HEADER ISOMERASE/DNA 14-MAR-18 6CQ2 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TOPOISOMERASE I IN TITLE 2 COMPLEX WITH OLIGONUCLEOTIDE MTS2-12 AND MAGNESIUM 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_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-HIS6-MOCR TEV-LIC; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 14 ORGANISM_TAXID: 83332 KEYWDS MYCOBACTERIUM TUBERCULOSIS, TOPOISOMERASE I, CO-CRYSTALLIZATION, KEYWDS 2 COMPLEX WITH OLIGONUCLEOTIDE AND MAGNESIUM, ISOMERASE, ISOMERASE-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.CAO,A.THIRUNAVUKKARAUS,K.TAN,Y.-C.TSE-DINH REVDAT 5 13-MAR-24 6CQ2 1 LINK REVDAT 4 04-DEC-19 6CQ2 1 REMARK REVDAT 3 05-SEP-18 6CQ2 1 JRNL REVDAT 2 04-JUL-18 6CQ2 1 JRNL REVDAT 1 30-MAY-18 6CQ2 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. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 15348 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 735 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 37.2823 - 5.1329 0.96 2984 159 0.1649 0.1919 REMARK 3 2 5.1329 - 4.0757 0.98 2915 159 0.1605 0.2365 REMARK 3 3 4.0757 - 3.5610 0.99 2971 124 0.1965 0.2627 REMARK 3 4 3.5610 - 3.2356 0.98 2901 143 0.2391 0.3877 REMARK 3 5 3.2356 - 3.0038 0.96 2842 150 0.2714 0.3294 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.450 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 : 0.002 5623 REMARK 3 ANGLE : 0.418 7682 REMARK 3 CHIRALITY : 0.037 867 REMARK 3 PLANARITY : 0.004 976 REMARK 3 DIHEDRAL : 14.183 3369 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 127 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.5353 4.1452 61.1706 REMARK 3 T TENSOR REMARK 3 T11: 0.4410 T22: 0.4949 REMARK 3 T33: 0.2290 T12: 0.1306 REMARK 3 T13: -0.0561 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 6.5082 L22: 4.9845 REMARK 3 L33: 3.3285 L12: 3.3362 REMARK 3 L13: -1.2336 L23: -0.9436 REMARK 3 S TENSOR REMARK 3 S11: 0.0694 S12: -0.6902 S13: 0.1215 REMARK 3 S21: 0.4356 S22: 0.0622 S23: 0.4654 REMARK 3 S31: -0.1509 S32: -0.4738 S33: -0.1000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 128 THROUGH 211 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.2717 1.7787 46.8423 REMARK 3 T TENSOR REMARK 3 T11: 0.2446 T22: 0.2244 REMARK 3 T33: 0.2773 T12: -0.0165 REMARK 3 T13: -0.1238 T23: -0.0715 REMARK 3 L TENSOR REMARK 3 L11: 1.6965 L22: 2.4947 REMARK 3 L33: 5.5094 L12: -0.4707 REMARK 3 L13: -0.7379 L23: -1.6062 REMARK 3 S TENSOR REMARK 3 S11: 0.0321 S12: -0.0884 S13: -0.1805 REMARK 3 S21: -0.0173 S22: 0.0658 S23: -0.0231 REMARK 3 S31: 0.1492 S32: -0.2087 S33: -0.0756 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 212 THROUGH 351 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.0982 -6.2098 12.9104 REMARK 3 T TENSOR REMARK 3 T11: 0.7344 T22: 0.2988 REMARK 3 T33: 0.3750 T12: 0.0860 REMARK 3 T13: -0.0507 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.9247 L22: 0.2299 REMARK 3 L33: 4.9730 L12: 0.7824 REMARK 3 L13: 0.2194 L23: 0.5759 REMARK 3 S TENSOR REMARK 3 S11: -0.0463 S12: 0.2062 S13: -0.0475 REMARK 3 S21: -0.4004 S22: 0.0473 S23: 0.0679 REMARK 3 S31: 0.0927 S32: -0.3175 S33: 0.0344 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 352 THROUGH 431 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.8370 -10.6289 37.7117 REMARK 3 T TENSOR REMARK 3 T11: 0.7081 