HEADER ISOMERASE/DNA 15-MAR-18 6CQI TITLE 2.42A CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TOPOISOMERASE I TITLE 2 IN COMPLEX WITH AN OLIGONUCLEOTIDE MTS2-11 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA TOPOISOMERASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA TOPOISOMERASE I,OMEGA-PROTEIN,RELAXING ENZYME,SWIVELASE, COMPND 5 UNTWISTING ENZYME; COMPND 6 EC: 5.99.1.2; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(P*TP*TP*CP*CP*GP*CP*TP*TP*GP*A)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: TOPA, RV3646C, MTCY15C10.06; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: T7 EXPRESS CRYSTAL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-HIS6-MOCR TEV-LIC; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 15 ORGANISM_TAXID: 1773 KEYWDS MYCOBACTERIUM TUBERCULOSIS, TOPOISOMERASE I, CO-CRYSTAL, COMPLEX WITH KEYWDS 2 OLIGONUCLEOTIDE, ISOMERASE-DNA COMPLEX, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.CAO,A.THIRUNAVUKKARASU,K.TAN,Y.-C.TSE-DINH REVDAT 5 04-OCT-23 6CQI 1 REMARK REVDAT 4 04-DEC-19 6CQI 1 REMARK REVDAT 3 05-SEP-18 6CQI 1 JRNL REVDAT 2 04-JUL-18 6CQI 1 JRNL REVDAT 1 30-MAY-18 6CQI 0 JRNL AUTH N.CAO,K.TAN,T.ANNAMALAI,A.JOACHIMIAK,Y.C.TSE-DINH JRNL TITL INVESTIGATING MYCOBACTERIAL TOPOISOMERASE I MECHANISM FROM JRNL TITL 2 THE ANALYSIS OF METAL AND DNA SUBSTRATE INTERACTIONS AT THE JRNL TITL 3 ACTIVE SITE. JRNL REF NUCLEIC ACIDS RES. V. 46 7296 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29905859 JRNL DOI 10.1093/NAR/GKY492 REMARK 2 REMARK 2 RESOLUTION. 2.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 29706 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1484 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 46.8542 - 5.3804 0.98 2717 144 0.1943 0.2336 REMARK 3 2 5.3804 - 4.2715 0.99 2637 161 0.1893 0.2238 REMARK 3 3 4.2715 - 3.7318 1.00 2618 156 0.1916 0.2255 REMARK 3 4 3.7318 - 3.3907 0.98 2609 141 0.2301 0.2960 REMARK 3 5 3.3907 - 3.1477 0.99 2601 141 0.2610 0.3651 REMARK 3 6 3.1477 - 2.9622 0.99 2644 117 0.2778 0.3745 REMARK 3 7 2.9622 - 2.8138 0.99 2605 140 0.2781 0.3140 REMARK 3 8 2.8138 - 2.6914 0.98 2608 114 0.3057 0.3750 REMARK 3 9 2.6914 - 2.5878 0.98 2558 143 0.3098 0.3643 REMARK 3 10 2.5878 - 2.4985 0.93 2418 116 0.3118 0.3890 REMARK 3 11 2.4985 - 2.4204 0.83 2207 111 0.3284 0.3137 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.90 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 : 0.004 5377 REMARK 3 ANGLE : 0.656 7360 REMARK 3 CHIRALITY : 0.042 845 REMARK 3 PLANARITY : 0.004 936 REMARK 3 DIHEDRAL : 13.538 3183 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 16 THROUGH 211 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.5421 1.2537 54.8104 REMARK 3 T TENSOR REMARK 3 T11: 0.4389 T22: 0.4679 REMARK 3 T33: 0.3508 T12: 0.0216 REMARK 3 T13: 0.0239 T23: 0.0205 REMARK 3 L TENSOR REMARK 3 L11: 1.0229 L22: 1.7410 REMARK 3 L33: 4.7943 L12: -0.4666 REMARK 3 