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 L 1 613 UNP P00579 RPOD_ECOLI 1 613 SEQRES 1 L 33 ALA ARG THR ILE ARG ILE PRO VAL HIS MET ILE GLU THR SEQRES 2 L 33 ILE ASN LYS LEU ASN ARG ILE SER ARG GLN MET LEU GLN SEQRES 3 L 33 GLU MET GLY ARG GLU PRO THR ATOM 1 N ALA L 447 -89.361 119.037 229.625 1.00189.71 ATOM 2 CA ALA L 447 -88.786 118.843 228.285 1.00189.66 ATOM 3 C ALA L 447 -89.111 117.484 227.597 1.00188.44 ATOM 4 O ALA L 447 -89.960 117.414 226.705 1.00184.89 ATOM 5 CB ALA L 447 -87.285 119.082 228.319 1.00194.20 ATOM 6 N ARG L 448 -88.422 116.424 228.035 1.00191.73 ATOM 7 CA ARG L 448 -88.567 115.068 227.503 1.00191.63 ATOM 8 C ARG L 448 -89.863 114.335 227.872 1.00188.74 ATOM 9 O ARG L 448 -90.315 114.337 229.029 1.00189.01 ATOM 10 CB ARG L 448 -87.394 114.187 227.954 1.00196.76 ATOM 11 CG ARG L 448 -86.009 114.604 227.487 1.00200.43 ATOM 12 CD ARG L 448 -84.983 113.572 227.946 1.00205.62 ATOM 13 NE ARG L 448 -83.601 114.006 227.739 1.00209.89 ATOM 14 CZ ARG L 448 -82.529 113.340 228.170 1.00215.18 ATOM 15 NH1 ARG L 448 -82.671 112.201 228.844 1.00216.94 ATOM 16 NH2 ARG L 448 -81.310 113.819 227.933 1.00219.04 ATOM 17 N THR L 449 -90.452 113.728 226.846 1.00186.19 ATOM 18 CA THR L 449 -91.501 112.724 227.005 1.00184.25 ATOM 19 C THR L 449 -91.119 111.715 228.091 1.00187.95 ATOM 20 O THR L 449 -91.914 111.391 228.967 1.00187.33 ATOM 21 CB THR L 449 -91.705 111.940 225.694 1.00182.84 ATOM 22 OG1 THR L 449 -91.790 112.844 224.588 1.00180.47 ATOM 23 CG2 THR L 449 -92.964 111.116 225.761 1.00180.17 ATOM 24 N ILE L 450 -89.886 111.232 228.014 1.00192.16 ATOM 25 CA ILE L 450 -89.330 110.314 228.993 1.00196.55 ATOM 26 C ILE L 450 -88.714 111.063 230.174 1.00199.33 ATOM 27 O ILE L 450 -87.653 111.649 230.012 1.00201.72 ATOM 28 CB ILE L 450 -88.197 109.490 228.346 1.00200.46 ATOM 29 CG1 ILE L 450 -87.226 110.403 227.576 1.00201.35 ATOM 30 CG2 ILE L 450 -88.776 108.464 227.392 1.00198.81 ATOM 31 CD1 ILE L 450 -85.997 109.699 227.035 1.00206.01 ATOM 32 N ARG L 451 -89.353 111.037 231.347 1.00199.37 ATOM 33 CA ARG L 451 -88.749 111.641 232.562 1.00202.67 ATOM 34 C ARG L 451 -87.475 110.928 233.075 1.00208.66 ATOM 35 O ARG L 451 -87.455 109.710 233.216 1.00210.85 ATOM 36 CB ARG L 451 -89.768 111.791 233.718 1.00201.69 ATOM 37 CG ARG L 451 -90.060 110.534 234.540 1.00204.29 ATOM 38 CD ARG L 451 -90.195 110.862 236.024 1.00206.80 ATOM 39 NE ARG L 451 -91.273 110.121 236.682 1.00206.44 ATOM 40 CZ ARG L 451 -91.333 109.896 237.992 1.00209.97 ATOM 41 NH1 ARG L 451 -90.363 110.339 238.778 1.00214.06 ATOM 42 NH2 ARG L 451 -92.347 109.222 238.521 1.00209.74 