0.015667 0.000000 0.000000 0.000000 0.012599 0.000000 0.000000 0.000000 0.007057 0.00000 0.00000 0.00000 Feinberg, H. Changela, A. Mondragon, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 63.830 79.370 141.700 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking O4 P -3 94.971 PHOSPHATE ION non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C10 H15 N2 O8 P 322.208 THYMIDINE-5'-PHOSPHATE non-polymer C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Nat.Struct.Biol. NSBIEW 2024 1072-8368 6 961 968 10.1038/13333 10504732 Protein-nucleotide interactions in E. coli DNA topoisomerase I. 1999 10.2210/pdb1cy7/pdb pdb_00001cy7 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 IMAGE PLATE 1998-05-01 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.98 1.0 BL9-1 SSRL 0.98 SYNCHROTRON SSRL BEAMLINE BL9-1 67542.500 DNA TOPOISOMERASE I 5.99.1.2 67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I GLY-SER ATTACHED AT N-TERMINUS DUE TO CONSTRUCT 1 man polymer 94.971 PHOSPHATE ION 1 syn non-polymer 322.208 THYMIDINE-5'-PHOSPHATE 3 syn non-polymer 18.015 water 127 nat water no no GSMGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHN WEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELN IDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQV THQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYIT YMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQF VACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFS EASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEA EWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSI GSMGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHN WEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELN IDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQV THQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYIT YMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQF VACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFS EASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEA EWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSI A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Escherichia Escherichia coli K12 Escherichia sample 83333 Escherichia coli 562 Escherichia coli DH5 ALPHA PLASMID PGEX-2T 1 2.66 53.69 VAPOR DIFFUSION, HANGING DROP 5.0 2.3M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K 277 database_2 struct_ref_seq_dif struct_site repository Initial release Version format compliance Source and taxonomy Version format compliance Database references Derived calculations 1 0 2000-03-08 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-12-21 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3'-5'-ADENOSINE DIPHOSPHATE COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpT Complex of E.coli DNA topoisomerase I with 5'pTpTpTp3' Complex of E.coli DNA topoisomerase I with TpTpTp3' COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3'-THYMIDINE MONOPHOSPHATE COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE AND 3'- THYMIDINE MONOPHOSPHATE CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM RCSB Y RCSB 1999-08-31 REL PO4 PHOSPHATE ION TMP THYMIDINE-5'-PHOSPHATE HOH water PO4 700 2 PO4 PO4 700 A TMP 600 3 TMP TMP 600 A TMP 601 3 TMP TMP 601 A TMP 602 3 TMP TMP 