L13: 0.3063 L23: -0.8743 REMARK 3 S TENSOR REMARK 3 S11: -0.1017 S12: -0.2428 S13: -0.1363 REMARK 3 S21: 0.1881 S22: 0.2989 S23: 0.2476 REMARK 3 S31: -0.0059 S32: -0.7805 S33: -0.1677 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 212 THROUGH 573 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3819 -6.7035 20.6018 REMARK 3 T TENSOR REMARK 3 T11: 0.8906 T22: 0.9649 REMARK 3 T33: 0.5111 T12: -0.2602 REMARK 3 T13: -0.0374 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 2.1315 L22: 1.5859 REMARK 3 L33: 5.7737 L12: 0.8811 REMARK 3 L13: -1.4453 L23: -0.9935 REMARK 3 S TENSOR REMARK 3 S11: -0.2835 S12: 0.4765 S13: -0.3483 REMARK 3 S21: -0.6066 S22: 0.2040 S23: 0.1541 REMARK 3 S31: 1.1629 S32: -1.7822 S33: 0.1249 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 574 THROUGH 704 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.5403 11.6765 28.3251 REMARK 3 T TENSOR REMARK 3 T11: 0.7332 T22: 0.5119 REMARK 3 T33: 0.5137 T12: -0.0831 REMARK 3 T13: 0.1442 T23: -0.1428 REMARK 3 L TENSOR REMARK 3 L11: 1.3379 L22: 3.2116 REMARK 3 L33: 7.7469 L12: -0.3343 REMARK 3 L13: 0.6320 L23: -3.5240 REMARK 3 S TENSOR REMARK 3 S11: 0.1182 S12: 0.2354 S13: 0.1650 REMARK 3 S21: -0.2481 S22: -0.2090 S23: -0.3787 REMARK 3 S31: -0.4715 S32: 0.8292 S33: 0.0847 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.7776 9.1135 48.5601 REMARK 3 T TENSOR REMARK 3 T11: 0.8860 T22: 0.7850 REMARK 3 T33: 0.4892 T12: 0.1530 REMARK 3 T13: 0.2598 T23: -0.0185 REMARK 3 L TENSOR REMARK 3 L11: 7.1102 L22: 5.9503 REMARK 3 L33: 4.2810 L12: 3.5823 REMARK 3 L13: 0.0893 L23: -0.8531 REMARK 3 S TENSOR REMARK 3 S11: 1.0713 S12: -0.5709 S13: 1.0982 REMARK 3 S21: 1.2961 S22: -0.3335 S23: 1.1438 REMARK 3 S31: -1.8433 S32: -1.7202 S33: -0.4246 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 6CQI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1000233224. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID 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 : SILICON 111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29799 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.420 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.64100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 5UKT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM PHOSPHATE DIBASIC, 20% REMARK 280 W/V POLYETHYLENE GLYCOL 3,350, PH 8.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 289K 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 22.48850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL 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 SER A -1 REMARK 465 ASN A 0 REMARK 465 ALA A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 PRO A 4 REMARK 465 LYS A 5 REMARK 465 THR A 6 REMARK 465 LYS A 7 REMARK 465 GLY A 8 REMARK 465 ARG A 9 REMARK 465 GLY A 10 REMARK 465 SER A 11 REMARK 465 GLY A 12 REMARK 465 GLY A 13 REMARK 465 ASN A 14 REMARK 465 GLY A 15 REMARK 465 ALA A 234 REMARK 