HEADER TRANSCRIPTION/DNA/RNA 31-DEC-69 4YLO TITLE E. coli Transcription Initiation Complex - 16-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. 6.00 ANGSTORMS DBREF 4YLO F 1 613 UNP P00579 RPOD_ECOLI 1 613 SEQRES 1 F 32 ARG THR ILE ARG ILE PRO VAL HIS MET ILE GLU THR ILE SEQRES 2 F 32 ASN LYS LEU ASN ARG ILE SER ARG GLN MET LEU GLN GLU SEQRES 3 F 32 MET GLY ARG GLU PRO THR ATOM 1 N ARG F 448 -24.654 48.247 4.738 1.00206.51 ATOM 2 CA ARG F 448 -24.535 49.541 4.042 1.00204.69 ATOM 3 C ARG F 448 -23.229 50.305 4.275 1.00201.89 ATOM 4 O ARG F 448 -22.629 50.243 5.359 1.00202.15 ATOM 5 CB ARG F 448 -25.690 50.466 4.463 1.00207.46 ATOM 6 CG ARG F 448 -27.080 49.835 4.437 1.00210.97 ATOM 7 CD ARG F 448 -28.174 50.892 4.544 1.00213.49 ATOM 8 NE ARG F 448 -29.362 50.542 3.757 1.00215.81 ATOM 9 CZ ARG F 448 -30.450 51.306 3.640 1.00218.49 ATOM 10 NH1 ARG F 448 -30.510 52.474 4.271 1.00219.19 ATOM 11 NH2 ARG F 448 -31.481 50.903 2.896 1.00220.79 ATOM 12 N THR F 449 -22.820 51.035 3.238 1.00199.50 ATOM 13 CA THR F 449 -21.695 51.954 3.299 1.00197.09 ATOM 14 C THR F 449 -21.863 52.918 4.478 1.00198.79 ATOM 15 O THR F 449 -20.945 53.156 5.250 1.00198.10 ATOM 16 CB THR F 449 -21.614 52.767 1.999 1.00195.25 ATOM 17 OG1 THR F 449 -21.805 51.898 0.871 1.00194.54 ATOM 18 CG2 THR F 449 -20.279 53.457 1.890 1.00192.50 ATOM 19 N ILE F 450 -23.057 53.460 4.594 1.00201.31 ATOM 20 CA ILE F 450 -23.400 54.312 5.690 1.00203.54 ATOM 21 C ILE F 450 -24.132 53.455 6.694 1.00206.50 ATOM 22 O ILE F 450 -25.249 53.022 6.435 1.00208.58 ATOM 23 CB ILE F 450 -24.333 55.405 5.188 1.00204.99 ATOM 24 CG1 ILE F 450 -25.375 54.814 4.212 1.00205.99 ATOM 25 CG2 ILE F 450 -23.509 56.486 4.520 1.00202.59 ATOM 26 CD1 ILE F 450 -24.827 54.181 2.939 1.00203.14 ATOM 27 N ARG F 451 -23.514 53.205 7.843 1.00206.97 ATOM 28 CA ARG F 451 -24.192 52.530 8.967 1.00210.24 ATOM 29 C ARG F 451 -25.448 53.269 9.455 1.00213.68 ATOM 30 O ARG F 451 -25.433 54.491 9.621 1.00213.98 ATOM 31 CB ARG F 451 -23.260 52.426 10.181 1.00210.46 ATOM 32 CG ARG F 451 -23.105 53.756 10.922 1.00211.42 ATOM 33 CD ARG F 451 -23.110 53.651 12.453 1.00214.34 ATOM 34 NE ARG F 451 -23.101 54.981 13.096 1.00215.71 ATOM 35 CZ ARG F 451 -22.885 55.214 14.396 1.00218.04 ATOM 36 NH1 ARG F 451 -22.650 54.203 15.223 1.00219.29 ATOM 37 NH2 ARG F 451 -22.897 56.461 14.874 1.00219.40 ATOM 38 N ILE F 452 -26.518 52.532 9.730 1.00216.58 ATOM 39 CA ILE F 452 -27.738 53.164 10.218 1.00220.23 ATOM 40 C ILE F 452 -28.207 52.584 11.529 1.00223.65 ATOM 41 O ILE F 452 -28.579 51.429 11.576 1.00224.79 ATOM 42 CB ILE F 452 -28.882 53.029 9.209 1.00221.43 ATOM 43 CG1 ILE F 452 -28.631 53.942 8.007 1.00218.99 ATOM 44 CG2 ILE F 452 -30.210 53.344 9.877 1.00225.94 ATOM 45 CD1 ILE F 452 -28.240 55.362 8.366 1.00218.74 ATOM 46 N PRO F 453 -28.161 53.380 12.602 1.00225.46 ATOM 47 CA PRO F 453 -28.734 52.920 13.836 1.00229.20 ATOM 48 C PRO F 453 -30.218 52.674 13.805 1.00232.85 ATOM 49 O PRO F 453 -30.959 53.052 12.904 1.00233.10 ATOM 50 CB PRO F 453 -28.417 54.041 14.809 1.00230.41 ATOM 51 CG PRO F 453 -27.080 54.464 14.354 1.00226.43 ATOM 52 CD PRO F 453 -27.173 54.437 12.849 1.00223.68 ATOM 53 N VAL F 454 -30.610 52.047 14.888 1.00236.02 ATOM 54 CA VAL F 454 -31.802 51.258 14.973 1.00239.45 ATOM 55 C VAL F 454 -33.056 52.026 14.634 1.00242.15 ATOM 56 O VAL F 454 -33.837 51.610 13.762 1.00242.82 ATOM 57 CB VAL F 454 -31.912 50.688 16.396 1.00242.76 ATOM 58 CG1 VAL F 454 -31.400 49.247 16.434 1.00241.96 ATOM 59 CG2 VAL F 454 -31.132 51.580 17.363 1.00242.60 ATOM 60 N HIS F 455 -33.259 53.138 15.339 1.00244.06 ATOM 61 CA HIS F 455 -34.488 53.915 15.212 1.00247.45 ATOM 62 C HIS F 455 -34.772 54.273 13.755 1.00245.64 ATOM 63 O HIS F 455 -35.908 54.166 13.254 1.00248.26 ATOM 64 CB HIS F 455 -34.423 55.179 16.095 1.00249.24 ATOM 65 CG HIS F 455 -34.894 54.974 17.509 1.00253.50 ATOM 66 ND1 HIS F 455 -36.239 54.971 17.854 1.00258.32 ATOM 67 CD2 HIS F 455 -34.197 54.793 18.666 1.00253.93 ATOM 68 CE1 HIS F 455 -36.352 54.784 19.158 1.00261.44 ATOM 69 NE2 HIS F 455 -35.127 54.674 19.675 1.00258.88 ATOM 70 N MET F 456 -33.684 54.637 13.087 1.00241.25 ATOM 71 CA MET F 456 -33.662 55.044 11.699 1.00238.89 ATOM 72 C MET F 456 -34.211 53.922 10.847 1.00238.96 ATOM 73 O MET F 456 -35.129 54.094 10.026 1.00240.58 ATOM 74 CB MET F 456 -32.198 55.274 11.320 1.00234.04 ATOM 75 CG MET F 456 -31.944 56.086 10.053 1.00231.51 ATOM 76 SD MET F 456 -31.855 57.900 10.234 1.00232.34 ATOM 77 CE MET F 456 -30.699 58.118 11.600 1.00231.50 ATOM 78 N ILE F 457 -33.608 52.768 11.064 1.00237.42 ATOM 79 CA ILE F 457 -33.949 51.578 10.342 1.00237.40 ATOM 80 C ILE F 457 -35.433 51.256 10.439 1.00242.19 ATOM 81 O ILE F 457 -36.145 51.052 9.431 1.00243.03 ATOM 82 CB ILE F 457 -33.166 50.425 10.958 1.00236.29 ATOM 83 CG1 ILE F 457 -31.672 50.697 10.809 1.00231.73 ATOM 84 CG2 ILE F 457 -33.571 49.109 10.328 1.00236.94 ATOM 85 CD1 ILE F 457 -31.263 50.939 9.374 1.00228.27 ATOM 86 N GLU F 