HEADER TRANSCRIPTION/DNA/RNA 31-DEC-69 4YLP TITLE E. coli Transcription Initiation Complex - 16-bp spacer and 5-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 4YLP 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 -41.924 84.918 91.673 1.00175.49 ATOM 2 CA ARG R 448 -42.906 83.866 91.642 1.00174.85 ATOM 3 C ARG R 448 -43.193 83.218 93.013 1.00172.44 ATOM 4 O ARG R 448 -42.372 83.222 93.938 1.00172.14 ATOM 5 CB ARG R 448 -42.492 82.868 90.552 1.00178.55 ATOM 6 CG ARG R 448 -41.883 83.600 89.348 1.00181.41 ATOM 7 CD ARG R 448 -41.496 82.688 88.192 1.00185.54 ATOM 8 NE ARG R 448 -41.027 83.452 87.031 1.00188.40 ATOM 9 CZ ARG R 448 -40.980 82.969 85.791 1.00192.18 ATOM 10 NH1 ARG R 448 -41.378 81.725 85.536 1.00193.58 ATOM 11 NH2 ARG R 448 -40.542 83.735 84.803 1.00194.89 ATOM 12 N THR R 449 -44.433 82.768 93.139 1.00170.85 ATOM 13 CA THR R 449 -44.900 81.950 94.249 1.00169.14 ATOM 14 C THR R 449 -43.890 80.904 94.662 1.00171.10 ATOM 15 O THR R 449 -43.529 80.749 95.822 1.00170.12 ATOM 16 CB THR R 449 -46.096 81.132 93.764 1.00169.26 ATOM 17 OG1 THR R 449 -47.122 82.015 93.301 1.00167.85 ATOM 18 CG2 THR R 449 -46.617 80.241 94.865 1.00167.87 ATOM 19 N ILE R 450 -43.458 80.175 93.659 1.00174.29 ATOM 20 CA ILE R 450 -42.519 79.118 93.797 1.00176.96 ATOM 21 C ILE R 450 -41.138 79.711 93.506 1.00178.89 ATOM 22 O ILE R 450 -40.830 79.988 92.353 1.00181.05 ATOM 23 CB ILE R 450 -42.914 78.101 92.741 1.00179.71 ATOM 24 CG1 ILE R 450 -43.355 78.869 91.487 1.00180.25 ATOM 25 CG2 ILE R 450 -44.092 77.282 93.247 1.00178.36 ATOM 26 CD1 ILE R 450 -43.982 78.025 90.405 1.00182.86 ATOM 27 N ARG R 451 -40.336 79.942 94.549 1.00178.31 ATOM 28 CA ARG R 451 -39.026 80.636 94.429 1.00180.00 ATOM 29 C ARG R 451 -37.958 79.933 93.557 1.00184.35 ATOM 30 O ARG R 451 -37.773 78.719 93.642 1.00186.35 ATOM 31 CB ARG R 451 -38.424 80.943 95.822 1.00178.81 ATOM 32 CG ARG R 451 -37.426 79.915 96.388 1.00181.44 ATOM 33 CD ARG R 451 -35.950 80.298 96.188 1.00184.31 ATOM 34 NE ARG R 451 -35.050 79.667 97.165 1.00186.06 ATOM 35 CZ ARG R 451 -33.720 79.772 97.161 1.00189.03 ATOM 36 NH1 ARG R 451 -33.096 80.476 96.224 1.00190.61 ATOM 37 NH2 ARG R 451 -33.007 79.162 98.099 1.00190.73 ATOM 38 N ILE R 452 -37.211 80.706 92.768 1.00186.12 ATOM 39 CA ILE R 452 -36.259 80.128 91.797 1.00190.55 ATOM 40 C ILE R 452 -34.805 80.647 91.915 1.00192.77 ATOM 41 O ILE R 452 -34.561 81.813 91.662 1.00192.32 ATOM 42 CB ILE R 452 -36.770 80.366 90.350 1.00191.97 