465 ALA A 235 REMARK 465 PRO A 236 REMARK 465 ASN A 384 REMARK 465 DC B 12 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 SER A 16 OG REMARK 470 ARG A 18 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 30 NE CZ NH1 NH2 REMARK 470 LYS A 31 CD CE NZ REMARK 470 SER A 38 OG REMARK 470 ASP A 78 CG OD1 OD2 REMARK 470 GLU A 88 CG CD OE1 OE2 REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 ARG A 130 CD NE CZ NH1 NH2 REMARK 470 HIS A 139 ND1 CD2 CE1 NE2 REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 470 ILE A 141 CG1 CG2 CD1 REMARK 470 ILE A 146 CG1 CG2 CD1 REMARK 470 ARG A 147 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 151 CG CD OE1 OE2 REMARK 470 ASP A 155 CG OD1 OD2 REMARK 470 LYS A 189 CE NZ REMARK 470 ILE A 221 CG1 CG2 CD1 REMARK 470 LEU A 222 CG CD1 CD2 REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 VAL A 229 CG1 CG2 REMARK 470 ASP A 231 CG OD1 OD2 REMARK 470 PRO A 237 CG CD REMARK 470 LEU A 243 CG CD1 CD2 REMARK 470 ARG A 250 NE CZ NH1 NH2 REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 ASP A 267 CG OD1 OD2 REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 ILE A 270 CG1 CG2 CD1 REMARK 470 LEU A 284 CG CD1 CD2 REMARK 470 GLN A 288 CG CD OE1 NE2 REMARK 470 LEU A 289 CG CD1 CD2 REMARK 470 GLU A 295 CD OE1 OE2 REMARK 470 LYS A 297 CG CD CE NZ REMARK 470 GLU A 352 CG CD OE1 OE2 REMARK 470 ASN A 356 OD1 ND2 REMARK 470 ARG A 363 NH1 NH2 REMARK 470 ASP A 368 CG OD1 OD2 REMARK 470 GLU A 369 CG CD OE1 OE2 REMARK 470 TYR A 370 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 376 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 377 CG CD OE1 NE2 REMARK 470 THR A 379 OG1 CG2 REMARK 470 LYS A 381 CG CD CE NZ REMARK 470 VAL A 382 CG1 CG2 REMARK 470 LYS A 383 CG CD CE NZ REMARK 470 GLN A 386 CG CD OE1 NE2 REMARK 470 GLU A 387 CG CD OE1 OE2 REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 ASP A 403 CG OD1 OD2 REMARK 470 ARG A 406 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 410 CG OD1 OD2 REMARK 470 ASN A 413 CG OD1 ND2 REMARK 470 ARG A 436 CG CD NE CZ NH1 NH2 REMARK 470 MET A 438 CG SD CE REMARK 470 ARG A 443 CZ NH1 NH2 REMARK 470 MET A 447 SD CE REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 LEU A 462 CD1 CD2 REMARK 470 LYS A 469 NZ REMARK 470 VAL A 475 CG1 CG2 REMARK 470 VAL A 479 CG1 CG2 REMARK 470 GLU A 482 CG CD OE1 OE2 REMARK 470 GLU A 487 CG CD OE1 OE2 REMARK 470 ARG A 488 NE CZ NH1 NH2 REMARK 470 ARG A 489 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 490 CD1 CD2 REMARK 470 HIS A 492 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 493 CG CD1 CD2 REMARK 470 GLN A 497 CG CD OE1 NE2 REMARK 470 ARG A 498 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 499 CG CD1 CD2 REMARK 470 ASP A 500 CG OD1 OD2 REMARK 470 ILE A 501 CG1 CG2 CD1 REMARK 470 GLU A 503 CG CD OE1 OE2 REMARK 470 LYS A 553 CG CD CE NZ REMARK 470 VAL A 615 CG1 CG2 REMARK 470 SER A 622 OG REMARK 470 LYS