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 L 1 613 UNP P00579 RPOD_ECOLI 1 613 SEQRES 1 L 32 ARG THR ILE ARG ILE PRO VAL HIS MET ILE GLU THR ILE SEQRES 2 L 32 ASN LYS LEU ASN ARG ILE SER ARG GLN MET LEU GLN GLU SEQRES 3 L 32 MET GLY ARG GLU PRO THR ATOM 1 N ARG L 448 -86.259 117.817 227.532 1.00190.41 ATOM 2 CA ARG L 448 -86.580 116.554 226.871 1.00188.83 ATOM 3 C ARG L 448 -87.903 115.910 227.265 1.00187.05 ATOM 4 O ARG L 448 -88.371 115.987 228.416 1.00187.52 ATOM 5 CB ARG L 448 -85.471 115.512 227.050 1.00190.38 ATOM 6 CG ARG L 448 -84.435 115.477 225.928 1.00191.11 ATOM 7 CD ARG L 448 -83.362 114.441 226.233 1.00192.95 ATOM 8 NE ARG L 448 -82.019 115.034 226.252 1.00195.41 ATOM 9 CZ ARG L 448 -80.909 114.388 226.617 1.00197.64 ATOM 10 NH1 ARG L 448 -80.976 113.109 226.990 1.00197.76 ATOM 11 NH2 ARG L 448 -79.731 115.018 226.604 1.00199.94 ATOM 12 N THR L 449 -88.475 115.242 226.275 1.00185.21 ATOM 13 CA THR L 449 -89.685 114.469 226.443 1.00183.55 ATOM 14 C THR L 449 -89.490 113.424 227.544 1.00184.67 ATOM 15 O THR L 449 -90.332 113.265 228.419 1.00184.43 ATOM 16 CB THR L 449 -90.027 113.785 225.116 1.00181.95 ATOM 17 OG1 THR L 449 -89.290 114.425 224.060 1.00182.31 ATOM 18 CG2 THR L 449 -91.517 113.886 224.838 1.00179.88 ATOM 19 N ILE L 450 -88.359 112.736 227.499 1.00186.15 ATOM 20 CA ILE L 450 -87.978 111.788 228.516 1.00187.75 ATOM 21 C ILE L 450 -87.225 112.544 229.575 1.00189.94 ATOM 22 O ILE L 450 -86.096 112.951 229.337 1.00191.36 ATOM 23 CB ILE L 450 -86.982 110.804 227.932 1.00188.76 ATOM 24 CG1 ILE L 450 -86.190 111.511 226.817 1.00188.81 ATOM 25 CG2 ILE L 450 -87.728 109.595 227.410 1.00187.44 ATOM 26 CD1 ILE L 450 -84.729 111.102 226.707 1.00191.12 ATOM 27 N ARG L 451 -87.845 112.711 230.739 1.00190.42 ATOM 28 CA ARG L 451 -87.229 113.398 231.878 1.00192.77 ATOM 29 C ARG L 451 -85.932 112.740 232.348 1.00195.35 ATOM 30 O ARG L 451 -85.877 111.530 232.559 1.00195.86 ATOM 31 CB ARG L 451 -88.194 113.464 233.075 1.00193.07 ATOM 32 CG ARG L 451 -87.821 112.558 234.253 1.00195.38 ATOM 33 CD ARG L 451 -88.497 112.989 235.554 1.00196.53 ATOM 34 NE ARG L 451 -88.169 112.124 236.692 1.00199.01 ATOM 35 CZ ARG L 451 -88.743 112.202 237.894 1.00200.43 ATOM 36 NH1 ARG L 451 -89.672 113.113 238.137 1.00199.63 ATOM 37 NH2 ARG L 451 -88.381 111.377 238.865 1.00202.94 ATOM 38 N ILE L 452 -84.895 113.549 232.531 1.00197.21 ATOM 39 CA ILE L 452 -83.600 113.030 232.931 1.00199.88 ATOM 40 C ILE L 452 -83.176 113.578 234.267 1.00202.55 ATOM 41 O ILE L 452 -83.095 114.789 234.450 1.00203.03 ATOM 42 CB ILE