ATOM 43 N ILE L 452 -86.420 111.692 233.360 1.00211.57 ATOM 44 CA ILE L 452 -85.165 111.119 233.858 1.00217.60 ATOM 45 C ILE L 452 -84.875 111.573 235.270 1.00220.80 ATOM 46 O ILE L 452 -84.578 112.737 235.489 1.00220.63 ATOM 47 CB ILE L 452 -83.960 111.540 233.002 1.00219.58 ATOM 48 CG1 ILE L 452 -84.079 110.974 231.588 1.00217.53 ATOM 49 CG2 ILE L 452 -82.667 111.084 233.655 1.00226.19 ATOM 50 CD1 ILE L 452 -84.269 109.477 231.543 1.00219.16 ATOM 51 N PRO L 453 -84.988 110.660 236.231 1.00223.92 ATOM 52 CA PRO L 453 -84.656 111.038 237.575 1.00227.56 ATOM 53 C PRO L 453 -83.177 111.191 237.843 1.00233.07 ATOM 54 O PRO L 453 -82.311 110.908 237.012 1.00234.73 ATOM 55 CB PRO L 453 -85.251 109.914 238.407 1.00229.45 ATOM 56 CG PRO L 453 -86.431 109.501 237.604 1.00224.27 ATOM 57 CD PRO L 453 -85.897 109.509 236.206 1.00222.70 ATOM 58 N VAL L 454 -82.958 111.646 239.058 1.00236.08 ATOM 59 CA VAL L 454 -81.777 112.356 239.484 1.00240.23 ATOM 60 C VAL L 454 -80.475 111.689 239.112 1.00245.18 ATOM 61 O VAL L 454 -79.590 112.281 238.461 1.00246.03 ATOM 62 CB VAL L 454 -81.802 112.447 241.017 1.00243.99 ATOM 63 CG1 VAL L 454 -81.088 113.704 241.488 1.00245.91 ATOM 64 CG2 VAL L 454 -83.241 112.414 241.514 1.00240.40 ATOM 65 N HIS L 455 -80.354 110.457 239.584 1.00248.96 ATOM 66 CA HIS L 455 -79.118 109.714 239.458 1.00254.83 ATOM 67 C HIS L 455 -78.790 109.507 237.990 1.00253.04 ATOM 68 O HIS L 455 -77.639 109.687 237.541 1.00256.39 ATOM 69 CB HIS L 455 -79.227 108.369 240.202 1.00259.02 ATOM 70 CG HIS L 455 -79.181 108.486 241.703 1.00262.97 ATOM 71 ND1 HIS L 455 -78.577 107.540 242.507 1.00269.71 ATOM 72 CD2 HIS L 455 -79.660 109.436 242.541 1.00261.51 ATOM 73 CE1 HIS L 455 -78.690 107.900 243.773 1.00272.17 ATOM 74 NE2 HIS L 455 -79.341 109.049 243.822 1.00267.29 ATOM 75 N MET L 456 -79.843 109.171 237.252 1.00247.80 ATOM 76 CA MET L 456 -79.780 108.939 235.827 1.00245.42 ATOM 77 C MET L 456 -79.171 110.143 235.135 1.00244.20 ATOM 78 O MET L 456 -78.208 110.038 234.355 1.00246.87 ATOM 79 CB MET L 456 -81.203 108.736 235.320 1.00239.14 ATOM 80 CG MET L 456 -81.308 108.496 233.826 1.00236.23 ATOM 81 SD MET L 456 -80.680 106.882 233.308 1.00241.03 ATOM 82 CE MET L 456 -81.819 105.759 234.130 1.00240.51 ATOM 83 N ILE L 457 -79.757 111.295 235.435 1.00240.44 ATOM 84 CA ILE L 457 -79.350 112.545 234.825 1.00238.88 ATOM 85 C ILE L 457 -77.872 112.833 235.075 1.00244.89 ATOM 86 O ILE L 457 -77.131 113.168 234.136 1.00245.76 ATOM 87 CB ILE L 457 -80.226 113.714 235.324 1.00234.73 ATOM 88 CG1 ILE L 457 -81.521 113.788 234.513 1.00228.17 ATOM 89 CG2 ILE L 457 -79.482 115.040 