ATOM 43 CG1 ILE R 452 -38.187 79.779 90.138 1.00190.43 ATOM 44 CG2 ILE R 452 -35.756 79.877 89.322 1.00196.87 ATOM 45 CD1 ILE R 452 -38.301 78.266 90.224 1.00192.31 ATOM 46 N PRO R 453 -33.846 79.784 92.314 1.00195.42 ATOM 47 CA PRO R 453 -32.466 80.261 92.292 1.00198.05 ATOM 48 C PRO R 453 -31.812 80.492 90.946 1.00201.71 ATOM 49 O PRO R 453 -32.331 80.214 89.860 1.00202.95 ATOM 50 CB PRO R 453 -31.695 79.193 93.067 1.00200.23 ATOM 51 CG PRO R 453 -32.700 78.661 94.012 1.00197.13 ATOM 52 CD PRO R 453 -33.987 78.632 93.223 1.00195.32 ATOM 53 N VAL R 454 -30.610 80.986 91.105 1.00203.77 ATOM 54 CA VAL R 454 -29.945 81.810 90.143 1.00206.25 ATOM 55 C VAL R 454 -29.752 81.099 88.836 1.00210.29 ATOM 56 O VAL R 454 -30.089 81.617 87.757 1.00211.13 ATOM 57 CB VAL R 454 -28.552 82.129 90.696 1.00208.52 ATOM 58 CG1 VAL R 454 -28.315 83.641 90.693 1.00207.55 ATOM 59 CG2 VAL R 454 -28.433 81.563 92.117 1.00207.05 ATOM 60 N HIS R 455 -29.168 79.912 88.951 1.00213.21 ATOM 61 CA HIS R 455 -28.795 79.140 87.787 1.00217.90 ATOM 62 C HIS R 455 -30.025 78.812 86.980 1.00217.08 ATOM 63 O HIS R 455 -30.046 78.931 85.742 1.00219.88 ATOM 64 CB HIS R 455 -28.054 77.859 88.200 1.00221.11 ATOM 65 CG HIS R 455 -26.557 77.994 88.211 1.00225.05 ATOM 66 ND1 HIS R 455 -25.735 77.247 87.391 1.00230.58 ATOM 67 CD2 HIS R 455 -25.735 78.792 88.936 1.00224.57 ATOM 68 CE1 HIS R 455 -24.473 77.576 87.614 1.00233.25 ATOM 69 NE2 HIS R 455 -24.446 78.512 88.546 1.00229.70 ATOM 70 N MET R 456 -31.060 78.435 87.719 1.00213.37 ATOM 71 CA MET R 456 -32.334 78.061 87.164 1.00212.21 ATOM 72 C MET R 456 -32.824 79.183 86.274 1.00211.44 ATOM 73 O MET R 456 -33.236 78.981 85.118 1.00213.83 ATOM 74 CB MET R 456 -33.313 77.906 88.316 1.00207.51 ATOM 75 CG MET R 456 -33.990 76.551 88.417 1.00208.16 ATOM 76 SD MET R 456 -32.994 75.378 89.365 1.00210.68 ATOM 77 CE MET R 456 -32.170 76.487 90.537 1.00208.11 ATOM 78 N ILE R 457 -32.770 80.376 86.843 1.00208.41 ATOM 79 CA ILE R 457 -33.307 81.549 86.199 1.00207.26 ATOM 80 C ILE R 457 -32.600 81.825 84.888 1.00211.95 ATOM 81 O ILE R 457 -33.252 82.029 83.841 1.00213.15 ATOM 82 CB ILE R 457 -33.183 82.764 87.120 1.00203.89 ATOM 83 CG1 ILE R 457 -34.395 82.835 88.043 1.00198.97 ATOM 84 CG2 ILE R 457 -33.084 84.040 86.305 1.00204.85 ATOM 85 CD1 ILE R 457 -35.687 83.192 87.329 1.00197.58 ATOM 86 N GLU R 458 -31.266 81.806 84.950 1.00214.91 ATOM 87 CA GLU R 458 -30.456 82.103 83.760 1.00219.76 ATOM 88 C GLU R 458 -30.828 