458 -35.886 51.206 11.685 1.00245.57 ATOM 87 CA GLU F 458 -37.264 50.841 11.962 1.00250.55 ATOM 88 C GLU F 458 -38.235 51.753 11.231 1.00252.56 ATOM 89 O GLU F 458 -39.252 51.316 10.672 1.00255.32 ATOM 90 CB GLU F 458 -37.542 50.871 13.459 1.00253.94 ATOM 91 CG GLU F 458 -37.171 49.587 14.171 1.00254.30 ATOM 92 CD GLU F 458 -38.094 49.299 15.334 1.00259.53 ATOM 93 OE1 GLU F 458 -38.404 50.237 16.105 1.00261.72 ATOM 94 OE2 GLU F 458 -38.513 48.130 15.466 1.00261.65 ATOM 95 N THR F 459 -37.904 53.031 11.235 1.00251.41 ATOM 96 CA THR F 459 -38.769 53.991 10.595 1.00253.55 ATOM 97 C THR F 459 -38.856 53.756 9.085 1.00251.73 ATOM 98 O THR F 459 -39.937 53.821 8.509 1.00254.91 ATOM 99 CB THR F 459 -38.273 55.389 10.921 1.00252.64 ATOM 100 OG1 THR F 459 -36.844 55.375 10.854 1.00247.67 ATOM 101 CG2 THR F 459 -38.699 55.768 12.345 1.00256.45 ATOM 102 N ILE F 460 -37.719 53.443 8.471 1.00246.90 ATOM 103 CA ILE F 460 -37.662 53.157 7.043 1.00244.91 ATOM 104 C ILE F 460 -38.630 52.044 6.691 1.00247.91 ATOM 105 O ILE F 460 -39.401 52.109 5.717 1.00249.65 ATOM 106 CB ILE F 460 -36.284 52.617 6.693 1.00239.77 ATOM 107 CG1 ILE F 460 -35.209 53.519 7.283 1.00236.99 ATOM 108 CG2 ILE F 460 -36.151 52.459 5.191 1.00237.64 ATOM 109 CD1 ILE F 460 -33.916 52.797 7.569 1.00233.25 ATOM 110 N ASN F 461 -38.561 51.017 7.524 1.00248.76 ATOM 111 CA ASN F 461 -39.398 49.833 7.406 1.00251.89 ATOM 112 C ASN F 461 -40.887 50.121 7.396 1.00257.30 ATOM 113 O ASN F 461 -41.656 49.610 6.568 1.00259.48 ATOM 114 CB ASN F 461 -39.104 48.982 8.616 1.00252.60 ATOM 115 CG ASN F 461 -37.762 49.321 9.208 1.00248.58 ATOM 116 OD1 ASN F 461 -36.925 49.912 8.523 1.00244.64 ATOM 117 ND2 ASN F 461 -37.552 48.980 10.477 1.00249.79 ATOM 118 N LYS F 462 -41.270 50.964 8.343 1.00259.69 ATOM 119 CA LYS F 462 -42.654 51.366 8.489 1.00265.16 ATOM 120 C LYS F 462 -43.136 51.989 7.174 1.00265.56 ATOM 121 O LYS F 462 -44.218 51.679 6.641 1.00269.44 ATOM 122 CB LYS F 462 -42.772 52.374 9.636 1.00267.00 ATOM 123 CG LYS F 462 -42.021 51.960 10.903 1.00265.79 ATOM 124 CD LYS F 462 -42.013 53.052 11.975 1.00267.34 ATOM 125 CE LYS F 462 -41.245 52.628 13.234 1.00266.38 ATOM 126 NZ LYS F 462 -41.221 53.649 14.329 1.00268.21 ATOM 127 N LEU F 463 -42.276 52.865 6.665 1.00261.61 ATOM 128 CA LEU F 463 -42.522 53.635 5.473 1.00261.48 ATOM 129 C LEU F 463 -42.968 52.758 4.349 1.00262.19 ATOM 130 O LEU F 463 -44.015 52.994 3.709 1.00266.03 ATOM 131 CB LEU F 463 -41.215 54.285 5.026 1.00256.01 ATOM 