235.231 1.00235.70 ATOM 90 CD1 ILE L 457 -81.308 114.106 233.047 1.00225.92 ATOM 91 N GLU L 458 -77.457 112.684 236.335 1.00249.28 ATOM 92 CA GLU L 458 -76.066 112.923 236.730 1.00255.53 ATOM 93 C GLU L 458 -75.096 112.126 235.868 1.00259.36 ATOM 94 O GLU L 458 -74.085 112.649 235.314 1.00261.95 ATOM 95 CB GLU L 458 -75.857 112.535 238.197 1.00260.15 ATOM 96 CG GLU L 458 -76.080 113.677 239.168 1.00259.54 ATOM 97 CD GLU L 458 -75.103 114.807 238.939 1.00261.43 ATOM 98 OE1 GLU L 458 -73.880 114.550 238.987 1.00267.18 ATOM 99 OE2 GLU L 458 -75.562 115.947 238.708 1.00257.42 ATOM 100 N THR L 459 -75.419 110.846 235.749 1.00259.99 ATOM 101 CA THR L 459 -74.519 109.972 235.039 1.00264.36 ATOM 102 C THR L 459 -74.493 110.319 233.541 1.00261.20 ATOM 103 O THR L 459 -73.424 110.331 232.949 1.00265.19 ATOM 104 CB THR L 459 -74.762 108.489 235.362 1.00266.90 ATOM 105 OG1 THR L 459 -76.165 108.275 235.552 1.00261.44 ATOM 106 CG2 THR L 459 -74.038 108.124 236.657 1.00273.57 ATOM 107 N ILE L 460 -75.638 110.668 232.950 1.00254.40 ATOM 108 CA ILE L 460 -75.651 111.044 231.526 1.00251.52 ATOM 109 C ILE L 460 -74.797 112.287 231.233 1.00252.87 ATOM 110 O ILE L 460 -74.120 112.360 230.193 1.00254.54 ATOM 111 CB ILE L 460 -77.075 111.238 230.957 1.00244.07 ATOM 112 CG1 ILE L 460 -78.039 110.193 231.515 1.00242.54 ATOM 113 CG2 ILE L 460 -77.058 111.146 229.437 1.00242.31 ATOM 114 CD1 ILE L 460 -79.490 110.497 231.217 1.00235.47 ATOM 115 N ASN L 461 -74.821 113.254 232.153 1.00252.53 ATOM 116 CA ASN L 461 -74.029 114.480 231.979 1.00254.07 ATOM 117 C ASN L 461 -72.550 114.197 231.891 1.00261.21 ATOM 118 O ASN L 461 -71.831 114.748 231.033 1.00262.75 ATOM 119 CB ASN L 461 -74.250 115.435 233.136 1.00253.46 ATOM 120 CG ASN L 461 -75.674 115.423 233.616 1.00247.97 ATOM 121 OD1 ASN L 461 -76.586 115.101 232.856 1.00243.29 ATOM 122 ND2 ASN L 461 -75.879 115.756 234.886 1.00248.81 ATOM 123 N LYS L 462 -72.108 113.335 232.803 1.00265.90 ATOM 124 CA LYS L 462 -70.722 112.904 232.834 1.00273.37 ATOM 125 C LYS L 462 -70.367 112.235 231.498 1.00274.49 ATOM 126 O LYS L 462 -69.337 112.546 230.899 1.00278.44 ATOM 127 CB LYS L 462 -70.455 111.958 234.018 1.00278.12 ATOM 128 CG LYS L 462 -70.184 112.651 235.350 1.00280.38 ATOM 129 CD LYS L 462 -70.050 111.647 236.489 1.00284.92 ATOM 130 CE LYS L 462 -69.726 112.335 237.807 1.00287.73 ATOM 131 NZ LYS L 462 -69.902 111.426 238.974 1.00291.05 ATOM 132 N LEU L 463 -71.258 111.340 231.050 1.00271.10 ATOM 133 CA LEU L 463 -71.136 110.566 229.808 1.00271.69 ATOM 134 C LEU L 463 -70.725 111.451 228.675 1.00270.95 ATOM 135 O LEU L 463 -69.704 111.226 