L 452 -82.507 113.377 231.920 1.00200.36 ATOM 43 CG1 ILE L 452 -82.921 112.939 230.514 1.00197.89 ATOM 44 CG2 ILE L 452 -81.189 112.752 232.345 1.00203.31 ATOM 45 CD1 ILE L 452 -83.429 111.517 230.424 1.00197.06 ATOM 46 N PRO L 453 -82.928 112.674 235.211 1.00204.50 ATOM 47 CA PRO L 453 -82.416 113.037 236.506 1.00207.52 ATOM 48 C PRO L 453 -81.043 113.662 236.430 1.00209.78 ATOM 49 O PRO L 453 -80.272 113.440 235.498 1.00209.65 ATOM 50 CB PRO L 453 -82.328 111.697 237.241 1.00209.16 ATOM 51 CG PRO L 453 -83.375 110.861 236.604 1.00206.43 ATOM 52 CD PRO L 453 -83.350 111.265 235.158 1.00203.93 ATOM 53 N VAL L 454 -80.776 114.432 237.469 1.00212.10 ATOM 54 CA VAL L 454 -79.575 115.198 237.648 1.00214.69 ATOM 55 C VAL L 454 -78.323 114.398 237.368 1.00216.55 ATOM 56 O VAL L 454 -77.497 114.800 236.558 1.00216.80 ATOM 57 CB VAL L 454 -79.506 115.672 239.109 1.00217.61 ATOM 58 CG1 VAL L 454 -78.247 116.487 239.358 1.00220.63 ATOM 59 CG2 VAL L 454 -80.761 116.456 239.469 1.00216.15 ATOM 60 N HIS L 455 -78.188 113.267 238.054 1.00218.10 ATOM 61 CA HIS L 455 -76.998 112.418 237.996 1.00220.52 ATOM 62 C HIS L 455 -76.575 112.135 236.559 1.00218.90 ATOM 63 O HIS L 455 -75.389 112.246 236.151 1.00220.71 ATOM 64 CB HIS L 455 -77.313 111.067 238.676 1.00221.48 ATOM 65 CG HIS L 455 -77.144 111.054 240.170 1.00224.79 ATOM 66 ND1 HIS L 455 -76.340 110.135 240.816 1.00228.14 ATOM 67 CD2 HIS L 455 -77.693 111.819 241.144 1.00225.49 ATOM 68 CE1 HIS L 455 -76.387 110.346 242.119 1.00230.78 ATOM 69 NE2 HIS L 455 -77.201 111.363 242.345 1.00229.25 ATOM 70 N MET L 456 -77.597 111.763 235.797 1.00215.58 ATOM 71 CA MET L 456 -77.411 111.333 234.429 1.00213.89 ATOM 72 C MET L 456 -76.938 112.508 233.631 1.00213.45 ATOM 73 O MET L 456 -76.010 112.398 232.838 1.00214.31 ATOM 74 CB MET L 456 -78.716 110.800 233.834 1.00210.50 ATOM 75 CG MET L 456 -78.589 110.248 232.409 1.00208.91 ATOM 76 SD MET L 456 -77.871 108.588 232.201 1.00210.78 ATOM 77 CE MET L 456 -79.054 107.547 233.067 1.00210.15 ATOM 78 N ILE L 457 -77.595 113.633 233.856 1.00212.32 ATOM 79 CA ILE L 457 -77.238 114.848 233.186 1.00212.12 ATOM 80 C ILE L 457 -75.773 115.197 233.437 1.00215.57 ATOM 81 O ILE L 457 -75.049 115.556 232.505 1.00215.91 ATOM 82 CB ILE L 457 -78.159 115.975 233.653 1.00211.07 ATOM 83 CG1 ILE L 457 -79.573 115.425 233.872 1.00208.55 ATOM 84 CG2 ILE L 457 -78.171 117.104 232.629 1.00209.91 ATOM 85 CD1 ILE L 457 -80.210 114.923 232.596 1.00205.49 ATOM 86 N GLU L 458 -75.351 115.063 234.698 1.00218.31 ATOM 87 CA GLU L 458 -73.959 115.262 235.132 1.00222.05 