132 CG LEU F 463 -41.157 55.803 4.841 1.00256.06 ATOM 133 CD1 LEU F 463 -39.779 56.208 4.334 1.00250.45 ATOM 134 CD2 LEU F 463 -42.244 56.271 3.874 1.00259.72 ATOM 135 N ASN F 464 -42.149 51.759 4.071 1.00258.66 ATOM 136 CA ASN F 464 -42.428 51.036 2.850 1.00258.90 ATOM 137 C ASN F 464 -43.640 50.149 2.964 1.00264.12 ATOM 138 O ASN F 464 -44.367 49.958 1.982 1.00266.57 ATOM 139 CB ASN F 464 -41.205 50.334 2.268 1.00253.75 ATOM 140 CG ASN F 464 -40.491 51.194 1.233 1.00250.10 ATOM 141 OD1 ASN F 464 -40.973 51.373 0.105 1.00251.31 ATOM 142 ND2 ASN F 464 -39.336 51.736 1.611 1.00245.87 ATOM 143 N ARG F 465 -43.859 49.635 4.170 1.00266.07 ATOM 144 CA ARG F 465 -45.023 48.792 4.386 1.00271.40 ATOM 145 C ARG F 465 -46.319 49.579 4.108 1.00276.53 ATOM 146 O ARG F 465 -47.246 49.089 3.428 1.00280.32 ATOM 147 CB ARG F 465 -44.994 48.154 5.786 1.00272.72 ATOM 148 CG ARG F 465 -43.856 47.153 5.984 1.00268.69 ATOM 149 CD ARG F 465 -44.092 46.225 7.170 1.00271.39 ATOM 150 NE ARG F 465 -44.044 46.922 8.453 1.00272.16 ATOM 151 CZ ARG F 465 -44.254 46.340 9.629 1.00274.77 ATOM 152 NH1 ARG F 465 -44.528 45.045 9.688 1.00276.86 ATOM 153 NH2 ARG F 465 -44.191 47.054 10.744 1.00275.52 ATOM 154 N ILE F 466 -46.359 50.820 4.581 1.00276.82 ATOM 155 CA ILE F 466 -47.557 51.631 4.398 1.00281.95 ATOM 156 C ILE F 466 -47.709 52.124 2.957 1.00281.67 ATOM 157 O ILE F 466 -48.833 52.345 2.459 1.00286.60 ATOM 158 CB ILE F 466 -47.620 52.799 5.402 1.00283.06 ATOM 159 CG1 ILE F 466 -47.530 52.262 6.833 1.00283.87 ATOM 160 CG2 ILE F 466 -48.905 53.590 5.223 1.00288.92 ATOM 161 CD1 ILE F 466 -47.873 53.277 7.901 1.00286.55 ATOM 162 N SER F 467 -46.555 52.270 2.306 1.00276.05 ATOM 163 CA SER F 467 -46.474 52.773 0.945 1.00274.99 ATOM 164 C SER F 467 -47.370 51.991 0.009 1.00278.64 ATOM 165 O SER F 467 -48.061 52.593 -0.826 1.00281.60 ATOM 166 CB SER F 467 -45.031 52.722 0.434 1.00268.34 ATOM 167 OG SER F 467 -44.184 53.546 1.215 1.00265.16 ATOM 168 N ARG F 468 -47.349 50.661 0.159 1.00278.70 ATOM 169 CA ARG F 468 -48.127 49.757 -0.713 1.00282.19 ATOM 170 C ARG F 468 -49.619 50.012 -0.642 1.00289.25 ATOM 171 O ARG F 468 -50.320 50.126 -1.664 1.00292.43 ATOM 172 CB ARG F 468 -47.938 48.310 -0.292 1.00281.91 ATOM 173 CG ARG F 468 -46.646 47.677 -0.731 1.00276.12 ATOM 174 CD ARG F 468 -46.420 46.438 0.102 1.00276.09 ATOM 175 NE ARG F 468 -45.304 45.668 -0.407 1.00271.48 ATOM 176 CZ ARG F 468 -44.411 45.068 0.371 1.00268.42 ATOM 177 NH1 ARG F 468 -44.496 45.172 1.696 