HEADER TRANSCRIPTION/DNA/RNA 31-DEC-69 4YLN TITLE E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA COMPND MOL_ID: 5; COMPND 2 MOLECULE: RNA polymerase sigma factor RpoD; COMPND 3 CHAIN: F, L, R; COMPND 4 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 5.50 ANGSTORMS DBREF 4YLN R 1 613 UNP P00579 RPOD_ECOLI 1 613 SEQRES 1 R 32 ARG THR ILE ARG ILE PRO VAL HIS MET ILE GLU THR ILE SEQRES 2 R 32 ASN LYS LEU ASN ARG ILE SER ARG GLN MET LEU GLN GLU SEQRES 3 R 32 MET GLY ARG GLU PRO THR ATOM 1 N ARG R 448 -41.729 86.837 90.979 1.00184.61 ATOM 2 CA ARG R 448 -42.533 85.630 91.017 1.00183.49 ATOM 3 C ARG R 448 -42.706 84.959 92.380 1.00182.26 ATOM 4 O ARG R 448 -41.853 85.039 93.268 1.00182.85 ATOM 5 CB ARG R 448 -41.948 84.607 90.054 1.00185.20 ATOM 6 CG ARG R 448 -41.288 85.215 88.830 1.00187.18 ATOM 7 CD ARG R 448 -40.706 84.101 87.976 1.00189.10 ATOM 8 NE ARG R 448 -40.239 84.571 86.674 1.00191.15 ATOM 9 CZ ARG R 448 -39.930 83.763 85.661 1.00193.10 ATOM 10 NH1 ARG R 448 -40.048 82.443 85.805 1.00193.28 ATOM 11 NH2 ARG R 448 -39.512 84.274 84.505 1.00195.11 ATOM 12 N THR R 449 -43.856 84.311 92.508 1.00180.78 ATOM 13 CA THR R 449 -44.198 83.473 93.647 1.00179.74 ATOM 14 C THR R 449 -43.099 82.458 93.949 1.00181.28 ATOM 15 O THR R 449 -42.619 82.344 95.074 1.00181.41 ATOM 16 CB THR R 449 -45.486 82.687 93.337 1.00178.59 ATOM 17 OG1 THR R 449 -46.533 83.595 92.968 1.00177.50 ATOM 18 CG2 THR R 449 -45.918 81.879 94.529 1.00177.59 ATOM 19 N ILE R 450 -42.722 81.710 92.923 1.00182.73 ATOM 20 CA ILE R 450 -41.593 80.809 92.996 1.00184.76 ATOM 21 C ILE R 450 -40.350 81.602 92.651 1.00186.47 ATOM 22 O ILE R 450 -40.166 81.969 91.500 1.00187.39 ATOM 23 CB ILE R 450 -41.737 79.699 91.950 1.00186.00 ATOM 24 CG1 ILE R 450 -42.342 80.283 90.661 1.00185.84 ATOM 25 CG2 ILE R 450 -42.613 78.590 92.504 1.00185.14 ATOM 26 CD1 ILE R 450 -41.887 79.608 89.379 1.00188.19 ATOM 27 N ARG R 451 -39.501 81.869 93.637 1.00187.13 ATOM 28 CA ARG R 451 -38.273 82.641 93.401 1.00189.00 ATOM 29 C ARG R 451 -37.268 81.891 92.509 1.00191.63 ATOM 30 O ARG R 451 -37.086 80.687 92.662 1.00192.58 ATOM 31 CB ARG R 451 -37.596 83.005 94.726 1.00189.49 ATOM 32 CG ARG R 451 -36.357 82.178 95.072 1.00192.06 ATOM 33 CD ARG R 451 -35.068 82.822 94.571 1.00194.49 ATOM 34 NE ARG R 451 -33.877 82.303 95.240 1.00197.04 ATOM 35 CZ ARG R 451 -32.629 82.585 94.877 1.00199.72 ATOM 36 NH1 ARG R 451 -32.389 83.379 93.842 1.00200.18 ATOM 37 NH2 ARG R 451 -31.614 82.067 95.548 1.00202.20 ATOM 38 N ILE R 452 -36.615 82.605 91.595 1.00193.04 ATOM 39 CA ILE R 452 -35.665 81.977 90.660 1.00195.78 ATOM 40 C ILE R 452 -34.226 82.477 90.838 1.00198.21 ATOM 41 O ILE R 452 -33.970 83.676 90.797 1.00198.20 ATOM 42 CB ILE R 452 -36.127 82.143 89.189 1.00196.03 ATOM 43 CG1 ILE R 452 -37.525 81.533 88.975 1.00194.10 ATOM 44 CG2 ILE R 452 -35.118 81.537 88.222 1.00199.17 ATOM 45 CD1 ILE R 452 -37.555 80.018 88.872 1.00195.18 ATOM 46 N PRO R 453 -33.285 81.545 91.048 1.00200.55 ATOM 47 CA PRO R 453 -31.907 81.959 91.255 1.00203.15 ATOM 48 C PRO R 453 -31.208 82.443 90.012 1.00205.21 ATOM 49 O PRO R 453 -31.649 82.274 88.886 1.00205.18 ATOM 50 CB PRO R 453 -31.222 80.690 91.757 1.00205.29 ATOM 51 CG PRO R 453 -31.985 79.594 91.104 1.00204.83 ATOM 52 CD PRO R 453 -33.415 80.076 91.029 1.00201.34 ATOM 53 N VAL R 454 -30.083 83.042 90.290 1.00207.27 ATOM 54 CA VAL R 454 -29.305 83.787 89.365 1.00209.33 ATOM 55 C VAL R 454 -29.095 83.096 88.026 1.00211.20 ATOM 56 O VAL R 454 -29.434 83.615 86.933 1.00211.10 ATOM 57 CB VAL R 454 -27.959 83.913 90.055 1.00212.09 ATOM 58 CG1 VAL R 454 -28.168 84.630 91.379 1.00210.58 ATOM 59 CG2 VAL R 454 -27.421 82.514 90.340 1.00214.05 ATOM 60 N HIS R 455 -28.516 81.909 88.117 1.00213.27 ATOM 61 CA HIS R 455 -28.062 81.262 86.902 1.00215.93 ATOM 62 C HIS R 455 -29.300 80.806 86.121 1.00214.13 ATOM 63 O HIS R 455 -29.342 80.861 84.887 1.00215.36 ATOM 64 CB HIS R 455 -27.010 80.136 87.159 1.00219.30 ATOM 65 CG HIS R 455 -25.563 80.522 86.881 1.00222.97 ATOM 66 ND1 HIS R 455 -24.897 80.168 85.719 1.00226.18 ATOM 67 CD2 HIS R 455 -24.645 81.179 87.638 1.00224.22 ATOM 68 CE1 HIS R 455 -23.651 80.613 85.761 1.00229.12 ATOM 69 NE2 HIS R 455 -23.472 81.230 86.916 1.00228.03 ATOM 70 N MET R 456 -30.333 80.439 86.871 1.00211.29 ATOM 71 CA MET R 456 -31.608 80.032 86.308 1.00209.41 ATOM 72 C MET R 456 -32.223 81.145 85.472 1.00208.15 ATOM 73 O MET R 456 -32.669 80.940 84.337 1.00208.82 ATOM 74 CB MET R 456 -32.553 79.727 87.460 1.00206.45 ATOM 75 CG MET R 456 -33.099 78.308 87.464 1.00206.67 ATOM 76 SD MET R 456 -31.749 77.117 87.280 1.00211.11 ATOM 77 CE MET R 456 -30.462 77.798 88.338 1.00212.23 ATOM 78 N ILE R 457 -32.225 82.334 86.055 1.00206.65 ATOM 79 CA ILE R 457 -32.752 83.494 85.391 1.00205.71 ATOM 80 C ILE R 457 -31.993 83.773 84.105 1.00208.68 ATOM 81 O ILE R 457 -32.602 84.035 83.058 1.00208.77 ATOM 82 CB ILE R 457 -32.684 84.713 86.303 1.00204.30 ATOM 83 CG1 ILE R 457 -33.335 84.401 87.647 1.00201.75 ATOM 84 CG2 ILE R 457 -33.440 85.863 85.662 1.00203.23 