T22: 0.6892 REMARK 3 T33: 0.3143 T12: -0.1964 REMARK 3 T13: -0.0124 T23: 0.0894 REMARK 3 L TENSOR REMARK 3 L11: 7.5687 L22: 8.1757 REMARK 3 L33: 7.1467 L12: 1.0828 REMARK 3 L13: 0.2788 L23: 1.8202 REMARK 3 S TENSOR REMARK 3 S11: -0.0597 S12: -0.0215 S13: -0.2990 REMARK 3 S21: 0.3189 S22: 0.0186 S23: 0.4236 REMARK 3 S31: 0.9577 S32: -1.3628 S33: 0.0418 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 432 THROUGH 608 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.1824 -3.1151 21.5748 REMARK 3 T TENSOR REMARK 3 T11: 0.6357 T22: 0.3665 REMARK 3 T33: 0.3089 T12: 0.0298 REMARK 3 T13: 0.0334 T23: -0.0433 REMARK 3 L TENSOR REMARK 3 L11: 1.0737 L22: 1.6291 REMARK 3 L33: 3.1261 L12: 0.7175 REMARK 3 L13: 1.0987 L23: 1.3169 REMARK 3 S TENSOR REMARK 3 S11: 0.0087 S12: -0.0037 S13: -0.1977 REMARK 3 S21: -0.3630 S22: 0.0998 S23: -0.0527 REMARK 3 S31: 0.2057 S32: -0.1708 S33: -0.1262 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 609 THROUGH 643 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.0046 9.1722 36.0241 REMARK 3 T TENSOR REMARK 3 T11: 0.7972 T22: 0.7629 REMARK 3 T33: 0.5734 T12: -0.1535 REMARK 3 T13: 0.2403 T23: -0.1223 REMARK 3 L TENSOR REMARK 3 L11: 2.7097 L22: 6.5574 REMARK 3 L33: 2.2373 L12: 0.8538 REMARK 3 L13: 0.3373 L23: -2.8173 REMARK 3 S TENSOR REMARK 3 S11: -0.0920 S12: 0.1910 S13: 0.2886 REMARK 3 S21: -1.6689 S22: -0.3265 S23: -1.3906 REMARK 3 S31: 0.2313 S32: 1.1346 S33: 0.3747 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 644 THROUGH 704 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.5977 26.6865 14.2433 REMARK 3 T TENSOR REMARK 3 T11: 1.0088 T22: 0.4624 REMARK 3 T33: 0.3637 T12: -0.0766 REMARK 3 T13: 0.1093 T23: 0.0391 REMARK 3 L TENSOR REMARK 3 L11: 5.4686 L22: 6.7507 REMARK 3 L33: 4.7327 L12: 0.0791 REMARK 3 L13: 1.9590 L23: 1.2659 REMARK 3 S TENSOR REMARK 3 S11: 0.2054 S12: -0.1460 S13: 0.3864 REMARK 3 S21: -0.1846 S22: 0.0551 S23: -0.2929 REMARK 3 S31: -0.3718 S32: 0.0561 S33: -0.2514 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 10 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1391 11.0043 48.1965 REMARK 3 T TENSOR REMARK 3 T11: 0.4623 T22: 0.5492 REMARK 3 T33: 0.6033 T12: 0.4448 REMARK 3 T13: -0.0540 T23: 0.1302 REMARK 3 L TENSOR REMARK 3 L11: 3.1856 L22: 4.0483 REMARK 3 L33: 4.7933 L12: 3.5714 REMARK 3 L13: -2.2817 L23: -2.9087 REMARK 3 S TENSOR REMARK 3 S11: 0.0841 S12: -0.7771 S13: 1.0902 REMARK 3 S21: 1.3955 S22: 0.3958 S23: 0.8595 REMARK 3 S31: -2.1576 S32: -1.2334 S33: -0.3065 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 6CQ2 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_1000233207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.9792 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15372 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 37.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.81600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 0.1 M MES NAOH, REMARK 280 30% (W/V) PEG 2000 MME, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 22.34150 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: 3330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 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 388 REMARK 465 DC B 11 REMARK 465 DT B 12 REMARK 465 DT B 13 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 GLU