1.00269.39 ATOM 178 NH2 ARG F 468 -43.422 44.386 -0.177 1.00264.58 ATOM 179 N GLN F 469 -50.077 50.051 0.605 1.00291.86 ATOM 180 CA GLN F 469 -51.445 50.330 0.948 1.00298.67 ATOM 181 C GLN F 469 -51.865 51.623 0.261 1.00300.45 ATOM 182 O GLN F 469 -52.821 51.655 -0.547 1.00305.13 ATOM 183 CB GLN F 469 -51.511 50.434 2.477 1.00299.63 ATOM 184 CG GLN F 469 -52.544 51.374 3.083 1.00305.03 ATOM 185 CD GLN F 469 -52.318 51.569 4.576 1.00304.75 ATOM 186 OE1 GLN F 469 -51.466 50.908 5.180 1.00300.98 ATOM 187 NE2 GLN F 469 -53.073 52.485 5.177 1.00309.00 ATOM 188 N MET F 470 -51.102 52.673 0.564 1.00296.77 ATOM 189 CA MET F 470 -51.429 54.014 0.094 1.00298.49 ATOM 190 C MET F 470 -51.505 54.106 -1.424 1.00298.55 ATOM 191 O MET F 470 -52.432 54.745 -1.974 1.00303.42 ATOM 192 CB MET F 470 -50.464 55.074 0.656 1.00294.20 ATOM 193 CG MET F 470 -50.896 55.679 1.992 1.00297.14 ATOM 194 SD MET F 470 -50.338 57.378 2.283 1.00295.42 ATOM 195 CE MET F 470 -51.526 58.319 1.323 1.00301.53 ATOM 196 N LEU F 471 -50.540 53.465 -2.089 1.00293.45 ATOM 197 CA LEU F 471 -50.461 53.475 -3.542 1.00292.94 ATOM 198 C LEU F 471 -51.699 52.787 -4.107 1.00299.14 ATOM 199 O LEU F 471 -52.272 53.215 -5.135 1.00302.28 ATOM 200 CB LEU F 471 -49.198 52.727 -3.979 1.00286.57 ATOM 201 CG LEU F 471 -48.408 53.219 -5.192 1.00282.82 ATOM 202 CD1 LEU F 471 -46.941 52.853 -5.041 1.00275.77 ATOM 203 CD2 LEU F 471 -48.976 52.661 -6.487 1.00285.70 ATOM 204 N GLN F 472 -52.125 51.740 -3.404 1.00301.25 ATOM 205 CA GLN F 472 -53.200 50.940 -3.952 1.00306.92 ATOM 206 C GLN F 472 -54.576 51.572 -3.742 1.00314.24 ATOM 207 O GLN F 472 -55.461 51.411 -4.581 1.00319.20 ATOM 208 CB GLN F 472 -53.133 49.505 -3.465 1.00306.76 ATOM 209 CG GLN F 472 -53.417 49.357 -1.998 1.00308.31 ATOM 210 CD GLN F 472 -53.895 47.975 -1.694 1.00311.29 ATOM 211 OE1 GLN F 472 -54.722 47.780 -0.801 1.00315.86 ATOM 212 NE2 GLN F 472 -53.394 46.999 -2.455 1.00309.05 ATOM 213 N GLU F 473 -54.746 52.327 -2.661 1.00315.15 ATOM 214 CA GLU F 473 -56.025 53.006 -2.434 1.00322.24 ATOM 215 C GLU F 473 -56.135 54.386 -3.076 1.00323.23 ATOM 216 O GLU F 473 -57.233 54.790 -3.466 1.00329.61 ATOM 217 CB GLU F 473 -56.337 53.082 -0.951 1.00324.04 ATOM 218 CG GLU F 473 -56.320 51.726 -0.289 1.00323.88 ATOM 219 CD GLU F 473 -55.402 51.723 0.920 1.00319.12 ATOM 220 OE1 GLU F 473 -54.980 50.612 1.362 1.00317.02 ATOM 221 OE2 GLU F 473 -55.086 52.836 1.406 1.00317.67 ATOM 222 N MET F 474 -55.017 55.105 -3.212 1.00317.31 ATOM 