ATOM 85 CD1 ILE R 457 -34.812 84.736 87.664 1.00198.80 ATOM 86 N GLU R 458 -30.664 83.689 84.196 1.00211.35 ATOM 87 CA GLU R 458 -29.790 83.835 83.020 1.00214.68 ATOM 88 C GLU R 458 -30.256 82.947 81.857 1.00215.85 ATOM 89 O GLU R 458 -30.409 83.395 80.688 1.00217.06 ATOM 90 CB GLU R 458 -28.351 83.399 83.356 1.00217.70 ATOM 91 CG GLU R 458 -27.356 84.481 83.802 1.00218.89 ATOM 92 CD GLU R 458 -25.903 83.975 83.820 1.00222.67 ATOM 93 OE1 GLU R 458 -25.321 83.734 82.734 1.00225.60 ATOM 94 OE2 GLU R 458 -25.323 83.819 84.918 1.00223.01 ATOM 95 N THR R 459 -30.466 81.677 82.198 1.00215.78 ATOM 96 CA THR R 459 -30.824 80.675 81.200 1.00217.38 ATOM 97 C THR R 459 -32.177 81.010 80.560 1.00215.40 ATOM 98 O THR R 459 -32.331 80.935 79.332 1.00217.32 ATOM 99 CB THR R 459 -30.786 79.241 81.780 1.00217.93 ATOM 100 OG1 THR R 459 -31.035 79.293 83.192 1.00215.25 ATOM 101 CG2 THR R 459 -29.411 78.594 81.550 1.00222.00 ATOM 102 N ILE R 460 -33.135 81.411 81.396 1.00211.86 ATOM 103 CA ILE R 460 -34.441 81.849 80.922 1.00209.94 ATOM 104 C ILE R 460 -34.328 82.914 79.829 1.00211.36 ATOM 105 O ILE R 460 -34.941 82.803 78.747 1.00212.39 ATOM 106 CB ILE R 460 -35.256 82.465 82.071 1.00206.23 ATOM 107 CG1 ILE R 460 -34.968 81.745 83.388 1.00205.19 ATOM 108 CG2 ILE R 460 -36.740 82.423 81.744 1.00204.34 ATOM 109 CD1 ILE R 460 -35.377 82.541 84.608 1.00202.27 ATOM 110 N ASN R 461 -33.535 83.944 80.127 1.00211.68 ATOM 111 CA ASN R 461 -33.373 85.069 79.206 1.00213.12 ATOM 112 C ASN R 461 -32.780 84.640 77.871 1.00216.84 ATOM 113 O ASN R 461 -33.236 85.073 76.782 1.00218.03 ATOM 114 CB ASN R 461 -32.479 86.132 79.824 1.00213.30 ATOM 115 CG ASN R 461 -32.588 86.164 81.329 1.00210.63 ATOM 116 OD1 ASN R 461 -33.523 85.604 81.909 1.00208.16 ATOM 117 ND2 ASN R 461 -31.623 86.806 81.975 1.00211.35 ATOM 118 N LYS R 462 -31.758 83.786 77.982 1.00218.92 ATOM 119 CA LYS R 462 -31.070 83.219 76.830 1.00222.82 ATOM 120 C LYS R 462 -32.089 82.546 75.925 1.00223.24 ATOM 121 O LYS R 462 -32.083 82.740 74.696 1.00225.82 ATOM 122 CB LYS R 462 -30.032 82.172 77.269 1.00224.74 ATOM 123 CG LYS R 462 -28.633 82.691 77.614 1.00226.62 ATOM 124 CD LYS R 462 -27.627 81.536 77.733 1.00229.54 ATOM 125 CE LYS R 462 -26.241 81.979 78.209 1.00231.50 ATOM 126 NZ LYS R 462 -25.232 80.875 78.298 1.00234.79 ATOM 127 N LEU R 463 -32.971 81.776 76.568 1.00220.86 ATOM 128 CA LEU R 463 -34.035 81.044 75.898 1.00221.05 ATOM 129 C LEU R 463 -34.804 81.947 74.980 1.00221.14 ATOM 130 O LEU R 463 -35.038 81.640 73.804 1.00223.79 