189 1 8 HELIX 6 AA6 LYS A 200 TYR A 202 5 3 HELIX 7 AA7 LEU A 239 LYS A 243 5 5 HELIX 8 AA8 ASP A 248 CYS A 266 1 19 HELIX 9 AA9 GLY A 282 LYS A 292 1 11 HELIX 10 AB1 ARG A 340 GLU A 355 1 16 HELIX 11 AB2 LYS A 368 ASN A 374 1 7 HELIX 12 AB3 GLN A 400 PHE A 404 5 5 HELIX 13 AB4 SER A 411 ALA A 418 1 8 HELIX 14 AB5 SER A 419 CYS A 421 5 3 SHEET 1 AA1 2 LEU A 73 ASP A 81 0 SHEET 2 AA1 2 GLY A 85 PHE A 93 -1 O ASN A 87 N VAL A 79 SHEET 1 AA2 3 LYS A 216 THR A 217 0 SHEET 2 AA2 3 HIS A 204 MET A 211 -1 N MET A 211 O LYS A 216 SHEET 3 AA2 3 LYS A 221 HIS A 224 -1 O LYS A 221 N LYS A 207 SHEET 1 AA3 8 LYS A 216 THR A 217 0 SHEET 2 AA3 8 HIS A 204 MET A 211 -1 N MET A 211 O LYS A 216 SHEET 3 AA3 8 SER A 190 CYS A 199 -1 N THR A 197 O PHE A 206 SHEET 4 AA3 8 TYR A 230 PRO A 237 -1 O THR A 234 N THR A 194 SHEET 5 AA3 8 ILE A 131 ASN A 137 -1 N ASN A 136 O THR A 231 SHEET 6 AA3 8 CYS A 120 ASP A 126 -1 N ASP A 126 O ILE A 131 SHEET 7 AA3 8 LYS A 270 PHE A 273 1 O MET A 272 N VAL A 123 SHEET 8 AA3 8 LYS A 276 LYS A 277 -1 O LYS A 276 N PHE A 273 SHEET 1 AA4 2 GLU A 145 HIS A 146 0 SHEET 2 AA4 2 VAL A 151 TYR A 152 -1 O VAL A 151 N HIS A 146 SHEET 1 AA5 5 ILE A 305 ASN A 310 0 SHEET 2 AA5 5 TRP A 313 LEU A 319 -1 O LEU A 317 N ILE A 305 SHEET 3 AA5 5 ILE A 376 CYS A 382 -1 O PHE A 379 N CYS A 316 SHEET 4 AA5 5 GLN A 325 VAL A 330 1 N PHE A 329 O CYS A 382 SHEET 5 AA5 5 ILE A 333 ALA A 334 -1 O ILE A 333 N VAL A 330 SHEET 1 AA6 2 GLY A 338 GLY A 339 0 SHEET 2 AA6 2 ASN A 396 MET A 397 1 O MET A 397 N GLY A 338 LINK OE2 GLU A 103 MG MG A 504 1555 1555 2.87 LINK OD1 ASN A 107 MG MG A 504 1555 1555 2.07 LINK O3B ADP A 501 MG MG A 504 1555 1555 2.41 LINK O2A ADP A 501 MG MG A 504 1555 1555 1.99 CRYST1 103.021 103.021 66.693 90.00 90.00 120.00 P 3 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 0.009707 0.005604 0.000000 0.00000 SCALE2 0.000000 0.011208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014994 0.00000