A 627 CG CD CE NZ REMARK 470 GLU A 634 CG CD OE1 OE2 REMARK 470 ASP A 637 CG OD1 OD2 REMARK 470 ARG A 639 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 640 OE1 OE2 REMARK 470 SER A 643 OG REMARK 470 LYS A 645 CG CD CE NZ REMARK 470 LEU A 669 CG CD1 CD2 REMARK 470 THR A 674 OG1 CG2 REMARK 470 GLU A 676 CG CD OE1 OE2 REMARK 470 SER A 685 OG REMARK 470 ASP A 686 CG OD1 OD2 REMARK 470 ILE A 688 CG1 CG2 CD1 REMARK 470 GLU A 700 CD OE1 OE2 REMARK 470 THR A 704 OG1 CG2 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 OD2 ASP A 649 NH1 ARG A 668 1.90 REMARK 500 CB ASP A 649 NH1 ARG A 668 2.04 REMARK 500 OH TYR A 378 O SER A 430 2.07 REMARK 500 O ASP A 231 N ASP A 233 2.14 REMARK 500 O ARG A 436 OG1 THR A 463 2.16 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 ASP A 612 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 LEU A 684 CB - CG - CD2 ANGL. DEV. = -13.9 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 HIS A 139 -82.07 -91.45 REMARK 500 VAL A 186 -77.95 -107.79 REMARK 500 ASP A 220 -158.38 -157.68 REMARK 500 SER A 228 -64.45 -103.17 REMARK 500 SER A 230 -94.22 -67.81 REMARK 500 PRO A 232 24.17 -50.32 REMARK 500 THR A 244 -41.25 -131.11 REMARK 500 LYS A 265 41.90 33.67 REMARK 500 LEU A 284 91.95 -162.91 REMARK 500 TYR A 378 79.39 -112.27 REMARK 500 ARG A 380 -157.57 -93.32 REMARK 500 GLN A 386 87.13 -154.00 REMARK 500 ASN A 413 74.19 -151.90 REMARK 500 GLN A 431 50.88 -112.40 REMARK 500 HIS A 450 6.31 -159.15 REMARK 500 HIS A 613 128.50 -179.60 REMARK 500 LEU A 646 -77.59 -103.69 REMARK 500 ASP A 649 -163.47 -79.22 REMARK 500 ASP A 673 -74.82 -76.33 REMARK 500 THR A 674 40.75 -77.30 REMARK 500 ALA A 682 102.52 -162.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 806 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D5H RELATED DB: PDB REMARK 900 APO FORM DBREF 6CQI A 2 704 UNP P9WG49 TOP1_MYCTU 2 704 DBREF 6CQI B 2 12 PDB 6CQI 6CQI 2 12 SEQADV 6CQI SER A -1 UNP P9WG49 EXPRESSION TAG SEQADV 6CQI ASN A 0 UNP P9WG49 EXPRESSION TAG SEQADV 6CQI ALA A 1 UNP P9WG49 EXPRESSION TAG SEQRES 1 A 706 SER ASN ALA ALA ASP PRO LYS THR LYS GLY ARG GLY SER SEQRES 2 A 706 GLY GLY ASN GLY SER GLY ARG ARG LEU VAL ILE VAL GLU SEQRES 3 A 706 SER PRO THR LYS ALA ARG LYS LEU ALA SER TYR LEU GLY SEQRES 4 A 706 SER GLY TYR ILE VAL GLU SER SER ARG GLY HIS ILE ARG SEQRES 5 A 706 ASP LEU PRO ARG ALA ALA SER ASP VAL PRO ALA LYS TYR SEQRES 6 A 706 LYS SER GLN PRO TRP ALA ARG LEU GLY VAL ASN VAL ASP SEQRES 7 A 706 ALA ASP PHE GLU PRO LEU TYR ILE ILE SER PRO GLU LYS SEQRES 8 A 706 ARG SER THR VAL SER GLU LEU ARG GLY LEU LEU LYS ASP SEQRES 9 A 706 VAL ASP GLU LEU TYR LEU ALA THR ASP GLY ASP ARG GLU SEQRES 10 A 706 GLY GLU ALA ILE ALA TRP HIS LEU LEU GLU THR LEU LYS SEQRES 11 A 706 PRO ARG ILE PRO VAL LYS ARG MET VAL PHE HIS GLU ILE SEQRES 12 A 706 THR GLU PRO ALA ILE ARG ALA ALA ALA GLU HIS PRO ARG SEQRES 13 A 706 ASP LEU ASP ILE ASP LEU VAL ASP ALA GLN GLU THR ARG SEQRES 