ATOM 131 CB LEU R 463 -35.078 80.577 76.901 1.00217.54 ATOM 132 CG LEU R 463 -34.732 80.061 78.296 1.00215.71 ATOM 133 CD1 LEU R 463 -36.032 79.800 79.040 1.00212.32 ATOM 134 CD2 LEU R 463 -33.868 78.796 78.211 1.00218.65 ATOM 135 N ASN R 464 -35.209 83.076 75.540 1.00218.47 ATOM 136 CA ASN R 464 -36.139 83.934 74.829 1.00218.23 ATOM 137 C ASN R 464 -35.539 84.566 73.617 1.00221.69 ATOM 138 O ASN R 464 -36.185 84.664 72.548 1.00223.40 ATOM 139 CB ASN R 464 -36.686 84.995 75.751 1.00214.89 ATOM 140 CG ASN R 464 -37.274 84.389 76.989 1.00211.59 ATOM 141 OD1 ASN R 464 -38.451 84.010 77.014 1.00210.10 ATOM 142 ND2 ASN R 464 -36.442 84.223 78.009 1.00210.75 ATOM 143 N ARG R 465 -34.288 84.984 73.797 1.00222.96 ATOM 144 CA ARG R 465 -33.550 85.629 72.718 1.00226.47 ATOM 145 C ARG R 465 -33.604 84.768 71.459 1.00229.94 ATOM 146 O ARG R 465 -33.913 85.223 70.321 1.00232.29 ATOM 147 CB ARG R 465 -32.076 85.807 73.105 1.00227.89 ATOM 148 CG ARG R 465 -31.819 86.345 74.509 1.00224.91 ATOM 149 CD ARG R 465 -30.355 86.740 74.695 1.00227.04 ATOM 150 NE ARG R 465 -29.463 85.587 74.830 1.00228.86 ATOM 151 CZ ARG R 465 -28.137 85.636 74.708 1.00231.77 ATOM 152 NH1 ARG R 465 -27.526 86.784 74.434 1.00233.19 ATOM 153 NH2 ARG R 465 -27.419 84.530 74.851 1.00233.54 ATOM 154 N ILE R 466 -33.280 83.506 71.689 1.00230.56 ATOM 155 CA ILE R 466 -33.107 82.608 70.585 1.00234.37 ATOM 156 C ILE R 466 -34.468 82.225 70.035 1.00234.06 ATOM 157 O ILE R 466 -34.625 82.030 68.831 1.00237.42 ATOM 158 CB ILE R 466 -32.281 81.370 70.976 1.00235.70 ATOM 159 CG1 ILE R 466 -31.227 81.750 72.024 1.00234.52 ATOM 160 CG2 ILE R 466 -31.616 80.773 69.744 1.00240.76 ATOM 161 CD1 ILE R 466 -30.468 80.575 72.610 1.00235.56 ATOM 162 N SER R 467 -35.444 82.126 70.931 1.00230.23 ATOM 163 CA SER R 467 -36.803 81.764 70.565 1.00229.64 ATOM 164 C SER R 467 -37.312 82.728 69.536 1.00231.23 ATOM 165 O SER R 467 -37.895 82.332 68.520 1.00233.81 ATOM 166 CB SER R 467 -37.715 81.843 71.787 1.00225.03 ATOM 167 OG SER R 467 -37.278 80.970 72.810 1.00223.58 ATOM 168 N ARG R 468 -37.086 84.008 69.778 1.00230.04 ATOM 169 CA ARG R 468 -37.689 84.963 68.874 1.00231.50 ATOM 170 C ARG R 468 -37.027 84.933 67.501 1.00236.44 ATOM 171 O ARG R 468 -37.694 85.003 66.459 1.00238.92 ATOM 172 CB ARG R 468 -37.726 86.353 69.492 1.00229.18 ATOM 173 CG ARG R 468 -38.805 86.480 70.565 1.00224.89 ATOM 174 CD ARG R 468 -38.917 87.901 71.124 1.00223.05 ATOM 175 NE ARG R 468 -40.183 88.153 71.827 1.00219.85 ATOM 176 CZ ARG R 468 -40.544 89.321 