223 CA MET F 474 -55.059 56.401 -3.909 1.00318.22 ATOM 224 C MET F 474 -55.240 56.196 -5.414 1.00319.37 ATOM 225 O MET F 474 -55.937 56.970 -6.088 1.00323.91 ATOM 226 CB MET F 474 -53.803 57.247 -3.629 1.00311.84 ATOM 227 CG MET F 474 -53.971 58.760 -3.809 1.00313.83 ATOM 228 SD MET F 474 -53.352 59.474 -5.353 1.00311.28 ATOM 229 CE MET F 474 -53.432 61.234 -5.010 1.00313.34 ATOM 230 N GLY F 475 -54.620 55.140 -5.927 1.00315.59 ATOM 231 CA GLY F 475 -54.592 54.903 -7.360 1.00315.82 ATOM 232 C GLY F 475 -53.217 55.186 -7.928 1.00308.63 ATOM 233 O GLY F 475 -52.838 54.626 -8.936 1.00306.83 ATOM 234 N ARG F 476 -52.460 56.049 -7.275 1.00304.70 ATOM 235 CA ARG F 476 -51.123 56.317 -7.735 1.00297.95 ATOM 236 C ARG F 476 -50.205 56.453 -6.548 1.00292.97 ATOM 237 O ARG F 476 -50.004 55.525 -5.805 1.00291.39 ATOM 238 CB ARG F 476 -51.074 57.582 -8.602 1.00298.73 ATOM 239 CG ARG F 476 -49.706 57.853 -9.222 1.00292.09 ATOM 240 CD ARG F 476 -49.436 56.982 -10.445 1.00290.77 ATOM 241 NE ARG F 476 -48.031 56.582 -10.563 1.00283.55 ATOM 242 CZ ARG F 476 -47.079 57.291 -11.176 1.00279.56 ATOM 243 NH1 ARG F 476 -47.358 58.462 -11.741 1.00281.98 ATOM 244 NH2 ARG F 476 -45.838 56.823 -11.224 1.00273.35 ATOM 245 N GLU F 477 -49.640 57.635 -6.371 1.00290.74 ATOM 246 CA GLU F 477 -48.599 57.810 -5.370 1.00285.55 ATOM 247 C GLU F 477 -49.051 58.650 -4.185 1.00288.30 ATOM 248 O GLU F 477 -49.910 59.521 -4.315 1.00293.27 ATOM 249 CB GLU F 477 -47.332 58.411 -5.996 1.00279.86 ATOM 250 CG GLU F 477 -46.639 57.516 -7.014 1.00276.12 ATOM 251 CD GLU F 477 -45.998 56.288 -6.393 1.00272.38 ATOM 252 OE1 GLU F 477 -45.556 55.402 -7.161 1.00270.07 ATOM 253 OE2 GLU F 477 -45.932 56.204 -5.144 1.00271.96 ATOM 254 N PRO F 478 -48.480 58.371 -3.012 1.00285.38 ATOM 255 CA PRO F 478 -48.667 59.287 -1.890 1.00287.16 ATOM 256 C PRO F 478 -47.709 60.495 -1.961 1.00283.61 ATOM 257 O PRO F 478 -46.489 60.313 -1.885 1.00277.72 ATOM 258 CB PRO F 478 -48.331 58.413 -0.678 1.00285.19 ATOM 259 CG PRO F 478 -47.341 57.423 -1.196 1.00279.71 ATOM 260 CD PRO F 478 -47.696 57.178 -2.639 1.00280.92 ATOM 261 N THR F 479 -48.252 61.710 -2.123 1.00287.39 ATOM 262 CA THR F 479 -47.451 62.951 -1.974 1.00285.00 ATOM 263 C THR F 479 -46.963 63.048 -0.517 1.00283.25 ATOM 264 O THR F 479 -47.637 62.517 0.382 1.00286.13 ATOM 265 CB THR F 479 -48.224 64.236 -2.412 1.00290.27 ATOM 266 OG1 THR F 479 -49.517 64.278 -1.795 1.00296.79 ATOM 267 CG2 THR F 479 -48.401 64.297 -3.932 1.00291.04 TER