602 A HOH 1 4 HOH HOH 701 A HOH 2 4 HOH HOH 702 A HOH 3 4 HOH HOH 703 A HOH 4 4 HOH HOH 704 A HOH 5 4 HOH HOH 705 A HOH 6 4 HOH HOH 706 A HOH 7 4 HOH HOH 707 A HOH 8 4 HOH HOH 708 A HOH 9 4 HOH HOH 709 A HOH 10 4 HOH HOH 710 A HOH 11 4 HOH HOH 711 A HOH 12 4 HOH HOH 712 A HOH 13 4 HOH HOH 713 A HOH 14 4 HOH HOH 714 A HOH 15 4 HOH HOH 715 A HOH 16 4 HOH HOH 716 A HOH 17 4 HOH HOH 717 A HOH 18 4 HOH HOH 718 A HOH 19 4 HOH HOH 719 A HOH 20 4 HOH HOH 720 A HOH 21 4 HOH HOH 721 A HOH 22 4 HOH HOH 722 A HOH 23 4 HOH HOH 723 A HOH 24 4 HOH HOH 724 A HOH 25 4 HOH HOH 725 A HOH 26 4 HOH HOH 726 A HOH 27 4 HOH HOH 727 A HOH 28 4 HOH HOH 728 A HOH 29 4 HOH HOH 729 A HOH 30 4 HOH HOH 730 A HOH 31 4 HOH HOH 731 A HOH 32 4 HOH HOH 732 A HOH 33 4 HOH HOH 733 A HOH 34 4 HOH HOH 734 A HOH 35 4 HOH HOH 735 A HOH 36 4 HOH HOH 736 A HOH 37 4 HOH HOH 737 A HOH 38 4 HOH HOH 738 A HOH 39 4 HOH HOH 739 A HOH 40 4 HOH HOH 740 A HOH 41 4 HOH HOH 741 A HOH 42 4 HOH HOH 742 A HOH 43 4 HOH HOH 743 A HOH 44 4 HOH HOH 744 A HOH 45 4 HOH HOH 745 A HOH 46 4 HOH HOH 746 A HOH 47 4 HOH HOH 747 A HOH 48 4 HOH HOH 748 A HOH 49 4 HOH HOH 749 A HOH 50 4 HOH HOH 750 A HOH 51 4 HOH HOH 751 A HOH 52 4 HOH HOH 752 A HOH 53 4 HOH HOH 753 A HOH 54 4 HOH HOH 754 A HOH 55 4 HOH HOH 755 A HOH 56 4 HOH HOH 756 A HOH 57 4 HOH HOH 757 A HOH 58 4 HOH HOH 758 A HOH 59 4 HOH HOH 759 A HOH 60 4 HOH HOH 760 A HOH 61 4 HOH HOH 761 A HOH 62 4 HOH HOH 762 A HOH 63 4 HOH HOH 763 A HOH 64 4 HOH HOH 764 A HOH 65 4 HOH HOH 765 A HOH 66 4 HOH HOH 766 A HOH 67 4 HOH HOH 767 A HOH 68 4 HOH HOH 768 A HOH 69 4 HOH HOH 769 A HOH 70 4 HOH HOH 770 A HOH 71 4 HOH HOH 771 A HOH 72 4 HOH HOH 772 A HOH 73 4 HOH HOH 773 A HOH 74 4 HOH HOH 774 A HOH 75 4 HOH HOH 775 A HOH 76 4 HOH HOH 776 A HOH 77 4 HOH HOH 777 A HOH 78 4 HOH HOH 778 A HOH 79 4 HOH HOH 779 A HOH 80 4 HOH HOH 780 A HOH 81 4 HOH HOH 781 A HOH 82 4 HOH HOH 782 A HOH 83 4 HOH HOH 783 A HOH 84 4 HOH HOH 784 A HOH 85 4 HOH HOH 785 A HOH 86 4 HOH HOH 786 A HOH 87 4 HOH HOH 787 A HOH 88 4 HOH HOH 788 A HOH 89 4 HOH HOH 789 A HOH 90 4 HOH HOH 790 A HOH 91 4 HOH HOH 791 A HOH 92 4 HOH HOH 792 A HOH 93 4 HOH HOH 793 A HOH 94 4 HOH HOH 794 A HOH 95 4 HOH HOH 795 A HOH 96 4 HOH HOH 796 A HOH 97 4 HOH HOH 797 A HOH 98 4 HOH HOH 798 A HOH 99 4 HOH HOH 799 A HOH 100 4 HOH HOH 800 A HOH 101 4 HOH HOH 801 A HOH 102 4 HOH HOH 802 A HOH 103 4 HOH HOH 803 A HOH 104 4 HOH HOH 804 A HOH 105 4 HOH HOH 805 A HOH 106 4 HOH HOH 806 A HOH 107 4 HOH HOH 807 A HOH 108 4 HOH HOH 808 A HOH 109 4 HOH HOH 809 A HOH 110 4 HOH HOH 810 A HOH 111 4 HOH HOH 811 A HOH 112 4 HOH HOH 812 A HOH 113 4 HOH HOH 813 A HOH 114 4 HOH HOH 814 A HOH 115 4 HOH HOH 815 A HOH 116 4 HOH HOH 816 A HOH 117 4 HOH HOH 817 A HOH 118 4 HOH HOH 818 A HOH 119 4 HOH HOH 819 A HOH 120 4 HOH HOH 820 A HOH 121 4 HOH HOH 821 A HOH 122 4 HOH HOH 822 A HOH 123 4 HOH HOH 823 A HOH 124 4 HOH HOH 824 A HOH 125 4 HOH HOH 825 A HOH 126 4 HOH HOH 826 A HOH 127 4 HOH HOH 827 A n 1 -1 A n 2 0 A n 3 1 A GLY 2 n 4 GLY 2 A LYS 3 n 5 LYS 3 A ALA 4 n 6 ALA 4 A LEU 5 n 7 LEU 5 A VAL 6 n 8 VAL 6 A ILE 7 n 9 ILE 7 A VAL 8 n 10 VAL 8 A GLU 9 n 11 GLU 9 A SER 10 n 12 SER 10 A PRO 11 n 13 PRO 11 A ALA 12 n 14 ALA 12 A LYS 13 n 15 LYS 13 A ALA 14 n 16 ALA 14 A LYS 15 n 17 LYS 15 A