227.992 1.00275.99 ATOM 136 CB LEU L 463 -72.507 110.020 229.393 1.00265.47 ATOM 137 CG LEU L 463 -72.966 108.567 229.497 1.00266.25 ATOM 138 CD1 LEU L 463 -74.382 108.481 228.947 1.00258.95 ATOM 139 CD2 LEU L 463 -72.035 107.649 228.712 1.00271.98 ATOM 140 N ASN L 464 -71.557 112.464 228.474 1.00264.84 ATOM 141 CA ASN L 464 -71.440 113.238 227.265 1.00263.15 ATOM 142 C ASN L 464 -70.207 114.114 227.249 1.00268.03 ATOM 143 O ASN L 464 -69.569 114.299 226.198 1.00270.35 ATOM 144 CB ASN L 464 -72.742 113.968 226.946 1.00255.44 ATOM 145 CG ASN L 464 -73.817 113.011 226.456 1.00251.30 ATOM 146 OD1 ASN L 464 -73.788 112.559 225.310 1.00251.33 ATOM 147 ND2 ASN L 464 -74.755 112.675 227.332 1.00248.10 ATOM 148 N ARG L 465 -69.836 114.600 228.428 1.00270.14 ATOM 149 CA ARG L 465 -68.635 115.418 228.517 1.00275.21 ATOM 150 C ARG L 465 -67.344 114.596 228.230 1.00282.97 ATOM 151 O ARG L 465 -66.397 115.100 227.588 1.00286.87 ATOM 152 CB ARG L 465 -68.627 116.226 229.830 1.00275.31 ATOM 153 CG ARG L 465 -69.867 117.115 229.962 1.00268.09 ATOM 154 CD ARG L 465 -69.877 117.934 231.240 1.00268.45 ATOM 155 NE ARG L 465 -70.282 117.144 232.393 1.00268.77 ATOM 156 CZ ARG L 465 -70.138 117.542 233.649 1.00270.69 ATOM 157 NH1 ARG L 465 -69.596 118.724 233.918 1.00272.35 ATOM 158 NH2 ARG L 465 -70.533 116.755 234.636 1.00271.23 ATOM 159 N ILE L 466 -67.351 113.311 228.611 1.00285.28 ATOM 160 CA ILE L 466 -66.177 112.443 228.384 1.00293.01 ATOM 161 C ILE L 466 -66.095 111.992 226.924 1.00293.27 ATOM 162 O ILE L 466 -64.998 111.801 226.357 1.00299.51 ATOM 163 CB ILE L 466 -66.164 111.177 229.287 1.00296.24 ATOM 164 CG1 ILE L 466 -66.136 111.539 230.771 1.00297.15 ATOM 165 CG2 ILE L 466 -64.961 110.299 228.975 1.00304.52 ATOM 166 CD1 ILE L 466 -66.127 110.314 231.692 1.00300.75 ATOM 167 N SER L 467 -67.278 111.822 226.332 1.00286.68 ATOM 168 CA SER L 467 -67.393 111.381 224.942 1.00286.16 ATOM 169 C SER L 467 -66.601 112.297 224.025 1.00288.60 ATOM 170 O SER L 467 -65.959 111.808 223.092 1.00292.89 ATOM 171 CB SER L 467 -68.856 111.330 224.471 1.00278.07 ATOM 172 OG SER L 467 -69.587 110.292 225.096 1.00276.37 ATOM 173 N ARG L 468 -66.646 113.611 224.290 1.00286.24 ATOM 174 CA ARG L 468 -65.948 114.613 223.452 1.00288.42 ATOM 175 C ARG L 468 -64.430 114.384 223.407 1.00297.42 ATOM 176 O ARG L 468 -63.788 114.324 222.321 1.00301.21 ATOM 177 CB ARG L 468 -66.219 116.043 223.959 1.00285.01 ATOM 178 CG ARG L 468 -67.050 116.926 223.034 1.00279.22 ATOM 179 CD ARG L 468 -68.479 117.133 223.512 1.00271.39 ATOM 180 NE ARG L 468 -69.316 115.957 223.300 1.00268.31 ATOM 181 CZ ARG L 468 -70.641 115.963 223.388 1.00261.48 ATOM 182 NH1 ARG L 468 -71.274 117.089 223.669 1.00257.13 ATOM 183 NH2 ARG L 468 -71.336 114.852 223.185 1.00259.27 ATOM 184 N GLN L 469 -63.870 114.271 224.610 1.00301.05 ATOM 185 CA GLN L 469 -62.456 114.012 224.763 1.00309.84 ATOM 186 C GLN L 469 -62.099 112.750 223.975 1.00314.04 ATOM 187 O GLN L 469 -61.226 112.775 223.088 1.00319.26 ATOM 188 CB GLN L 469 -62.102 113.854 226.242 1.00312.67 ATOM 189 CG GLN L 469 -60.651 113.498 226.510 1.00322.17 ATOM 190 CD GLN L 469 -60.504 112.618 227.740 1.00325.30 ATOM 191 OE1 GLN L 469 -61.502 112.243 228.382 1.00320.36 ATOM 192 NE2 GLN L 469 -59.261 112.266 228.063 1.00333.88 ATOM 193 N MET L 470 -62.810 111.662 224.275 1.00311.84 ATOM 194 CA MET L 470 -62.470 110.374 223.672 1.00316.36 ATOM 195 C MET L 470 -62.580 110.344 222.146 1.00315.65 ATOM 196 O MET L 470 -61.708 109.761 221.487 1.00322.31 ATOM 197 CB MET L 470 -63.178 109.179 224.339 1.00314.78 ATOM 198 CG MET L 470 -62.332 108.523 225.434 1.00321.78 ATOM 199 SD MET L 470 -62.436 106.718 225.547 1.00325.60 ATOM 200 CE MET L 470 -61.448 106.183 224.146 1.00332.65 ATOM 201 N LEU L 471 -63.618 110.982 221.596 1.00308.09 ATOM 202 CA LEU L 471 -63.797 111.049 220.140 1.00307.09 ATOM 203 C LEU L 471 -62.576 111.778 219.560 1.00313.34 ATOM 204 O LEU L 471 -62.034 111.351 218.533 1.00317.92 ATOM 205 CB LEU L 471 -65.114 111.771 219.798 1.00298.00 ATOM 206 CG LEU L 471 -65.886 111.450 218.511 1.00294.44 ATOM 207 CD1 LEU L 471 -67.388 111.458 218.762 1.00285.67 ATOM 208 CD2 LEU L 471 -65.515 112.396 217.377 1.00295.52 ATOM 209 N GLN L 472 -62.109 112.825 220.255 1.00314.12 ATOM 210 CA GLN L 472 -60.977 113.617 219.731 1.00319.98 ATOM 211 C GLN L 472 -59.625 112.870 219.765 1.00329.84 ATOM 212 O GLN L 472 -58.837 112.884 218.795 1.00335.40 ATOM 213 CB GLN L 472 -60.879 115.013 220.380 1.00318.12 ATOM 214 CG GLN L 472 -60.213 115.065 221.743 1.00321.81 ATOM 215 CD GLN L 472 -59.710 116.451 222.071 1.00322.82 ATOM 216 OE1 GLN L 472 -60.378 117.218 222.764 1.00317.52 ATOM 217 NE2 GLN L 472 -58.533 116.786 221.558 1.00329.91 ATOM 218 N GLU L 473 -59.364 112.183 220.865 1.00332.41 ATOM 219 CA GLU L 473 -58.111 111.465 220.946 1.00341.97 ATOM 220 C GLU L 473 -58.092 110.212 220.058 1.00345.04 ATOM 221 O GLU L 473 -57.116 110.006 219.332 1.00352.36 ATOM 222 CB GLU L 473 -57.694 111.216 222.402 1.00344.92 ATOM 223 CG GLU L 473 -57.154 112.472 223.079 1.00345.86 ATOM 224 CD GLU L 473 -57.387 112.484 224.576 1.00344.30 ATOM 225 OE1 GLU L 473 -57.049 113.497 225.219 1.00344.61 ATOM 226 OE2 GLU L 473 -57.909 111.485 225.113 1.00343.02 ATOM 227 