72.366 1.00218.16 ATOM 177 NH1 ARG R 468 -39.746 90.387 72.303 1.00219.32 ATOM 178 NH2 ARG R 468 -41.721 89.421 72.971 1.00215.55 ATOM 179 N GLN R 469 -35.710 84.781 67.528 1.00238.05 ATOM 180 CA GLN R 469 -34.946 84.732 66.298 1.00242.89 ATOM 181 C GLN R 469 -35.429 83.558 65.437 1.00245.72 ATOM 182 O GLN R 469 -35.857 83.693 64.266 1.00249.00 ATOM 183 CB GLN R 469 -33.462 84.551 66.637 1.00243.99 ATOM 184 CG GLN R 469 -32.576 84.129 65.469 1.00249.23 ATOM 185 CD GLN R 469 -31.242 83.526 65.909 1.00250.34 ATOM 186 OE1 GLN R 469 -31.119 82.993 67.020 1.00247.54 ATOM 187 NE2 GLN R 469 -30.242 83.596 65.027 1.00254.74 ATOM 188 N MET R 470 -35.359 82.386 66.042 1.00244.68 ATOM 189 CA MET R 470 -35.533 81.179 65.284 1.00247.96 ATOM 190 C MET R 470 -36.962 80.976 64.866 1.00247.76 ATOM 191 O MET R 470 -37.201 80.293 63.865 1.00251.60 ATOM 192 CB MET R 470 -34.978 79.987 66.036 1.00247.42 ATOM 193 CG MET R 470 -33.462 79.985 65.987 1.00249.79 ATOM 194 SD MET R 470 -32.711 78.881 67.187 1.00248.45 ATOM 195 CE MET R 470 -33.456 77.318 66.716 1.00250.75 ATOM 196 N LEU R 471 -37.902 81.544 65.622 1.00243.64 ATOM 197 CA LEU R 471 -39.295 81.610 65.222 1.00243.47 ATOM 198 C LEU R 471 -39.343 82.249 63.842 1.00247.71 ATOM 199 O LEU R 471 -39.984 81.728 62.951 1.00250.74 ATOM 200 CB LEU R 471 -40.054 82.496 66.208 1.00238.75 ATOM 201 CG LEU R 471 -41.546 82.273 66.469 1.00236.72 ATOM 202 CD1 LEU R 471 -42.042 83.315 67.459 1.00232.43 ATOM 203 CD2 LEU R 471 -42.371 82.319 65.193 1.00240.39 ATOM 204 N GLN R 472 -38.651 83.369 63.650 1.00248.28 ATOM 205 CA GLN R 472 -38.798 84.030 62.356 1.00252.38 ATOM 206 C GLN R 472 -37.981 83.390 61.229 1.00257.74 ATOM 207 O GLN R 472 -38.411 83.369 60.054 1.00261.85 ATOM 208 CB GLN R 472 -38.609 85.533 62.439 1.00251.52 ATOM 209 CG GLN R 472 -37.406 85.954 63.224 1.00249.71 ATOM 210 CD GLN R 472 -37.252 87.434 63.159 1.00249.67 ATOM 211 OE1 GLN R 472 -36.141 87.950 63.207 1.00250.57 ATOM 212 NE2 GLN R 472 -38.373 88.136 63.020 1.00248.97 ATOM 213 N GLU R 473 -36.839 82.813 61.582 1.00258.01 ATOM 214 CA GLU R 473 -36.059 82.095 60.584 1.00263.20 ATOM 215 C GLU R 473 -36.740 80.833 60.083 1.00265.53 ATOM 216 O GLU R 473 -36.814 80.591 58.876 1.00270.45 ATOM 217 CB GLU R 473 -34.651 81.802 61.083 1.00263.28 ATOM 218 CG GLU R 473 -33.755 83.024 61.011 1.00263.67 ATOM 219 CD GLU R 473 -32.283 82.653 60.929 1.00266.31 ATOM 220 OE1 GLU R 473 -31.489 83.505 60.472 1.00268.46 ATOM 221 OE2 GLU R 473 -31.926 81.506 61.310 1.00266.50 ATOM 222 N MET