81.162 82.612 1.00223.36 ATOM 89 O GLU R 458 -31.009 81.569 81.440 1.00225.99 ATOM 90 CB GLU R 458 -28.940 82.032 84.047 1.00222.84 ATOM 91 CG GLU R 458 -28.301 83.361 84.467 1.00221.88 ATOM 92 CD GLU R 458 -26.820 83.490 84.101 1.00226.69 ATOM 93 OE1 GLU R 458 -26.409 82.978 83.036 1.00231.32 ATOM 94 OE2 GLU R 458 -26.064 84.129 84.871 1.00226.13 ATOM 95 N THR R 459 -30.985 79.903 82.979 1.00223.65 ATOM 96 CA THR R 459 -31.266 78.874 82.004 1.00227.49 ATOM 97 C THR R 459 -32.615 79.097 81.301 1.00226.24 ATOM 98 O THR R 459 -32.709 78.992 80.073 1.00230.22 ATOM 99 CB THR R 459 -31.200 77.514 82.697 1.00227.86 ATOM 100 OG1 THR R 459 -31.853 77.621 83.969 1.00222.43 ATOM 101 CG2 THR R 459 -29.736 77.127 82.932 1.00231.46 ATOM 102 N ILE R 460 -33.639 79.415 82.093 1.00221.02 ATOM 103 CA ILE R 460 -34.977 79.712 81.585 1.00219.37 ATOM 104 C ILE R 460 -34.945 80.773 80.504 1.00221.46 ATOM 105 O ILE R 460 -35.603 80.694 79.446 1.00223.88 ATOM 106 CB ILE R 460 -35.818 80.364 82.686 1.00213.32 ATOM 107 CG1 ILE R 460 -35.722 79.575 83.986 1.00210.78 ATOM 108 CG2 ILE R 460 -37.256 80.554 82.226 1.00211.74 ATOM 109 CD1 ILE R 460 -36.060 80.414 85.197 1.00205.54 ATOM 110 N ASN R 461 -34.197 81.812 80.822 1.00220.62 ATOM 111 CA ASN R 461 -34.167 82.967 79.963 1.00222.23 ATOM 112 C ASN R 461 -33.537 82.639 78.622 1.00228.54 ATOM 113 O ASN R 461 -34.011 83.101 77.584 1.00230.84 ATOM 114 CB ASN R 461 -33.456 84.092 80.687 1.00220.20 ATOM 115 CG ASN R 461 -33.788 84.100 82.168 1.00214.80 ATOM 116 OD1 ASN R 461 -34.727 83.422 82.602 1.00212.16 ATOM 117 ND2 ASN R 461 -33.021 84.849 82.954 1.00213.44 ATOM 118 N LYS R 462 -32.500 81.802 78.667 1.00231.57 ATOM 119 CA LYS R 462 -31.834 81.298 77.475 1.00237.97 ATOM 120 C LYS R 462 -32.843 80.700 76.515 1.00240.20 ATOM 121 O LYS R 462 -32.835 80.982 75.314 1.00244.54 ATOM 122 CB LYS R 462 -30.848 80.190 77.850 1.00240.37 ATOM 123 CG LYS R 462 -29.767 80.584 78.841 1.00238.85 ATOM 124 CD LYS R 462 -28.930 79.375 79.234 1.00241.36 ATOM 125 CE LYS R 462 -27.988 79.695 80.386 1.00239.45 ATOM 126 NZ LYS R 462 -27.293 78.476 80.892 1.00241.64 ATOM 127 N LEU R 463 -33.715 79.873 77.073 1.00237.43 ATOM 128 CA LEU R 463 -34.663 79.129 76.274 1.00239.72 ATOM 129 C LEU R 463 -35.493 80.059 75.418 1.00240.11 ATOM 130 O LEU R 463 -35.641 79.867 74.195 1.00245.15 ATOM 131 CB LEU R 463 -35.593 78.379 77.200 1.00235.55 ATOM 132 CG LEU R 463 -34.876 78.122 78.511 1.00232.53 ATOM 133 CD1 LEU R 463 -35.753 