ATOM 88 C GLU L 458 -72.996 114.535 234.228 1.00222.85 ATOM 89 O GLU L 458 -72.019 115.085 233.664 1.00224.34 ATOM 90 CB GLU L 458 -73.735 114.606 236.502 1.00224.73 ATOM 91 CG GLU L 458 -74.403 115.235 237.707 1.00225.35 ATOM 92 CD GLU L 458 -73.778 114.750 239.006 1.00229.12 ATOM 93 OE1 GLU L 458 -72.822 113.936 238.938 1.00231.18 ATOM 94 OE2 GLU L 458 -74.230 115.183 240.095 1.00230.25 ATOM 95 N THR L 459 -73.260 113.241 234.159 1.00222.20 ATOM 96 CA THR L 459 -72.386 112.378 233.425 1.00223.32 ATOM 97 C THR L 459 -72.393 112.734 231.928 1.00221.24 ATOM 98 O THR L 459 -71.343 112.748 231.301 1.00222.99 ATOM 99 CB THR L 459 -72.720 110.912 233.716 1.00223.32 ATOM 100 OG1 THR L 459 -74.115 110.822 234.020 1.00220.57 ATOM 101 CG2 THR L 459 -71.934 110.434 234.932 1.00227.18 ATOM 102 N ILE L 460 -73.562 113.080 231.385 1.00217.79 ATOM 103 CA ILE L 460 -73.703 113.439 229.968 1.00215.80 ATOM 104 C ILE L 460 -72.767 114.585 229.631 1.00217.60 ATOM 105 O ILE L 460 -71.994 114.567 228.654 1.00218.46 ATOM 106 CB ILE L 460 -75.116 113.975 229.673 1.00212.28 ATOM 107 CG1 ILE L 460 -76.187 112.995 230.153 1.00210.51 ATOM 108 CG2 ILE L 460 -75.265 114.293 228.191 1.00210.48 ATOM 109 CD1 ILE L 460 -77.558 113.618 230.296 1.00207.76 ATOM 110 N ASN L 461 -72.855 115.588 230.485 1.00218.41 ATOM 111 CA ASN L 461 -72.118 116.810 230.300 1.00220.17 ATOM 112 C ASN L 461 -70.609 116.610 230.397 1.00223.88 ATOM 113 O ASN L 461 -69.837 117.152 229.586 1.00225.07 ATOM 114 CB ASN L 461 -72.629 117.813 231.315 1.00220.41 ATOM 115 CG ASN L 461 -74.118 117.657 231.552 1.00217.25 ATOM 116 OD1 ASN L 461 -74.789 116.895 230.844 1.00214.70 ATOM 117 ND2 ASN L 461 -74.641 118.358 232.553 1.00217.60 ATOM 118 N LYS L 462 -70.204 115.788 231.365 1.00225.84 ATOM 119 CA LYS L 462 -68.788 115.477 231.533 1.00229.60 ATOM 120 C LYS L 462 -68.303 114.775 230.258 1.00229.37 ATOM 121 O LYS L 462 -67.232 115.081 229.712 1.00231.65 ATOM 122 CB LYS L 462 -68.551 114.593 232.762 1.00231.72 ATOM 123 CG LYS L 462 -68.929 115.219 234.097 1.00232.58 ATOM 124 CD LYS L 462 -68.893 114.185 235.216 1.00234.34 ATOM 125 CE LYS L 462 -69.687 114.634 236.434 1.00234.25 ATOM 126 NZ LYS L 462 -69.820 113.563 237.462 1.00235.74 ATOM 127 N LEU L 463 -69.146 113.857 229.786 1.00226.69 ATOM 128 CA LEU L 463 -68.891 113.029 228.621 1.00226.27 ATOM 129 C LEU L 463 -68.555 113.885 227.449 1.00226.03 ATOM 130 O LEU L 463 -67.553 113.663 226.785 1.00228.18 ATOM 131 CB LEU L 463 -70.138 112.212 228.257 1.00222.85 ATOM 132 CG LEU L 463 -70.173 110.684 228.397 1.00223.29 ATOM 133 