A 88 OE1 OE2 REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 GLU A 151 CG CD OE1 OE2 REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 LYS A 224 CE NZ REMARK 470 ARG A 250 CZ NH1 NH2 REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 ASP A 368 OD1 OD2 REMARK 470 LYS A 381 CE NZ REMARK 470 VAL A 382 CG1 CG2 REMARK 470 LYS A 383 CG CD CE NZ REMARK 470 ASN A 384 CG OD1 ND2 REMARK 470 ASP A 410 CG OD1 OD2 REMARK 470 ASN A 413 CG OD1 ND2 REMARK 470 ASN A 597 CG OD1 ND2 REMARK 470 ARG A 599 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 615 CG1 CG2 REMARK 470 ASP A 617 CG OD1 OD2 REMARK 470 LYS A 627 CG CD CE NZ REMARK 470 GLU A 640 CG CD OE1 OE2 REMARK 470 LYS A 645 CG CD CE NZ REMARK 470 THR A 674 OG1 CG2 REMARK 470 GLU A 676 CG CD OE1 OE2 REMARK 470 ASP A 686 CG OD1 OD2 REMARK 470 THR A 704 OG1 CG2 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 VAL A 23 -163.31 -113.96 REMARK 500 ALA A 109 45.22 -109.31 REMARK 500 LYS A 128 70.32 51.89 REMARK 500 HIS A 139 -72.54 -101.15 REMARK 500 PRO A 153 -161.42 -72.88 REMARK 500 VAL A 186 -84.13 -121.23 REMARK 500 ASP A 231 94.73 -160.03 REMARK 500 THR A 253 -151.35 -122.69 REMARK 500 LEU A 284 -35.85 -145.42 REMARK 500 ARG A 380 -145.42 -120.18 REMARK 500 VAL A 382 -60.46 -166.59 REMARK 500 LYS A 383 68.41 -164.16 REMARK 500 ASN A 384 -78.95 59.60 REMARK 500 ASP A 410 -151.08 -106.26 REMARK 500 SER A 441 88.93 -152.18 REMARK 500 SER A 448 56.90 -97.24 REMARK 500 LYS A 553 65.64 -108.20 REMARK 500 ASN A 597 -69.32 55.55 REMARK 500 SER A 618 -179.45 -69.06 REMARK 500 LEU A 633 38.24 -92.79 REMARK 500 GLU A 634 -45.55 -161.35 REMARK 500 LEU A 646 -73.73 -97.22 REMARK 500 ASP A 686 5.29 -62.71 REMARK 500 LEU A 693 78.64 -103.38 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 801 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 24 OE1 REMARK 620 2 ASP A 111 OD1 104.7 REMARK 620 3 HOH A 903 O 125.3 71.9 REMARK 620 4 DC B 6 O3' 108.1 144.8 78.8 REMARK 620 5 DT B 7 OP1 138.6 93.2 95.6 70.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 233 OD1 REMARK 620 2 ASP A 233 OD2 49.3 REMARK 620 3 ASP A 507 OD1 93.3 78.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 802 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 296 OE1 REMARK 620 2 GLU A 296 OE2 62.6 REMARK 620 3 GLU A 503 OE1 100.1 60.2 REMARK 620 4 GLU A 503 OE2 99.5 58.2 2.1 REMARK 620 5 HOH A 902 O 132.2 74.3 36.8 36.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 804 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 589 OE1 REMARK 620 2 GLU A 589 OE2 65.3 REMARK 620 3 GLU A 598 OE1 66.6 131.6 REMARK 620 4 GLU A 598 OE2 114.6 175.2 49.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 805 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D5H RELATED DB: PDB REMARK 900 APO FORM DBREF 6CQ2 A 2 704 UNP P9WG49 TOP1_MYCTU 2 704 DBREF 6CQ2 B 1 13 PDB 6CQ2 6CQ2 1 13 SEQADV 6CQ2 SER A -1 UNP P9WG49 EXPRESSION TAG SEQADV 6CQ2 ASN A 0 UNP P9WG49 EXPRESSION TAG SEQADV 6CQ2 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 13 DT DT DC DC DG DC DT DT DG DA DC DT DT HET MG A 801 1 HET MG A 802 1 HET MG A 803 1 HET MG A 804 1 HET PO4 A 805 5 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 3 MG 4(MG 2+) FORMUL 7 PO4 O4 P 3- FORMUL 8 HOH *14(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 ASP A 