THR 16 n 18 THR 16 A ILE 17 n 19 ILE 17 A ASN 18 n 20 ASN 18 A LYS 19 n 21 LYS 19 A TYR 20 n 22 TYR 20 A LEU 21 n 23 LEU 21 A GLY 22 n 24 GLY 22 A SER 23 n 25 SER 23 A ASP 24 n 26 ASP 24 A TYR 25 n 27 TYR 25 A VAL 26 n 28 VAL 26 A VAL 27 n 29 VAL 27 A LYS 28 n 30 LYS 28 A SER 29 n 31 SER 29 A SER 30 n 32 SER 30 A VAL 31 n 33 VAL 31 A GLY 32 n 34 GLY 32 A HIS 33 n 35 HIS 33 A ILE 34 n 36 ILE 34 A ARG 35 n 37 ARG 35 A ASP 36 n 38 ASP 36 A LEU 37 n 39 LEU 37 A PRO 38 n 40 PRO 38 A THR 39 n 41 THR 39 A n 42 40 A n 43 41 A n 44 42 A n 45 43 A n 46 44 A n 47 45 A n 48 46 A n 49 47 A n 50 48 A n 51 49 A n 52 50 A n 53 51 A n 54 52 A n 55 53 A n 56 54 A n 57 55 A n 58 56 A n 59 57 A n 60 58 A n 61 59 A n 62 60 A n 63 61 A ASP 62 n 64 ASP 62 A GLU 63 n 65 GLU 63 A ARG 64 n 66 ARG 64 A GLY 65 n 67 GLY 65 A ALA 66 n 68 ALA 66 A LEU 67 n 69 LEU 67 A VAL 68 n 70 VAL 68 A ASN 69 n 71 ASN 69 A ARG 70 n 72 ARG 70 A MET 71 n 73 MET 71 A GLY 72 n 74 GLY 72 A VAL 73 n 75 VAL 73 A ASP 74 n 76 ASP 74 A PRO 75 n 77 PRO 75 A TRP 76 n 78 TRP 76 A HIS 77 n 79 HIS 77 A ASN 78 n 80 ASN 78 A TRP 79 n 81 TRP 79 A GLU 80 n 82 GLU 80 A ALA 81 n 83 ALA 81 A HIS 82 n 84 HIS 82 A TYR 83 n 85 TYR 83 A GLU 84 n 86 GLU 84 A VAL 85 n 87 VAL 85 A LEU 86 n 88 LEU 86 A PRO 87 n 89 PRO 87 A GLY 88 n 90 GLY 88 A LYS 89 n 91 LYS 89 A GLU 90 n 92 GLU 90 A LYS 91 n 93 LYS 91 A VAL 92 n 94 VAL 92 A VAL 93 n 95 VAL 93 A SER 94 n 96 SER 94 A GLU 95 n 97 GLU 95 A LEU 96 n 98 LEU 96 A LYS 97 n 99 LYS 97 A GLN 98 n 100 GLN 98 A LEU 99 n 101 LEU 99 A ALA 100 n 102 ALA 100 A GLU 101 n 103 GLU 101 A LYS 102 n 104 LYS 102 A ALA 103 n 105 ALA 103 A ASP 104 n 106 ASP 104 A HIS 105 n 107 HIS 105 A ILE 106 n 108 ILE 106 A TYR 107 n 109 TYR 107 A LEU 108 n 110 LEU 108 A ALA 109 n 111 ALA 109 A THR 110 n 112 THR 110 A ASP 111 n 113 ASP 111 A LEU 112 n 114 LEU 112 A ASP 113 n 115 ASP 113 A ARG 114 n 116 ARG 114 A GLU 115 n 117 GLU 115 A GLY 116 n 118 GLY 116 A GLU 117 n 119 GLU 117 A ALA 118 n 120 ALA 118 A ILE 119 n 121 ILE 119 A ALA 120 n 122 ALA 120 A TRP 121 n 123 TRP 121 A HIS 122 n 124 HIS 122 A LEU 123 n 125 LEU 123 A ARG 124 n 126 ARG 124 A GLU 125 n 127 GLU 125 A VAL 126 n 128 VAL 126 A ILE 127 n 129 ILE 127 A GLY 128 n 130 GLY 128 A GLY 129 n 131 GLY 129 A ASP 130 n 132 ASP 130 A ASP 131 n 133 ASP 131 A ALA 132 n 134 ALA 132 A ARG 133 n 135 ARG 133 A TYR 134 n 136 TYR 134 A SER 135 n 137 SER 135 A ARG 136 n 138 ARG 136 A VAL 137 n 139 VAL 137 A VAL 138 n 140 VAL 138 A PHE 139 n 141 PHE 139 A ASN 140 n 142 ASN 140 A GLU 141 n 143 GLU 141 A ILE 142 n 144 ILE 142 A THR 143 n 145 THR 143 A LYS 144 n 146 LYS 144 A ASN 145 n 147 ASN 145 A ALA 146 n 148 ALA 146 A ILE 147 n 149 ILE 147 A ARG 148 n 150 ARG 148 A GLN 149 n 151 GLN 149 A ALA 150 n 152 ALA 150 A PHE 151 n 153 PHE 151 A ASN 152 n 154 ASN 152 A LYS 153 n 155 LYS 153 A PRO 154 n 156 PRO 154 A GLY 155 n 157 GLY 155 A GLU 156 n 158 GLU 156 A LEU 157 n 159 LEU 157 A ASN 158 n 160 ASN 158 A ILE 159 n 161 ILE 159 A ASP 160 n 162 ASP 160 A ARG 161 n 163 ARG 161 A VAL 162 n 164 VAL 162 A ASN 163 n 165 ASN 163 A ALA 164 n 166 ALA 164 A GLN 165 n 167 GLN 165 A GLN 166 n 168 GLN 166 A ALA 167 n 169 ALA 167 A ARG 168 n 170 ARG 168 A ARG 169 n 171 ARG 169 A PHE 170 n 172 PHE 170 A MET 171 n 173 