CD1 LEU L 463 -71.516 110.144 227.926 1.00219.67 ATOM 134 CD2 LEU L 463 -69.051 110.019 227.613 1.00225.72 ATOM 135 N ASN L 464 -69.387 114.877 227.179 1.00223.66 ATOM 136 CA ASN L 464 -69.129 115.679 225.989 1.00223.52 ATOM 137 C ASN L 464 -67.798 116.453 226.038 1.00227.18 ATOM 138 O ASN L 464 -66.996 116.461 225.068 1.00228.72 ATOM 139 CB ASN L 464 -70.316 116.586 225.685 1.00220.46 ATOM 140 CG ASN L 464 -71.565 115.797 225.357 1.00216.99 ATOM 141 OD1 ASN L 464 -71.873 115.571 224.188 1.00215.51 ATOM 142 ND2 ASN L 464 -72.280 115.353 226.387 1.00215.92 ATOM 143 N ARG L 465 -67.563 117.095 227.181 1.00228.79 ATOM 144 CA ARG L 465 -66.362 117.896 227.324 1.00232.38 ATOM 145 C ARG L 465 -65.100 117.037 227.114 1.00235.48 ATOM 146 O ARG L 465 -64.162 117.417 226.385 1.00237.72 ATOM 147 CB ARG L 465 -66.361 118.678 228.659 1.00233.78 ATOM 148 CG ARG L 465 -67.392 119.819 228.733 1.00231.58 ATOM 149 CD ARG L 465 -67.330 120.615 230.041 1.00233.43 ATOM 150 NE ARG L 465 -67.308 119.746 231.223 1.00234.30 ATOM 151 CZ ARG L 465 -67.179 120.172 232.480 1.00236.34 ATOM 152 NH1 ARG L 465 -67.064 121.472 232.733 1.00237.70 ATOM 153 NH2 ARG L 465 -67.164 119.296 233.482 1.00237.27 ATOM 154 N ILE L 466 -65.110 115.845 227.694 1.00235.70 ATOM 155 CA ILE L 466 -63.938 114.982 227.620 1.00238.94 ATOM 156 C ILE L 466 -63.804 114.374 226.224 1.00238.27 ATOM 157 O ILE L 466 -62.697 114.161 225.707 1.00241.21 ATOM 158 CB ILE L 466 -63.991 113.894 228.705 1.00239.75 ATOM 159 CG1 ILE L 466 -64.126 114.553 230.080 1.00240.68 ATOM 160 CG2 ILE L 466 -62.752 113.013 228.648 1.00243.46 ATOM 161 CD1 ILE L 466 -64.476 113.597 231.197 1.00240.97 ATOM 162 N SER L 467 -64.956 114.158 225.600 1.00234.53 ATOM 163 CA SER L 467 -65.049 113.630 224.247 1.00233.49 ATOM 164 C SER L 467 -64.288 114.508 223.308 1.00235.22 ATOM 165 O SER L 467 -63.524 114.005 222.482 1.00237.14 ATOM 166 CB SER L 467 -66.500 113.636 223.770 1.00229.16 ATOM 167 OG SER L 467 -67.270 112.670 224.451 1.00227.50 ATOM 168 N ARG L 468 -64.546 115.811 223.399 1.00234.61 ATOM 169 CA ARG L 468 -63.874 116.773 222.522 1.00236.40 ATOM 170 C ARG L 468 -62.340 116.706 222.640 1.00240.98 ATOM 171 O ARG L 468 -61.608 116.693 221.631 1.00242.90 ATOM 172 CB ARG L 468 -64.374 118.185 222.810 1.00235.47 ATOM 173 CG ARG L 468 -65.874 118.333 222.615 1.00231.21 ATOM 174 CD ARG L 468 -66.370 119.666 223.146 1.00230.63 ATOM 175 NE ARG L 468 -67.622 120.061 222.510 1.00227.23 ATOM 176 CZ ARG L 468 -68.125 121.290 222.544 1.00226.68 ATOM 177 NH1 ARG L 468 -67.487 122.263 223.189 1.00229.31 ATOM 