14 A 706 ARG ILE LEU ASP ARG LEU TYR GLY TYR GLU VAL SER PRO SEQRES 15 A 706 VAL LEU TRP LYS LYS VAL ALA PRO LYS LEU SER ALA GLY SEQRES 16 A 706 ARG VAL GLN SER VAL ALA THR ARG ILE ILE VAL ALA ARG SEQRES 17 A 706 GLU ARG ASP ARG MET ALA PHE ARG SER ALA ALA TYR TRP SEQRES 18 A 706 ASP ILE LEU ALA LYS LEU ASP ALA SER VAL SER ASP PRO SEQRES 19 A 706 ASP ALA ALA PRO PRO THR PHE SER ALA ARG LEU THR ALA SEQRES 20 A 706 VAL ALA GLY ARG ARG VAL ALA THR GLY ARG ASP PHE ASP SEQRES 21 A 706 SER LEU GLY THR LEU ARG LYS GLY ASP GLU VAL ILE VAL SEQRES 22 A 706 LEU ASP GLU GLY SER ALA THR ALA LEU ALA ALA GLY LEU SEQRES 23 A 706 ASP GLY THR GLN LEU THR VAL ALA SER ALA GLU GLU LYS SEQRES 24 A 706 PRO TYR ALA ARG ARG PRO TYR PRO PRO PHE MET THR SER SEQRES 25 A 706 THR LEU GLN GLN GLU ALA SER ARG LYS LEU ARG PHE SER SEQRES 26 A 706 ALA GLU ARG THR MET SER ILE ALA GLN ARG LEU TYR GLU SEQRES 27 A 706 ASN GLY TYR ILE THR TYR MET ARG THR ASP SER THR THR SEQRES 28 A 706 LEU SER GLU SER ALA ILE ASN ALA ALA ARG THR GLN ALA SEQRES 29 A 706 ARG GLN LEU TYR GLY ASP GLU TYR VAL ALA PRO ALA PRO SEQRES 30 A 706 ARG GLN TYR THR ARG LYS VAL LYS ASN ALA GLN GLU ALA SEQRES 31 A 706 HIS GLU ALA ILE ARG PRO ALA GLY GLU THR PHE ALA THR SEQRES 32 A 706 PRO ASP ALA VAL ARG ARG GLU LEU ASP GLY PRO ASN ILE SEQRES 33 A 706 ASP ASP PHE ARG LEU TYR GLU LEU ILE TRP GLN ARG THR SEQRES 34 A 706 VAL ALA SER GLN MET ALA ASP ALA ARG GLY MET THR LEU SEQRES 35 A 706 SER LEU ARG ILE THR GLY MET SER GLY HIS GLN GLU VAL SEQRES 36 A 706 VAL PHE SER ALA THR GLY ARG THR LEU THR PHE PRO GLY SEQRES 37 A 706 PHE LEU LYS ALA TYR VAL GLU THR VAL ASP GLU LEU VAL SEQRES 38 A 706 GLY GLY GLU ALA ASP ASP ALA GLU ARG ARG LEU PRO HIS SEQRES 39 A 706 LEU THR PRO GLY GLN ARG LEU ASP ILE VAL GLU LEU THR SEQRES 40 A 706 PRO ASP GLY HIS ALA THR ASN PRO PRO ALA ARG TYR THR SEQRES 41 A 706 GLU ALA SER LEU VAL LYS ALA LEU GLU GLU LEU GLY ILE SEQRES 42 A 706 GLY ARG PRO SER THR TYR SER SER ILE ILE LYS THR ILE SEQRES 43 A 706 GLN ASP ARG GLY TYR VAL HIS LYS LYS GLY SER ALA LEU SEQRES 44 A 706 VAL PRO SER TRP VAL ALA PHE ALA VAL THR GLY LEU LEU SEQRES 45 A 706 GLU GLN HIS PHE GLY ARG LEU VAL ASP TYR ASP PHE THR SEQRES 46 A 706 ALA ALA MET GLU ASP GLU LEU ASP GLU ILE ALA ALA GLY SEQRES 47 A 706 ASN GLU ARG ARG THR ASN TRP LEU ASN ASN PHE TYR PHE SEQRES 48 A 706 GLY GLY ASP HIS GLY VAL PRO ASP SER VAL ALA ARG SER SEQRES 49 A 706 GLY GLY LEU LYS LYS LEU VAL GLY ILE ASN LEU GLU GLY SEQRES 50 A 706 ILE ASP ALA ARG GLU VAL ASN SER ILE LYS LEU PHE ASP SEQRES 51 A 706 ASP THR HIS GLY ARG PRO ILE TYR VAL ARG VAL GLY LYS SEQRES 52 A 706 ASN GLY PRO TYR LEU GLU ARG LEU VAL ALA GLY ASP THR SEQRES 53 A 706 GLY GLU PRO THR PRO GLN ARG ALA ASN LEU SER ASP SER SEQRES 54 A 706 ILE THR PRO ASP GLU LEU THR LEU GLN VAL ALA GLU GLU SEQRES 55 A 706 LEU PHE ALA THR SEQRES 1 B 11 DT DT DC DC DG DC DT DT DG DA DC HET FMT A 801 3 HET FMT A 802 3 HET GOL A 803 6 HET ACT A 