MET 171 A ASP 172 n 174 ASP 172 A ARG 173 n 175 ARG 173 A VAL 174 n 176 VAL 174 A VAL 175 n 177 VAL 175 A GLY 176 n 178 GLY 176 A TYR 177 n 179 TYR 177 A MET 178 n 180 MET 178 A VAL 179 n 181 VAL 179 A SER 180 n 182 SER 180 A PRO 181 n 183 PRO 181 A LEU 182 n 184 LEU 182 A LEU 183 n 185 LEU 183 A TRP 184 n 186 TRP 184 A LYS 185 n 187 LYS 185 A LYS 186 n 188 LYS 186 A ILE 187 n 189 ILE 187 A ALA 188 n 190 ALA 188 A ARG 189 n 191 ARG 189 A GLY 190 n 192 GLY 190 A LEU 191 n 193 LEU 191 A SER 192 n 194 SER 192 A ALA 193 n 195 ALA 193 A GLY 194 n 196 GLY 194 A ARG 195 n 197 ARG 195 A VAL 196 n 198 VAL 196 A GLN 197 n 199 GLN 197 A SER 198 n 200 SER 198 A VAL 199 n 201 VAL 199 A ALA 200 n 202 ALA 200 A VAL 201 n 203 VAL 201 A ARG 202 n 204 ARG 202 A LEU 203 n 205 LEU 203 A VAL 204 n 206 VAL 204 A VAL 205 n 207 VAL 205 A GLU 206 n 208 GLU 206 A ARG 207 n 209 ARG 207 A GLU 208 n 210 GLU 208 A ARG 209 n 211 ARG 209 A GLU 210 n 212 GLU 210 A ILE 211 n 213 ILE 211 A LYS 212 n 214 LYS 212 A ALA 213 n 215 ALA 213 A PHE 214 n 216 PHE 214 A VAL 215 n 217 VAL 215 A PRO 216 n 218 PRO 216 A GLU 217 n 219 GLU 217 A GLU 218 n 220 GLU 218 A PHE 219 n 221 PHE 219 A TRP 220 n 222 TRP 220 A GLU 221 n 223 GLU 221 A VAL 222 n 224 VAL 222 A ASP 223 n 225 ASP 223 A ALA 224 n 226 ALA 224 A SER 225 n 227 SER 225 A THR 226 n 228 THR 226 A THR 227 n 229 THR 227 A THR 228 n 230 THR 228 A PRO 229 n 231 PRO 229 A SER 230 n 232 SER 230 A GLY 231 n 233 GLY 231 A GLU 232 n 234 GLU 232 A ALA 233 n 235 ALA 233 A LEU 234 n 236 LEU 234 A ALA 235 n 237 ALA 235 A LEU 236 n 238 LEU 236 A GLN 237 n 239 GLN 237 A VAL 238 n 240 VAL 238 A THR 239 n 241 THR 239 A HIS 240 n 242 HIS 240 A GLN 241 n 243 GLN 241 A ASN 242 n 244 ASN 242 A ASP 243 n 245 ASP 243 A LYS 244 n 246 LYS 244 A PRO 245 n 247 PRO 245 A PHE 246 n 248 PHE 246 A ARG 247 n 249 ARG 247 A PRO 248 n 250 PRO 248 A VAL 249 n 251 VAL 249 A ASN 250 n 252 ASN 250 A LYS 251 n 253 LYS 251 A GLU 252 n 254 GLU 252 A GLN 253 n 255 GLN 253 A THR 254 n 256 THR 254 A GLN 255 n 257 GLN 255 A ALA 256 n 258 ALA 256 A ALA 257 n 259 ALA 257 A VAL 258 n 260 VAL 258 A SER 259 n 261 SER 259 A LEU 260 n 262 LEU 260 A LEU 261 n 263 LEU 261 A GLU 262 n 264 GLU 262 A LYS 263 n 265 LYS 263 A ALA 264 n 266 ALA 264 A ARG 265 n 267 ARG 265 A TYR 266 n 268 TYR 266 A SER 267 n 269 SER 267 A VAL 268 n 270 VAL 268 A LEU 269 n 271 LEU 269 A GLU 270 n 272 GLU 270 A ARG 271 n 273 ARG 271 A GLU 272 n 274 GLU 272 A ASP 273 n 275 ASP 273 A LYS 274 n 276 LYS 274 A PRO 275 n 277 PRO 275 A THR 276 n 278 THR 276 A THR 277 n 279 THR 277 A SER 278 n 280 SER 278 A LYS 279 n 281 LYS 279 A PRO 280 n 282 PRO 280 A GLY 281 n 283 GLY 281 A ALA 282 n 284 ALA 282 A PRO 283 n 285 PRO 283 A PHE 284 n 286 PHE 284 A ILE 285 n 287 ILE 285 A THR 286 n 288 THR 286 A SER 287 n 289 SER 287 A THR 288 n 290 THR 288 A LEU 289 n 291 LEU 289 A GLN 290 n 292 GLN 290 A GLN 291 n 293 GLN 291 A ALA 292 n 294 ALA 292 A ALA 293 n 295 ALA 293 A SER 294 n 296 SER 294 A THR 295 n 297 THR 295 A ARG 296 n 298 ARG 296 A LEU 297 n 299 LEU 297 A GLY 298 n 300 GLY 298 A PHE 299 n 301 PHE 299 A GLY 300 n 302 GLY 300 A VAL 301 n 303 VAL 301 A LYS 302 n 304 LYS 302 A LYS 303 n 305 LYS 303 A THR 304 n 306 THR 304 A MET 305 n 307 MET 305 A MET 306 n 308 MET 