178 NH2 ARG L 468 -69.268 121.539 221.923 1.00223.70 ATOM 179 N GLN L 469 -61.882 116.626 223.881 1.00242.84 ATOM 180 CA GLN L 469 -60.462 116.546 224.147 1.00247.33 ATOM 181 C GLN L 469 -59.872 115.312 223.455 1.00248.74 ATOM 182 O GLN L 469 -58.921 115.390 222.658 1.00251.50 ATOM 183 CB GLN L 469 -60.236 116.482 225.657 1.00248.85 ATOM 184 CG GLN L 469 -58.822 116.139 226.084 1.00253.56 ATOM 185 CD GLN L 469 -58.703 116.013 227.590 1.00255.01 ATOM 186 OE1 GLN L 469 -59.539 116.530 228.336 1.00253.00 ATOM 187 NE2 GLN L 469 -57.665 115.319 228.046 1.00258.72 ATOM 188 N MET L 470 -60.481 114.172 223.748 1.00246.94 ATOM 189 CA MET L 470 -59.986 112.906 223.242 1.00248.43 ATOM 190 C MET L 470 -60.020 112.814 221.720 1.00247.81 ATOM 191 O MET L 470 -59.115 112.224 221.120 1.00250.70 ATOM 192 CB MET L 470 -60.712 111.737 223.900 1.00246.68 ATOM 193 CG MET L 470 -60.536 111.728 225.408 1.00248.07 ATOM 194 SD MET L 470 -61.101 110.216 226.200 1.00247.37 ATOM 195 CE MET L 470 -60.076 109.002 225.373 1.00250.65 ATOM 196 N LEU L 471 -61.045 113.402 221.099 1.00244.34 ATOM 197 CA LEU L 471 -61.154 113.445 219.634 1.00243.77 ATOM 198 C LEU L 471 -59.994 114.286 219.091 1.00247.36 ATOM 199 O LEU L 471 -59.450 113.995 218.009 1.00249.14 ATOM 200 CB LEU L 471 -62.508 114.077 219.226 1.00239.53 ATOM 201 CG LEU L 471 -63.288 113.744 217.930 1.00237.18 ATOM 202 CD1 LEU L 471 -64.772 114.087 218.055 1.00232.78 ATOM 203 CD2 LEU L 471 -62.701 114.397 216.684 1.00239.10 ATOM 204 N GLN L 472 -59.614 115.321 219.842 1.00248.66 ATOM 205 CA GLN L 472 -58.554 116.183 219.333 1.00252.17 ATOM 206 C GLN L 472 -57.151 115.609 219.532 1.00256.76 ATOM 207 O GLN L 472 -56.256 115.915 218.760 1.00259.82 ATOM 208 CB GLN L 472 -58.697 117.667 219.723 1.00252.05 ATOM 209 CG GLN L 472 -58.886 117.968 221.196 1.00251.71 ATOM 210 CD GLN L 472 -59.863 119.106 221.412 1.00249.05 ATOM 211 OE1 GLN L 472 -59.905 119.709 222.483 1.00249.46 ATOM 212 NE2 GLN L 472 -60.671 119.396 220.392 1.00246.48 ATOM 213 N GLU L 473 -56.971 114.737 220.520 1.00257.42 ATOM 214 CA GLU L 473 -55.684 114.071 220.707 1.00261.87 ATOM 215 C GLU L 473 -55.529 112.786 219.884 1.00262.48 ATOM 216 O GLU L 473 -54.410 112.433 219.499 1.00266.46 ATOM 217 CB GLU L 473 -55.447 113.792 222.182 1.00263.04 ATOM 218 CG GLU L 473 -55.416 115.048 223.026 1.00263.35 ATOM 219 CD GLU L 473 -55.996 114.802 224.402 1.00261.94 ATOM 220 OE1 GLU L 473 -55.604 115.529 225.340 1.00263.77 ATOM 221 OE2 GLU L 473 -56.846 113.877 224.539 1.00259.19 ATOM 222 N MET L 474 -56.645 112.103 219.602 1.00258.75 