77.319 79.457 1.00228.84 ATOM 134 CD2 LEU R 463 -33.558 77.420 78.227 1.00237.50 ATOM 135 N ASN R 464 -36.026 81.084 76.064 1.00235.13 ATOM 136 CA ASN R 464 -36.979 81.942 75.398 1.00235.02 ATOM 137 C ASN R 464 -36.339 82.778 74.332 1.00239.58 ATOM 138 O ASN R 464 -36.935 83.067 73.292 1.00242.67 ATOM 139 CB ASN R 464 -37.698 82.838 76.392 1.00228.81 ATOM 140 CG ASN R 464 -38.985 82.215 76.886 1.00225.45 ATOM 141 OD1 ASN R 464 -39.891 81.903 76.098 1.00227.51 ATOM 142 ND2 ASN R 464 -39.078 82.022 78.195 1.00220.55 ATOM 143 N ARG R 465 -35.101 83.166 74.590 1.00240.36 ATOM 144 CA ARG R 465 -34.419 84.017 73.634 1.00244.81 ATOM 145 C ARG R 465 -34.060 83.259 72.329 1.00251.90 ATOM 146 O ARG R 465 -34.163 83.814 71.214 1.00256.15 ATOM 147 CB ARG R 465 -33.242 84.741 74.305 1.00243.67 ATOM 148 CG ARG R 465 -33.659 85.532 75.551 1.00237.17 ATOM 149 CD ARG R 465 -32.447 86.056 76.303 1.00236.35 ATOM 150 NE ARG R 465 -31.325 85.123 76.186 1.00239.92 ATOM 151 CZ ARG R 465 -30.072 85.399 76.531 1.00241.23 ATOM 152 NH1 ARG R 465 -29.771 86.591 77.025 1.00239.25 ATOM 153 NH2 ARG R 465 -29.120 84.481 76.380 1.00244.82 ATOM 154 N ILE R 466 -33.712 81.978 72.461 1.00253.45 ATOM 155 CA ILE R 466 -33.408 81.153 71.281 1.00260.39 ATOM 156 C ILE R 466 -34.685 80.785 70.519 1.00261.94 ATOM 157 O ILE R 466 -34.698 80.609 69.276 1.00268.09 ATOM 158 CB ILE R 466 -32.624 79.865 71.643 1.00262.17 ATOM 159 CG1 ILE R 466 -31.272 80.203 72.271 1.00261.75 ATOM 160 CG2 ILE R 466 -32.378 79.011 70.411 1.00269.66 ATOM 161 CD1 ILE R 466 -30.358 79.004 72.415 1.00265.02 ATOM 162 N SER R 467 -35.752 80.667 71.309 1.00256.49 ATOM 163 CA SER R 467 -37.077 80.332 70.818 1.00256.94 ATOM 164 C SER R 467 -37.476 81.209 69.639 1.00260.72 ATOM 165 O SER R 467 -38.034 80.695 68.660 1.00265.33 ATOM 166 CB SER R 467 -38.128 80.426 71.944 1.00249.90 ATOM 167 OG SER R 467 -38.227 79.215 72.691 1.00248.16 ATOM 168 N ARG R 468 -37.183 82.512 69.729 1.00259.17 ATOM 169 CA ARG R 468 -37.608 83.485 68.699 1.00262.49 ATOM 170 C ARG R 468 -37.009 83.170 67.318 1.00270.74 ATOM 171 O ARG R 468 -37.726 83.087 66.270 1.00275.19 ATOM 172 CB ARG R 468 -37.240 84.927 69.119 1.00259.69 ATOM 173 CG ARG R 468 -38.112 85.525 70.232 1.00252.49 ATOM 174 CD ARG R 468 -37.555 86.829 70.823 1.00249.74 ATOM 175 NE ARG R 468 -38.500 87.508 71.724 1.00243.79 ATOM 176 CZ ARG R 468 -38.358 87.636 73.046 1.00238.05 ATOM 177 NH1 ARG R 468 -37.300 87.143 73.679 1.00237.23 ATOM 178 NH2 ARG R 