306 A MET 307 n 309 MET 307 A ALA 308 n 310 ALA 308 A GLN 309 n 311 GLN 309 A ARG 310 n 312 ARG 310 A LEU 311 n 313 LEU 311 A TYR 312 n 314 TYR 312 A GLU 313 n 315 GLU 313 A ALA 314 n 316 ALA 314 A GLY 315 n 317 GLY 315 A TYR 316 n 318 TYR 316 A ILE 317 n 319 ILE 317 A THR 318 n 320 THR 318 A TYR 319 n 321 TYR 319 A MET 320 n 322 MET 320 A ARG 321 n 323 ARG 321 A THR 322 n 324 THR 322 A ASP 323 n 325 ASP 323 A SER 324 n 326 SER 324 A THR 325 n 327 THR 325 A ASN 326 n 328 ASN 326 A LEU 327 n 329 LEU 327 A SER 328 n 330 SER 328 A GLN 329 n 331 GLN 329 A ASP 330 n 332 ASP 330 A ALA 331 n 333 ALA 331 A VAL 332 n 334 VAL 332 A ASN 333 n 335 ASN 333 A MET 334 n 336 MET 334 A VAL 335 n 337 VAL 335 A ARG 336 n 338 ARG 336 A GLY 337 n 339 GLY 337 A TYR 338 n 340 TYR 338 A ILE 339 n 341 ILE 339 A SER 340 n 342 SER 340 A ASP 341 n 343 ASP 341 A ASN 342 n 344 ASN 342 A PHE 343 n 345 PHE 343 A GLY 344 n 346 GLY 344 A LYS 345 n 347 LYS 345 A LYS 346 n 348 LYS 346 A TYR 347 n 349 TYR 347 A LEU 348 n 350 LEU 348 A PRO 349 n 351 PRO 349 A GLU 350 n 352 GLU 350 A SER 351 n 353 SER 351 A PRO 352 n 354 PRO 352 A ASN 353 n 355 ASN 353 A GLN 354 n 356 GLN 354 A TYR 355 n 357 TYR 355 A n 358 356 A n 359 357 A n 360 358 A GLU 359 n 361 GLU 359 A ASN 360 n 362 ASN 360 A SER 361 n 363 SER 361 A GLN 362 n 364 GLN 362 A GLU 363 n 365 GLU 363 A ALA 364 n 366 ALA 364 A HIS 365 n 367 HIS 365 A GLU 366 n 368 GLU 366 A ALA 367 n 369 ALA 367 A ILE 368 n 370 ILE 368 A ARG 369 n 371 ARG 369 A PRO 370 n 372 PRO 370 A SER 371 n 373 SER 371 A ASP 372 n 374 ASP 372 A VAL 373 n 375 VAL 373 A ASN 374 n 376 ASN 374 A VAL 375 n 377 VAL 375 A MET 376 n 378 MET 376 A ALA 377 n 379 ALA 377 A GLU 378 n 380 GLU 378 A SER 379 n 381 SER 379 A LEU 380 n 382 LEU 380 A LYS 381 n 383 LYS 381 A ASP 382 n 384 ASP 382 A MET 383 n 385 MET 383 A GLU 384 n 386 GLU 384 A ALA 385 n 387 ALA 385 A ASP 386 n 388 ASP 386 A ALA 387 n 389 ALA 387 A GLN 388 n 390 GLN 388 A LYS 389 n 391 LYS 389 A LEU 390 n 392 LEU 390 A TYR 391 n 393 TYR 391 A GLN 392 n 394 GLN 392 A LEU 393 n 395 LEU 393 A ILE 394 n 396 ILE 394 A TRP 395 n 397 TRP 395 A ARG 396 n 398 ARG 396 A GLN 397 n 399 GLN 397 A PHE 398 n 400 PHE 398 A VAL 399 n 401 VAL 399 A ALA 400 n 402 ALA 400 A CYS 401 n 403 CYS 401 A GLN 402 n 404 GLN 402 A MET 403 n 405 MET 403 A THR 404 n 406 THR 404 A PRO 405 n 407 PRO 405 A ALA 406 n 408 ALA 406 A LYS 407 n 409 LYS 407 A TYR 408 n 410 TYR 408 A ASP 409 n 411 ASP 409 A SER 410 n 412 SER 410 A THR 411 n 413 THR 411 A THR 412 n 414 THR 412 A LEU 413 n 415 LEU 413 A THR 414 n 416 THR 414 A VAL 415 n 417 VAL 415 A GLY 416 n 418 GLY 416 A ALA 417 n 419 ALA 417 A GLY 418 n 420 GLY 418 A ASP 419 n 421 ASP 419 A PHE 420 n 422 PHE 420 A ARG 421 n 423 ARG 421 A LEU 422 n 424 LEU 422 A LYS 423 n 425 LYS 423 A ALA 424 n 426 ALA 424 A ARG 425 n 427 ARG 425 A GLY 426 n 428 GLY 426 A ARG 427 n 429 ARG 427 A ILE 428 n 430 ILE 428 A LEU 429 n 431 LEU 429 A ARG 430 n 432 ARG 430 A PHE 431 n 433 PHE 431 A ASP 432 n 434 ASP 432 A GLY 433 n 435 GLY 433 A TRP 434 n 436 TRP 434 A THR 435 n 437 THR 435 A LYS 436 n 438 LYS 436 A VAL 437 n 439 VAL 437 A MET 438 n 440 MET 438 A PRO 439 n 441 PRO 439 A ALA 440 n 442 ALA 440 A LEU 441 n 443 LEU 441 A n 444 442 A n 445 443 A n 446 