R 474 -37.256 80.030 61.002 1.00262.27 ATOM 223 CA MET R 474 -37.967 78.829 60.607 1.00264.39 ATOM 224 C MET R 474 -39.321 79.120 59.958 1.00265.28 ATOM 225 O MET R 474 -39.797 78.372 59.109 1.00269.17 ATOM 226 CB MET R 474 -38.128 77.877 61.792 1.00260.88 ATOM 227 CG MET R 474 -36.964 76.913 61.970 1.00262.82 ATOM 228 SD MET R 474 -36.907 75.579 60.745 1.00269.53 ATOM 229 CE MET R 474 -38.340 74.588 61.193 1.00267.78 ATOM 230 N GLY R 475 -39.945 80.218 60.364 1.00261.95 ATOM 231 CA GLY R 475 -41.300 80.486 59.943 1.00262.30 ATOM 232 C GLY R 475 -42.302 79.644 60.736 1.00259.29 ATOM 233 O GLY R 475 -43.438 79.501 60.332 1.00260.34 ATOM 234 N ARG R 476 -41.875 79.078 61.862 1.00255.80 ATOM 235 CA ARG R 476 -42.786 78.425 62.803 1.00252.29 ATOM 236 C ARG R 476 -42.231 78.523 64.231 1.00247.32 ATOM 237 O ARG R 476 -42.145 79.602 64.788 1.00244.26 ATOM 238 CB ARG R 476 -43.090 76.964 62.404 1.00255.38 ATOM 239 CG ARG R 476 -44.064 76.208 63.325 1.00252.24 ATOM 240 CD ARG R 476 -45.503 76.109 62.801 1.00253.54 ATOM 241 NE ARG R 476 -46.443 75.564 63.797 1.00250.01 ATOM 242 CZ ARG R 476 -47.023 74.363 63.732 1.00251.74 ATOM 243 NH1 ARG R 476 -46.776 73.552 62.709 1.00257.09 ATOM 244 NH2 ARG R 476 -47.859 73.976 64.692 1.00248.34 ATOM 245 N GLU R 477 -41.862 77.390 64.815 1.00246.87 ATOM 246 CA GLU R 477 -41.421 77.346 66.209 1.00242.46 ATOM 247 C GLU R 477 -40.078 76.646 66.360 1.00244.17 ATOM 248 O GLU R 477 -39.629 75.927 65.468 1.00248.68 ATOM 249 CB GLU R 477 -42.474 76.646 67.082 1.00239.47 ATOM 250 CG GLU R 477 -43.802 77.373 67.178 1.00237.18 ATOM 251 CD GLU R 477 -43.661 78.692 67.887 1.00233.46 ATOM 252 OE1 GLU R 477 -44.264 79.682 67.425 1.00233.59 ATOM 253 OE2 GLU R 477 -42.931 78.730 68.897 1.00230.75 ATOM 254 N PRO R 478 -39.423 76.858 67.501 1.00240.83 ATOM 255 CA PRO R 478 -38.213 76.102 67.796 1.00242.34 ATOM 256 C PRO R 478 -38.534 74.796 68.534 1.00241.55 ATOM 257 O PRO R 478 -39.192 74.840 69.574 1.00237.47 ATOM 258 CB PRO R 478 -37.424 77.058 68.697 1.00239.22 ATOM 259 CG PRO R 478 -38.449 77.943 69.333 1.00234.89 ATOM 260 CD PRO R 478 -39.705 77.895 68.510 1.00236.01 ATOM 261 N THR R 479 -38.094 73.650 68.001 1.00245.66 ATOM 262 CA THR R 479 -38.218 72.364 68.699 1.00245.56 ATOM 263 C THR R 479 -37.105 72.347 69.736 1.00243.95 ATOM 264 O THR R 479 -36.110 73.026 69.529 1.00244.79 ATOM 265 CB THR R 479 -38.099 71.165 67.729 1.00251.09 ATOM 266 OG1 THR R 479 -37.211 71.501 66.658 1.00255.13 ATOM 267 CG2 THR R 479 -39.458 70.807 67.134 1.00252.04 TER