N MET L 474 -59.164 109.411 220.078 1.00339.70 ATOM 228 CA MET L 474 -59.261 108.210 219.215 1.00342.14 ATOM 229 C MET L 474 -59.180 108.550 217.727 1.00342.64 ATOM 230 O MET L 474 -58.750 107.738 216.899 1.00347.95 ATOM 231 CB MET L 474 -60.561 107.410 219.470 1.00335.42 ATOM 232 CG MET L 474 -60.414 106.035 220.133 1.00339.63 ATOM 233 SD MET L 474 -60.216 104.598 219.041 1.00345.09 ATOM 234 CE MET L 474 -61.654 104.699 217.976 1.00335.79 ATOM 235 N GLY L 475 -59.618 109.760 217.395 1.00337.27 ATOM 236 CA GLY L 475 -59.815 110.128 216.008 1.00336.21 ATOM 237 C GLY L 475 -61.000 109.371 215.419 1.00330.51 ATOM 238 O GLY L 475 -61.160 109.301 214.217 1.00330.69 ATOM 239 N ARG L 476 -61.828 108.775 216.264 1.00325.78 ATOM 240 CA ARG L 476 -63.040 108.136 215.769 1.00319.80 ATOM 241 C ARG L 476 -64.085 108.070 216.875 1.00312.71 ATOM 242 O ARG L 476 -64.417 109.067 217.499 1.00308.22 ATOM 243 CB ARG L 476 -62.750 106.737 215.185 1.00325.26 ATOM 244 CG ARG L 476 -63.925 106.107 214.436 1.00319.87 ATOM 245 CD ARG L 476 -64.070 106.646 213.017 1.00318.96 ATOM 246 NE ARG L 476 -65.440 107.070 212.707 1.00309.74 ATOM 247 CZ ARG L 476 -66.405 106.271 212.257 1.00306.03 ATOM 248 NH1 ARG L 476 -66.168 104.982 212.064 1.00310.69 ATOM 249 NH2 ARG L 476 -67.613 106.763 212.005 1.00297.89 ATOM 250 N GLU L 477 -64.632 106.883 217.095 1.00311.89 ATOM 251 CA GLU L 477 -65.649 106.720 218.133 1.00305.64 ATOM 252 C GLU L 477 -65.160 105.743 219.192 1.00310.65 ATOM 253 O GLU L 477 -64.543 104.723 218.870 1.00317.09 ATOM 254 CB GLU L 477 -67.000 106.269 217.538 1.00298.84 ATOM 255 CG GLU L 477 -67.749 107.324 216.719 1.00292.40 ATOM 256 CD GLU L 477 -68.802 108.097 217.511 1.00284.39 ATOM 257 OE1 GLU L 477 -69.821 108.509 216.903 1.00278.06 ATOM 258 OE2 GLU L 477 -68.630 108.296 218.735 1.00284.61 ATOM 259 N PRO L 478 -65.420 106.059 220.467 1.00308.13 ATOM 260 CA PRO L 478 -65.084 105.140 221.556 1.00312.47 ATOM 261 C PRO L 478 -66.071 103.965 221.637 1.00309.65 ATOM 262 O PRO L 478 -67.263 104.175 221.879 1.00302.10 ATOM 263 CB PRO L 478 -65.169 106.027 222.805 1.00309.87 ATOM 264 CG PRO L 478 -66.090 107.147 222.436 1.00301.66 ATOM 265 CD PRO L 478 -66.010 107.328 220.946 1.00301.59 ATOM 266 N THR L 479 -65.571 102.740 221.443 1.00316.04 ATOM 267 CA THR L 479 -66.388 101.523 221.532 1.00314.66 ATOM 268 C THR L 479 -66.870 101.353 222.978 1.00312.67 ATOM 269 O THR L 479 -66.160 101.781 223.900 1.00315.97 ATOM 270 CB THR L 479 -65.600 100.266 221.068 1.00323.23 ATOM 271 OG1 THR L 479 -64.213 100.397 221.420 1.00331.46 ATOM 272 CG2 THR L 479 -65.701 100.078 219.556 1.00323.15 TER