444 A n 447 445 A n 448 446 A n 449 447 A n 450 448 A ILE 449 n 451 ILE 449 A LEU 450 n 452 LEU 450 A PRO 451 n 453 PRO 451 A ALA 452 n 454 ALA 452 A VAL 453 n 455 VAL 453 A ASN 454 n 456 ASN 454 A LYS 455 n 457 LYS 455 A GLY 456 n 458 GLY 456 A ASP 457 n 459 ASP 457 A ALA 458 n 460 ALA 458 A LEU 459 n 461 LEU 459 A THR 460 n 462 THR 460 A LEU 461 n 463 LEU 461 A VAL 462 n 464 VAL 462 A GLU 463 n 465 GLU 463 A LEU 464 n 466 LEU 464 A THR 465 n 467 THR 465 A PRO 466 n 468 PRO 466 A ALA 467 n 469 ALA 467 A GLN 468 n 470 GLN 468 A HIS 469 n 471 HIS 469 A PHE 470 n 472 PHE 470 A THR 471 n 473 THR 471 A LYS 472 n 474 LYS 472 A PRO 473 n 475 PRO 473 A PRO 474 n 476 PRO 474 A ALA 475 n 477 ALA 475 A ARG 476 n 478 ARG 476 A PHE 477 n 479 PHE 477 A SER 478 n 480 SER 478 A GLU 479 n 481 GLU 479 A ALA 480 n 482 ALA 480 A SER 481 n 483 SER 481 A LEU 482 n 484 LEU 482 A VAL 483 n 485 VAL 483 A LYS 484 n 486 LYS 484 A GLU 485 n 487 GLU 485 A LEU 486 n 488 LEU 486 A GLU 487 n 489 GLU 487 A LYS 488 n 490 LYS 488 A ARG 489 n 491 ARG 489 A GLY 490 n 492 GLY 490 A ILE 491 n 493 ILE 491 A GLY 492 n 494 GLY 492 A ARG 493 n 495 ARG 493 A PRO 494 n 496 PRO 494 A SER 495 n 497 SER 495 A THR 496 n 498 THR 496 A TYR 497 n 499 TYR 497 A ALA 498 n 500 ALA 498 A SER 499 n 501 SER 499 A ILE 500 n 502 ILE 500 A ILE 501 n 503 ILE 501 A SER 502 n 504 SER 502 A THR 503 n 505 THR 503 A ILE 504 n 506 ILE 504 A GLN 505 n 507 GLN 505 A ASP 506 n 508 ASP 506 A ARG 507 n 509 ARG 507 A GLY 508 n 510 GLY 508 A TYR 509 n 511 TYR 509 A VAL 510 n 512 VAL 510 A ARG 511 n 513 ARG 511 A VAL 512 n 514 VAL 512 A GLU 513 n 515 GLU 513 A ASN 514 n 516 ASN 514 A ARG 515 n 517 ARG 515 A ARG 516 n 518 ARG 516 A PHE 517 n 519 PHE 517 A TYR 518 n 520 TYR 518 A ALA 519 n 521 ALA 519 A GLU 520 n 522 GLU 520 A LYS 521 n 523 LYS 521 A MET 522 n 524 MET 522 A GLY 523 n 525 GLY 523 A GLU 524 n 526 GLU 524 A ILE 525 n 527 ILE 525 A VAL 526 n 528 VAL 526 A THR 527 n 529 THR 527 A ASP 528 n 530 ASP 528 A ARG 529 n 531 ARG 529 A LEU 530 n 532 LEU 530 A GLU 531 n 533 GLU 531 A GLU 532 n 534 GLU 532 A ASN 533 n 535 ASN 533 A PHE 534 n 536 PHE 534 A ARG 535 n 537 ARG 535 A GLU 536 n 538 GLU 536 A LEU 537 n 539 LEU 537 A MET 538 n 540 MET 538 A ASN 539 n 541 ASN 539 A TYR 540 n 542 TYR 540 A ASP 541 n 543 ASP 541 A PHE 542 n 544 PHE 542 A THR 543 n 545 THR 543 A ALA 544 n 546 ALA 544 A GLN 545 n 547 GLN 545 A MET 546 n 548 MET 546 A GLU 547 n 549 GLU 547 A ASN 548 n 550 ASN 548 A SER 549 n 551 SER 549 A LEU 550 n 552 LEU 550 A ASP 551 n 553 ASP 551 A GLN 552 n 554 GLN 552 A VAL 553 n 555 VAL 553 A ALA 554 n 556 ALA 554 A ASN 555 n 557 ASN 555 A HIS 556 n 558 HIS 556 A GLU 557 n 559 GLU 557 A ALA 558 n 560 ALA 558 A GLU 559 n 561 GLU 559 A TRP 560 n 562 TRP 560 A LYS 561 n 563 LYS 561 A ALA 562 n 564 ALA 562 A VAL 563 n 565 VAL 563 A LEU 564 n 566 LEU 564 A ASP 565 n 567 ASP 565 A HIS 566 n 568 HIS 566 A PHE 567 n 569 PHE 567 A PHE 568 n 570 PHE 568 A SER 569 n 571 SER 569 A ASP 570 n 572 ASP 570 A PHE 571 n 573 PHE 571 A THR 572 n 574 THR 572 A GLN 573 n 575 GLN 573 A GLN 574 n 576 GLN 574 A LEU 575 n 577 LEU 575 A ASP 576 n 578 ASP 576 A LYS 577 n 579 LYS 577 A ALA 578 n 580 ALA 578 A GLU 579 n 581 GLU 579 A LYS 580 n 582 LYS 580 A ASP 581 n 583 ASP 581 