102 1 14 HELIX 5 AA5 ASP A 113 LYS A 128 1 16 HELIX 6 AA6 THR A 142 HIS A 152 1 11 HELIX 7 AA7 ASP A 157 VAL A 186 1 30 HELIX 8 AA8 VAL A 195 ALA A 212 1 18 HELIX 9 AA9 THR A 253 PHE A 257 5 5 HELIX 10 AB1 ASP A 273 GLY A 283 1 11 HELIX 11 AB2 MET A 308 LYS A 319 1 12 HELIX 12 AB3 SER A 323 ASN A 337 1 15 HELIX 13 AB4 SER A 351 VAL A 371 1 21 HELIX 14 AB5 THR A 401 LEU A 409 1 9 HELIX 15 AB6 ILE A 414 GLN A 431 1 18 HELIX 16 AB7 PRO A 465 ALA A 470 5 6 HELIX 17 AB8 GLU A 519 GLY A 530 1 12 HELIX 18 AB9 THR A 536 ARG A 547 1 12 HELIX 19 AC1 SER A 560 PHE A 574 1 15 HELIX 20 AC2 GLY A 575 ASP A 579 5 5 HELIX 21 AC3 TYR A 580 ALA A 594 1 15 HELIX 22 AC4 ARG A 599 PHE A 609 1 11 HELIX 23 AC5 GLY A 623 ILE A 631 1 9 HELIX 24 AC6 ASP A 637 ASN A 642 1 6 HELIX 25 AC7 THR A 689 LEU A 693 5 5 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 VAL A 21 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 108 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 7 ALA A 217 ASP A 226 0 SHEET 2 AA3 7 THR A 238 VAL A 246 -1 O PHE A 239 N LEU A 225 SHEET 3 AA3 7 GLU A 452 ALA A 457 -1 O VAL A 454 N THR A 244 SHEET 4 AA3 7 LEU A 442 MET A 447 -1 N ILE A 444 O PHE A 455 SHEET 5 AA3 7 GLN A 288 ALA A 294 -1 N THR A 290 O THR A 445 SHEET 6 AA3 7 ARG A 498 ALA A 510 -1 O LEU A 499 N LEU A 289 SHEET 7 AA3 7 ALA A 217 ASP A 226 -1 N TYR A 218 O HIS A 509 SHEET 1 AA4 2 ARG A 250 VAL A 251 0 SHEET 2 AA4 2 VAL A 269 ILE A 270 1 O ILE A 270 N ARG A 250 SHEET 1 AA5 3 LYS A 297 ARG A 301 0 SHEET 2 AA5 3 ALA A 435 THR A 439 -1 O THR A 439 N LYS A 297 SHEET 3 AA5 3 ARG A 460 PHE A 464 -1 O THR A 461 N MET A 438 SHEET 1 AA6 3 TYR A 517 THR A 518 0 SHEET 2 AA6 3 ALA A 556 PRO A 559 -1 O LEU A 557 N TYR A 517 SHEET 3 AA6 3 VAL A 550 LYS A 553 -1 N HIS A 551 O VAL A 558 SHEET 1 AA7 4 ILE A 644 ASP A 648 0 SHEET 2 AA7 4 PRO A 654 VAL A 659 -1 O ILE A 655 N PHE A 647 SHEET 3 AA7 4 PRO A 664 VAL A 670 -1 O TYR A 665 N ARG A 658 SHEET 4 AA7 4 THR A 678 ASN A 683 -1 O THR A 678 N VAL A 670 LINK OE1 GLU A 24 MG MG A 801 1555 1555 2.01 LINK OD1 ASP A 111 MG MG A 801 1555 1555 1.90 LINK OD1 ASP A 233 MG MG A 803 1555 2545 2.66 LINK OD2 ASP A 233 MG MG A 803 1555 2545 2.60 LINK OE1 GLU A 296 MG MG A 802 1555 1555 2.26 LINK OE2 GLU A 296 MG MG A 802 1555 1555 1.93 LINK OE1 GLU A 503 MG MG A 802 1555 2555 2.51 LINK OE2 GLU A 503 MG MG A 802 1555 2555 1.91 LINK OD1 ASP A 507 MG MG A 803 1555 1555 2.33 LINK OE1 GLU A 589 MG MG A 804 1555 1555 2.07 LINK OE2 GLU A 589 MG MG A 804 1555 1555 2.00 LINK OE1 GLU A 598 MG MG A 804 1555 1555 2.90 LINK OE2 GLU A 598 MG MG A 804 1555 1555 1.95 LINK MG MG A 801 O HOH A 903 1555 1555 2.15 LINK MG MG A 801 O3' DC B 6 1555 1555 2.24 LINK MG MG A 801 OP1 DT B 7 1555 1555 2.09 LINK MG MG A 802 O HOH A 902 1555 1555 1.99 CISPEP 1 ALA A 235 PRO A 236 0 -3.46 CISPEP 2 GLU A 676 PRO A 677 0 -3.23 SITE 1 AC1 5 GLU A 24 ASP A 111 HOH A 903 DC B 6 SITE 2 AC1 5 DT B 7 SITE 1 AC2 3 GLU A 296 HIS A 492 HOH A 902 SITE 1 AC3 3 ASP A 220 ASP A 507 HIS A 509 SITE 1 AC4 3 GLU A 589 GLU A 598 HIS A 613 SITE 1 AC5 4 GLY A 112 HIS A 139 GLN A 386 HIS A 389 CRYST1 67.625 44.683 128.866 90.00 90.61 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 0.014787 0.000000 0.000158 0.00000 SCALE2 0.000000 0.022380 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007760 0.00000