468 -39.288 88.269 73.744 1.00233.38 ATOM 179 N GLN R 469 -35.684 82.996 67.348 1.00272.97 ATOM 180 CA GLN R 469 -34.933 82.644 66.158 1.00280.85 ATOM 181 C GLN R 469 -35.556 81.417 65.542 1.00284.55 ATOM 182 O GLN R 469 -35.975 81.423 64.370 1.00290.23 ATOM 183 CB GLN R 469 -33.473 82.298 66.478 1.00282.25 ATOM 184 CG GLN R 469 -32.746 81.678 65.280 1.00290.74 ATOM 185 CD GLN R 469 -31.632 80.701 65.651 1.00292.31 ATOM 186 OE1 GLN R 469 -31.522 80.256 66.795 1.00287.22 ATOM 187 NE2 GLN R 469 -30.808 80.350 64.666 1.00299.80 ATOM 188 N MET R 470 -35.613 80.376 66.368 1.00281.49 ATOM 189 CA MET R 470 -35.981 79.050 65.918 1.00285.27 ATOM 190 C MET R 470 -37.358 79.016 65.256 1.00286.65 ATOM 191 O MET R 470 -37.524 78.385 64.174 1.00293.40 ATOM 192 CB MET R 470 -35.872 78.048 67.079 1.00281.03 ATOM 193 CG MET R 470 -34.465 77.950 67.669 1.00280.70 ATOM 194 SD MET R 470 -34.334 77.107 69.268 1.00274.54 ATOM 195 CE MET R 470 -34.608 75.399 68.794 1.00279.72 ATOM 196 N LEU R 471 -38.315 79.698 65.904 1.00280.62 ATOM 197 CA LEU R 471 -39.701 79.760 65.436 1.00281.08 ATOM 198 C LEU R 471 -39.687 80.382 64.055 1.00287.85 ATOM 199 O LEU R 471 -40.339 79.867 63.122 1.00293.08 ATOM 200 CB LEU R 471 -40.564 80.597 66.396 1.00273.55 ATOM 201 CG LEU R 471 -42.011 80.961 66.024 1.00273.27 ATOM 202 CD1 LEU R 471 -42.872 81.139 67.272 1.00265.41 ATOM 203 CD2 LEU R 471 -42.039 82.227 65.171 1.00276.34 ATOM 204 N GLN R 472 -38.910 81.457 63.904 1.00288.32 ATOM 205 CA GLN R 472 -39.021 82.177 62.636 1.00294.54 ATOM 206 C GLN R 472 -38.302 81.489 61.467 1.00303.28 ATOM 207 O GLN R 472 -38.800 81.497 60.327 1.00309.48 ATOM 208 CB GLN R 472 -38.723 83.671 62.747 1.00292.68 ATOM 209 CG GLN R 472 -37.356 84.026 63.276 1.00291.26 ATOM 210 CD GLN R 472 -37.308 85.472 63.692 1.00287.73 ATOM 211 OE1 GLN R 472 -36.430 85.888 64.454 1.00284.52 ATOM 212 NE2 GLN R 472 -38.271 86.250 63.204 1.00288.55 ATOM 213 N GLU R 473 -37.175 80.848 61.763 1.00304.02 ATOM 214 CA GLU R 473 -36.437 80.135 60.729 1.00312.35 ATOM 215 C GLU R 473 -37.166 78.895 60.229 1.00316.22 ATOM 216 O GLU R 473 -37.340 78.749 59.009 1.00323.78 ATOM 217 CB GLU R 473 -35.007 79.797 61.170 1.00312.55 ATOM 218 CG GLU R 473 -33.999 80.905 60.911 1.00314.21 ATOM 219 CD GLU R 473 -32.590 80.505 61.299 1.00315.05 ATOM 220 OE1 GLU R 473 -31.686 81.359 61.212 1.00316.11 ATOM 221 OE2 GLU R 473 -32.385 79.336 61.687 1.00314.97 ATOM 222 N MET R 474 -37.583 77.998 61.131 1.00311.65 ATOM 223 