A PRO 582 n 584 PRO 582 A GLU 583 n 585 GLU 583 A GLU 584 n 586 GLU 584 A GLY 585 n 587 GLY 585 A GLY 586 n 588 GLY 586 A MET 587 n 589 MET 587 A ARG 588 n 590 ARG 588 A PRO 589 n 591 PRO 589 A ASN 590 n 592 ASN 590 A GLN 591 n 593 GLN 591 A MET 592 n 594 MET 592 A VAL 593 n 595 VAL 593 A LEU 594 n 596 LEU 594 A THR 595 n 597 THR 595 A SER 596 n 598 SER 596 A n 599 597 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N VAL 26 A N VAL 28 A O ALA 4 A O ALA 6 A O LEU 5 A O LEU 7 A N TYR 107 A N TYR 109 A N LEU 108 A N LEU 110 A O SER 135 A O SER 137 A O ASP 36 A O ASP 38 A N GLU 84 A N GLU 86 A O LYS 244 A O LYS 246 A N GLN 241 A N GLN 243 A N VAL 238 A N VAL 240 A O VAL 222 A O VAL 224 A O THR 227 A O THR 229 A N THR 460 A N THR 462 A N LEU 459 A N LEU 461 A O TYR 266 A O TYR 268 A O SER 278 A O SER 280 A N ALA 406 A N ALA 408 A O ALA 417 A O ALA 419 A N PHE 420 A N PHE 422 A O LYS 423 A O LYS 425 A N GLN 237 A N GLN 239 A N GLU 513 A N GLU 515 A O ARG 516 A O ARG 518 1 A GLY -1 A GLY 1 1 Y 1 A SER 0 A SER 2 1 Y 1 A MET 1 A MET 3 1 Y 1 A SER 40 A SER 42 1 Y 1 A GLY 41 A GLY 43 1 Y 1 A SER 42 A SER 44 1 Y 1 A ALA 43 A ALA 45 1 Y 1 A ALA 44 A ALA 46 1 Y 1 A LYS 45 A LYS 47 1 Y 1 A LYS 46 A LYS 48 1 Y 1 A SER 47 A SER 49 1 Y 1 A ALA 48 A ALA 50 1 Y 1 A ASP 49 A ASP 51 1 Y 1 A SER 50 A SER 52 1 Y 1 A THR 51 A THR 53 1 Y 1 A SER 52 A SER 54 1 Y 1 A THR 53 A THR 55 1 Y 1 A LYS 54 A LYS 56 1 Y 1 A THR 55 A THR 57 1 Y 1 A ALA 56 A ALA 58 1 Y 1 A LYS 57 A LYS 59 1 Y 1 A LYS 58 A LYS 60 1 Y 1 A PRO 59 A PRO 61 1 Y 1 A LYS 60 A LYS 62 1 Y 1 A LYS 61 A LYS 63 1 Y 1 A ALA 356 A ALA 358 1 Y 1 A SER 357 A SER 359 1 Y 1 A LYS 358 A LYS 360 1 Y 1 A ARG 442 A ARG 444 1 Y 1 A LYS 443 A LYS 445 1 Y 1 A GLY 444 A GLY 446 1 Y 1 A ASP 445 A ASP 447 1 Y 1 A GLU 446 A GLU 448 1 Y 1 A ASP 447 A ASP 449 1 Y 1 A ARG 448 A ARG 450 1 Y 1 A ILE 597 A ILE 599 1 Y 1 A C1' TMP 600 PLANAR 1 A C1' TMP 601 PLANAR 1 A C1' TMP 602 PLANAR 1 A ASP 36 179.82 -175.73 1 A GLU 63 90.25 138.20 1 A ARG 64 -163.46 97.77 1 A LYS 102 -82.72 37.98 1 A ALA 109 -108.26 49.50 1 A GLU 141 -172.37 143.66 1 A LYS 153 -116.74 78.64 1 A ILE 187 -117.62 -70.87 1 A ARG 247 -160.07 63.90 1 A LEU 269 -145.72 44.37 1 A GLU 270 140.37 136.91 1 A GLU 272 -36.27 94.47 1 A ASN 360 64.46 -160.27 1 A SER 361 -27.21 -74.26 1 A LYS 381 -67.07 -79.65 1 A ASP 382 -87.16 33.36 1 A PRO 494 -36.59 -38.83 1 A PHE 534 -140.60 55.13 1 A GLN 591 -68.29 -134.14 1 A MET 592 98.12 91.14 PROTEIN_REP.PA PROTEIN.TOP TMP_XPLOR_PAR.TXT TMP_XPLOR_TOP.TXT WATER_REP.PARA WATER.TOP ION.PARAM ION.TOP &_1_PARAMETER_INFILE_5 &_1_TOPOLOGY_INFILE_5 37.9 -4.05 0.00 0.00 2.97 0.00 1.08 REFINEMENT DONE WITH REFMAC. THE SOLVENT CORRECTION WAS CALCULATED WITH XPLOR AND APPLIED IN REFMAC. FINAL PARAMETERS OBTAINED WITH CNS 0.9 0.2950000 0.008 0.2340000 0.2370000 0.2340000 2.40 19.84 1294 25709 25373 5.1 87.9 RANDOM 1525570.43 0.00 1 RESTRAINED THROUGHOUT 2.0 R. A. ENGH AND R. HUBER, ACTA CRYST. SECT. A., 1991 FLAT MODEL 27.22 0.319 0.44 0.33 20.00 0.30 0.23 2.40 19.84 127 4680 68 0 4485 0.006 1.3 21.7 0.86 1.06 1.50 1.78 2.00 1.53 2.00 2.30 2.50 0.3240000 0.023 0.2650000 2.55 204 3930 6 4.9 86.9 37.8 2.4 30 1CY7 264320 28970 0 0 0.0500000 1 89.0 0.2080000 2.40 2.49 1 87.4 refinement