804 4 HET ACT A 805 4 HET ACT A 806 4 HETNAM FMT FORMIC ACID HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FMT 2(C H2 O2) FORMUL 5 GOL C3 H8 O3 FORMUL 6 ACT 3(C2 H3 O2 1-) FORMUL 9 HOH *18(H2 O) HELIX 1 AA1 SER A 25 GLY A 37 1 13 HELIX 2 AA2 ALA A 55 VAL A 59 5 5 HELIX 3 AA3 PRO A 60 LYS A 64 5 5 HELIX 4 AA4 LYS A 89 LEU A 100 1 12 HELIX 5 AA5 LYS A 101 VAL A 103 5 3 HELIX 6 AA6 ASP A 113 LYS A 128 1 16 HELIX 7 AA7 THR A 142 GLU A 151 1 10 HELIX 8 AA8 ASP A 157 VAL A 186 1 30 HELIX 9 AA9 VAL A 195 ALA A 212 1 18 HELIX 10 AB1 THR A 253 PHE A 257 5 5 HELIX 11 AB2 ASP A 273 ALA A 282 1 10 HELIX 12 AB3 MET A 308 ARG A 321 1 14 HELIX 13 AB4 SER A 323 ASN A 337 1 15 HELIX 14 AB5 SER A 351 GLY A 367 1 17 HELIX 15 AB6 THR A 401 LEU A 409 1 9 HELIX 16 AB7 ILE A 414 SER A 430 1 17 HELIX 17 AB8 PRO A 465 ALA A 470 5 6 HELIX 18 AB9 THR A 518 LEU A 529 1 12 HELIX 19 AC1 THR A 536 ARG A 547 1 12 HELIX 20 AC2 SER A 560 PHE A 574 1 15 HELIX 21 AC3 GLY A 575 ASP A 579 5 5 HELIX 22 AC4 ASP A 581 ALA A 595 1 15 HELIX 23 AC5 THR A 601 GLY A 610 1 10 HELIX 24 AC6 GLY A 624 LEU A 633 1 10 HELIX 25 AC7 ASP A 637 ASN A 642 1 6 HELIX 26 AC8 THR A 694 THR A 704 1 11 SHEET 1 AA1 4 TYR A 40 SER A 44 0 SHEET 2 AA1 4 ARG A 19 VAL A 23 1 N ARG A 19 O ILE A 41 SHEET 3 AA1 4 GLU A 105 LEU A 108 1 O TYR A 107 N LEU A 20 SHEET 4 AA1 4 VAL A 133 ARG A 135 1 O LYS A 134 N LEU A 106 SHEET 1 AA2 2 ARG A 50 ASP A 51 0 SHEET 2 AA2 2 ILE A 84 ILE A 85 -1 O ILE A 84 N ASP A 51 SHEET 1 AA3 2 VAL A 73 ASN A 74 0 SHEET 2 AA3 2 GLU A 80 PRO A 81 -1 O GLU A 80 N ASN A 74 SHEET 1 AA4 7 ALA A 217 LEU A 225 0 SHEET 2 AA4 7 PHE A 239 VAL A 246 -1 O PHE A 239 N LEU A 225 SHEET 3 AA4 7 GLN A 451 THR A 461 -1 O VAL A 454 N THR A 244 SHEET 4 AA4 7 MET A 438 SER A 448 -1 N LEU A 440 O GLY A 459 SHEET 5 AA4 7 GLN A 288 PRO A 298 -1 N THR A 290 O THR A 445 SHEET 6 AA4 7 ARG A 498 ALA A 510 -1 O LEU A 499 N LEU A 289 SHEET 7 AA4 7 ALA A 217 LEU A 225 -1 N ASP A 220 O ASP A 507 SHEET 1 AA5 2 ARG A 250 VAL A 251 0 SHEET 2 AA5 2 VAL A 269 ILE A 270 1 O ILE A 270 N ARG A 250 SHEET 1 AA6 2 VAL A 550 LYS A 553 0 SHEET 2 AA6 2 ALA A 556 PRO A 559 -1 O VAL A 558 N HIS A 551 SHEET 1 AA7 4 SER A 643 ASP A 648 0 SHEET 2 AA7 4 PRO A 654 GLY A 660 -1 O VAL A 657 N ILE A 644 SHEET 3 AA7 4 GLY A 663 GLY A 672 -1 O TYR A 665 N ARG A 658 SHEET 4 AA7 4 GLY A 675 ASN A 683 -1 O GLN A 680 N ARG A 668 CISPEP 1 GLU A 676 PRO A 677 0 -3.50 SITE 1 AC1 3 ASP A 51 LEU A 52 ARG A 54 SITE 1 AC2 4 HIS A 48 ARG A 50 ASP A 51 GLN A 164 SITE 1 AC3 6 ARG A 576 PHE A 582 TRP A 603 PHE A 607 SITE 2 AC3 6 SER A 618 VAL A 619 SITE 1 AC4 4 ARG A 50 TYR A 83 TRP A 121 GLU A 125 SITE 1 AC5 2 ASP A 76 LYS A 626 SITE 1 AC6 2 SER A 317 LYS A 552 CRYST1 68.777 44.977 129.229 90.00 90.60 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 0.014540 0.000000 0.000152 0.00000 SCALE2 0.000000 0.022234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007739 0.00000