CA MET R 474 -38.256 76.774 60.646 1.00315.85 ATOM 224 C MET R 474 -39.669 77.045 60.122 1.00316.63 ATOM 225 O MET R 474 -40.149 76.346 59.215 1.00323.03 ATOM 226 CB MET R 474 -38.231 75.588 61.647 1.00312.22 ATOM 227 CG MET R 474 -37.323 74.405 61.259 1.00318.44 ATOM 228 SD MET R 474 -38.090 72.924 60.531 1.00325.15 ATOM 229 CE MET R 474 -38.807 72.124 61.971 1.00317.40 ATOM 230 N GLY R 475 -40.321 78.068 60.676 1.00310.55 ATOM 231 CA GLY R 475 -41.711 78.332 60.350 1.00310.46 ATOM 232 C GLY R 475 -42.657 77.754 61.403 1.00303.97 ATOM 233 O GLY R 475 -43.806 78.164 61.499 1.00301.52 ATOM 234 N ARG R 476 -42.178 76.792 62.177 1.00301.59 ATOM 235 CA ARG R 476 -43.020 76.233 63.234 1.00295.51 ATOM 236 C ARG R 476 -42.309 76.314 64.587 1.00288.40 ATOM 237 O ARG R 476 -41.864 77.373 65.019 1.00284.53 ATOM 238 CB ARG R 476 -43.485 74.792 62.902 1.00299.90 ATOM 239 CG ARG R 476 -44.405 74.126 63.938 1.00294.38 ATOM 240 CD ARG R 476 -45.894 74.143 63.585 1.00295.02 ATOM 241 NE ARG R 476 -46.760 74.019 64.767 1.00287.77 ATOM 242 CZ ARG R 476 -47.263 72.878 65.238 1.00287.30 ATOM 243 NH1 ARG R 476 -46.996 71.726 64.637 1.00293.71 ATOM 244 NH2 ARG R 476 -48.037 72.892 66.317 1.00280.68 ATOM 245 N GLU R 477 -42.203 75.170 65.254 1.00287.08 ATOM 246 CA GLU R 477 -41.708 75.114 66.636 1.00280.28 ATOM 247 C GLU R 477 -40.412 74.293 66.764 1.00283.06 ATOM 248 O GLU R 477 -39.982 73.622 65.818 1.00290.24 ATOM 249 CB GLU R 477 -42.805 74.568 67.582 1.00275.10 ATOM 250 CG GLU R 477 -43.992 75.498 67.858 1.00270.40 ATOM 251 CD GLU R 477 -44.193 75.792 69.361 1.00261.91 ATOM 252 OE1 GLU R 477 -45.188 75.270 69.961 1.00258.92 ATOM 253 OE2 GLU R 477 -43.353 76.524 69.951 1.00258.51 ATOM 254 N PRO R 478 -39.773 74.360 67.940 1.00277.66 ATOM 255 CA PRO R 478 -38.597 73.549 68.243 1.00279.70 ATOM 256 C PRO R 478 -38.917 72.381 69.179 1.00277.29 ATOM 257 O PRO R 478 -39.179 72.599 70.365 1.00270.56 ATOM 258 CB PRO R 478 -37.695 74.541 68.971 1.00275.25 ATOM 259 CG PRO R 478 -38.650 75.462 69.672 1.00268.33 ATOM 260 CD PRO R 478 -39.987 75.391 68.972 1.00269.94 ATOM 261 N THR R 479 -38.885 71.152 68.654 1.00283.08 ATOM 262 CA THR R 479 -39.103 69.949 69.472 1.00281.91 ATOM 263 C THR R 479 -37.922 69.777 70.424 1.00279.66 ATOM 264 O THR R 479 -36.850 70.301 70.143 1.00281.40 ATOM 265 CB THR R 479 -39.262 68.660 68.617 1.00289.63 ATOM 266 OG1 THR R 479 -38.364 68.695 67.496 1.00296.68 ATOM 267 CG2 THR R 479 -40.703 68.486 68.120 1.00290.55 TER