X-PLOR refinement REFMAC refinement CNS 0.9 data reduction DENZO data scaling SCALEPACK COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE 1 N N 2 N N 3 N N 3 N N 3 N N 4 N N A SER 10 A SER 12 HELX_P A ASN 18 A ASN 20 1 1 9 A LYS 19 A LYS 21 HELX_P A LEU 21 A LEU 23 5 2 3 A ALA 66 A ALA 68 HELX_P A GLY 72 A GLY 74 1 3 7 A LYS 89 A LYS 91 HELX_P A GLU 101 A GLU 103 1 4 13 A ASP 113 A ASP 115 HELX_P A GLY 128 A GLY 130 1 5 16 A ASP 130 A ASP 132 HELX_P A ALA 132 A ALA 134 5 6 3 A THR 143 A THR 145 HELX_P A LYS 153 A LYS 155 1 7 11 A ASN 158 A ASN 160 HELX_P A ILE 187 A ILE 189 1 8 30 A VAL 196 A VAL 198 HELX_P A PHE 214 A PHE 216 1 9 19 A ASN 250 A ASN 252 HELX_P A ALA 264 A ALA 266 1 10 15 A ILE 285 A ILE 287 HELX_P A GLY 298 A GLY 300 1 11 14 A GLY 300 A GLY 302 HELX_P A ALA 314 A ALA 316 1 12 15 A SER 328 A SER 330 HELX_P A PHE 343 A PHE 345 1 13 16 A GLY 344 A GLY 346 HELX_P A LEU 348 A LEU 350 5 14 5 A MET 376 A MET 378 HELX_P A LEU 380 A LEU 382 5 15 5 A GLU 384 A GLU 386 HELX_P A CYS 401 A CYS 403 1 16 18 A ASP 432 A ASP 434 HELX_P A MET 438 A MET 440 5 17 7 A SER 478 A SER 480 HELX_P A ARG 489 A ARG 491 1 18 12 A THR 496 A THR 498 HELX_P A ARG 507 A ARG 509 1 19 12 A GLU 520 A GLU 522 HELX_P A PHE 534 A PHE 536 1 20 15 A ASN 539 A ASN 541 HELX_P A ASN 555 A ASN 557 1 21 17 A GLU 559 A GLU 561 HELX_P A THR 572 A THR 574 1 22 14 ISOMERASE DNA TOPOISOMERASE, RELAXING ENZYME, ISOMERASE TOP1_ECOLI UNP 1 P06612 1 597 1CY7 1 597 P06612 A 1 3 599 1 cloning artifact GLY -1 1CY7 A P06612 UNP 1 1 cloning artifact SER 0 1CY7 A P06612 UNP 2 4 2 8 2 parallel parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TYR 25 A TYR 27 A SER 29 A SER 31 A ALA 4 A ALA 6 A VAL 8 A VAL 10 A ILE 106 A ILE 108 A LEU 108 A LEU 110 A TYR 134 A TYR 136 A ARG 136 A ARG 138 A ARG 35 A ARG 37 A ASP 36 A ASP 38 A GLU 84 A GLU 86 A VAL 85 A VAL 87 A LYS 244 A LYS 246 A PRO 245 A PRO 247 A ALA 233 A ALA 235 A GLN 241 A GLN 243 A GLU 218 A GLU 220 A THR 227 A THR 229 A ALA 458 A ALA 460 A PHE 470 A PHE 472 A TYR 266 A TYR 268 A SER 278 A SER 280 A ALA 406 A ALA 408 A ALA 417 A ALA 419 A PHE 420 A PHE 422 A PHE 431 A PHE 433 A ALA 233 A ALA 235 A GLN 241 A GLN 243 A VAL 510 A VAL 512 A GLU 513 A GLU 515 A ARG 516 A ARG 518 A ALA 519 A ALA 521 BINDING SITE FOR RESIDUE PO4 A 700 A PO4 700 Software 5 BINDING SITE FOR RESIDUE TMP A 600 A TMP 600 Software 9 BINDING SITE FOR RESIDUE TMP A 601 A TMP 601 Software 7 BINDING SITE FOR RESIDUE TMP A 602 A TMP 602 Software 6 A ARG 202 A ARG 204 5 1_555 A ALA 458 A ALA 460 5 4_555 A ARG 535 A ARG 537 5 1_555 A ASN 539 A ASN 541 5 1_555 A HOH 759 F HOH 5 1_555 A LEU 112 A LEU 114 9 1_555 A ASP 113 A ASP 115 9 1_555 A ARG 114 A ARG 116 9 1_555 A GLU 115 A GLU 117 9 1_555 A ARG 161 A ARG 163 9 1_555 A GLN 165 A GLN 167 9 1_555 A ARG 168 A ARG 170 9 1_555 A HIS 365 A HIS 367 9 1_555 A SER 495 A SER 497 9 1_555 A ARG 296 A ARG 298 7 1_555 A LEU 393 A LEU 395 7 1_555 A ARG 396 A ARG 398 7 1_555 A GLN 397 A GLN 399 7 1_555 A TRP 434 A TRP 436 7 1_555 A MET 438 A MET 440 7 1_555 A PRO 439 A PRO 441 7 1_555 A GLN 291 A GLN 293 6 1_555 A THR 295 A THR 297 6 1_555 A SER 481 A SER 483 6 1_555 A ASN 514 A ASN 516 6 1_555 A ARG 516 A ARG 518 6 1_555 A HOH 801 F HOH 6 1_555 19 P 21 21 21