ATOM 223 CA MET L 474 -56.630 110.891 218.763 1.00259.14 ATOM 224 C MET L 474 -56.480 111.234 217.275 1.00259.64 ATOM 225 O MET L 474 -55.693 110.628 216.534 1.00262.71 ATOM 226 CB MET L 474 -57.921 110.064 218.948 1.00255.08 ATOM 227 CG MET L 474 -57.911 109.019 220.064 1.00255.70 ATOM 228 SD MET L 474 -57.225 107.394 219.650 1.00258.96 ATOM 229 CE MET L 474 -58.535 106.678 218.662 1.00254.97 ATOM 230 N GLY L 475 -57.238 112.231 216.853 1.00256.85 ATOM 231 CA GLY L 475 -57.384 112.513 215.442 1.00256.64 ATOM 232 C GLY L 475 -58.667 111.884 214.939 1.00252.62 ATOM 233 O GLY L 475 -59.022 112.033 213.791 1.00251.86 ATOM 234 N ARG L 476 -59.371 111.174 215.807 1.00250.22 ATOM 235 CA ARG L 476 -60.670 110.616 215.427 1.00246.28 ATOM 236 C ARG L 476 -61.588 110.608 216.629 1.00243.11 ATOM 237 O ARG L 476 -61.989 111.648 217.094 1.00241.49 ATOM 238 CB ARG L 476 -60.550 109.210 214.800 1.00247.40 ATOM 239 CG ARG L 476 -61.843 108.368 214.785 1.00243.70 ATOM 240 CD ARG L 476 -62.825 108.661 213.638 1.00240.90 ATOM 241 NE ARG L 476 -64.162 108.075 213.868 1.00237.02 ATOM 242 CZ ARG L 476 -64.738 107.135 213.112 1.00236.14 ATOM 243 NH1 ARG L 476 -64.119 106.649 212.036 1.00238.84 ATOM 244 NH2 ARG L 476 -65.950 106.685 213.433 1.00232.71 ATOM 245 N GLU L 477 -61.919 109.432 217.138 1.00242.45 ATOM 246 CA GLU L 477 -62.894 109.341 218.221 1.00239.41 ATOM 247 C GLU L 477 -62.386 108.517 219.404 1.00241.45 ATOM 248 O GLU L 477 -61.319 107.913 219.350 1.00245.12 ATOM 249 CB GLU L 477 -64.232 108.779 217.707 1.00235.64 ATOM 250 CG GLU L 477 -64.886 109.579 216.584 1.00233.45 ATOM 251 CD GLU L 477 -65.715 110.753 217.073 1.00230.57 ATOM 252 OE1 GLU L 477 -65.985 111.666 216.261 1.00229.69 ATOM 253 OE2 GLU L 477 -66.105 110.762 218.260 1.00229.40 ATOM 254 N PRO L 478 -63.138 108.529 220.503 1.00239.31 ATOM 255 CA PRO L 478 -62.854 107.613 221.603 1.00241.00 ATOM 256 C PRO L 478 -63.950 106.548 221.797 1.00238.47 ATOM 257 O PRO L 478 -65.104 106.889 222.048 1.00234.90 ATOM 258 CB PRO L 478 -62.796 108.555 222.813 1.00241.06 ATOM 259 CG PRO L 478 -63.546 109.797 222.398 1.00238.02 ATOM 260 CD PRO L 478 -63.962 109.657 220.958 1.00236.39 ATOM 261 N THR L 479 -63.592 105.273 221.665 1.00240.50 ATOM 262 CA THR L 479 -64.542 104.178 221.916 1.00238.72 ATOM 263 C THR L 479 -64.688 103.927 223.408 1.00239.19 ATOM 264 O THR L 479 -63.822 104.333 224.182 1.00241.80 ATOM 265 CB THR L 479 -64.131 102.875 221.208 1.00241.02 ATOM 266 OG1 THR L 479 -62.723 102.666 221.379 1.00245.61 ATOM 267 CG2 THR L 479 -64.477 102.943 219.719 1.00239.54 TER