0.014348 0.008284 0.000000 0.000000 0.016567 0.000000 0.000000 0.000000 0.011890 0.00000 0.00000 0.00000 Jovine, L. Hainzl, T. Oubridge, C. Scott, W.G. Li, J. Sixma, T.K. Wonacott, A. Skarzynski, T. Nagai, K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 69.697 69.697 84.102 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer Lu 3 174.967 LUTETIUM (III) ION LU non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer C10 H15 N5 O11 P2 443.201 n GUANOSINE-3',5'-DIPHOSPHATE RNA linking O4 S -2 96.063 SULFATE ION non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N O N 74 N P N 75 N O N 76 N O N 77 N O N 78 N C N 79 R C N 80 N O N 81 S C N 82 N O N 83 R C N 84 N O N 85 R C Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N C N 91 N O N 92 N N N 93 N C N 94 N N N 95 N N Y 96 N C N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N O N 112 N H N 113 N H N 114 N LU N 115 N MG N 116 N P N 117 N O N 118 N O N 119 N O N 120 N P N 121 N O N 122 N O N 123 N O N 124 N O N 125 N C N 126 R C N 127 N O N 128 S C N 129 N O N 130 R C N 131 N O N 132 R C Y 133 N N Y 134 N C Y 135 N N Y 136 N C N 137 N C N 138 N O N 139 N N N 140 N C N 141 N N N 142 N N Y 143 N C N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N S N 160 N O N 161 N O N 162 N O N 163 N O N 164 N O N 165 N P N 166 N O N 167 N O N 168 N O N 169 N C N 170 R C N 171 N O N 172 S C N 173 N O N 174 R C N 175 N O N 176 R C N 177 N N N 178 N C N 179 N O N 180 N N N 181 N C N 182 N O N 183 N C N 184 N C N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N doub N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing Y 147 N sing Y 148 N sing Y 149 N doub N 150 N sing Y 151 N sing N 152 N sing Y 153 N doub N 154 N doub N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N doub N 160 N sing N 161 N sing N 162 N sing N 163 N doub N 164 N doub N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N doub N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N doub N 194 N sing N 195 N sing N 196 N sing N 197 N doub N 198 N sing N 199 N doub N 200 N sing N 201 N sing UK Structure Fold.Des. FODEFH 1263 0969-2126 8 527 540 10.1016/S0969-2126(00)00137-4 10801497 Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA. 2000 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 56 1033 1037 10.1107/S0907444900006910 Crystallization and preliminary X-ray analysis of the conserved domain IV of E. coli 4.5S RNA 2000 10.2210/pdb1duh/pdb pdb_00001duh 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 IMAGE PLATE 1999-08-01 MARRESEARCH MAD M x-ray 1 1.0302 1.0 1.3366 1.0 1.3369 1.0 0.9968 1.0 1.3359 1.0 5.2R ELETTRA 1.0302, 1.3366, 1.3369, 0.9968, 1.3359 SYNCHROTRON ELETTRA BEAMLINE 5.2R 14663.736 4.5S RNA DOMAIN IV DOMAIN IV 1 syn polymer 174.967 LUTETIUM (III) ION 1 syn non-polymer 24.305 MAGNESIUM ION 1 syn non-polymer 96.063 SULFATE ION 2 syn non-polymer 18.015 water 6 nat water no yes CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGA(PGP) CUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAG A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n 1 4.15 76.9 VAPOR DIFFUSION, SITTING DROP 6.0 CRYSTALLIZED FROM 1.60-1.90 M (NH4)2SO4, 0.09 M MAGNESIUM ACETATE, 0.05 M SODIUM CACODYLATE PH 6.0, AT 303 K. CRYSTALS WERE STABILISED AT 292 K IN A SOLUTION OF 2.20 M (NH4)2SO4, 0.01 M MGCL2, 0.05 M BIS-TRIS-HCL PH 6.0. SOAK CONDITIONS: CRYSTALS WERE SOAKED IN STABILISATION SOLUTION CONTAINING 0.002 M LUTETIUM CHLORIDE HEXAHYDRATE. CRYOPROTECTION CONDITIONS: AFTER ADDITION OF 20% GLYCEROL (W/V) TO THE SOAK SOLUTION, CRYSTALS WERE FLASH-FROZEN IN LIQUID NITROGEN., VAPOR DIFFUSION, SITTING DROP, temperature 303.15K 303.15 MAGNESIUM ACETATE 1 SODIUM CACODYLATE 1 BIS-TRIS-HCL 1 (NH4)2SO4 1 MGCL2 1 LUCL3 1 (NH4)2SO4 2 BIS-TRIS-HCL 2 10.286 1 19 A 31 A 75 1.428 A_C31:PGP75_A 1 -13.615 0.569 -0.156 -0.528 1.281 1 20 A 32 A 74 4.093 A_U32:A74_A 2 -16.429 -0.039 0.276 -0.305 -0.876 1 19 A 33 A 73 0.198 A_C33:G73_A 3 -9.775 0.330 0.294 -0.321 5.243 1 20 A 34 A 72 10.563 A_U34:A72_A 4 -0.181 0.090 -0.205 -0.089 6.409 1 A 35 A 71 9.821 A_G35:C71_A 5 -7.541 0.339 1.035 0.088 0.363 1 28 A 36 A 70 3.557 A_U36:G70_A 6 -7.213 1.988 0.561 -0.384 -5.645 1 28 A 37 A 69 2.583 A_U37:G69_A 7 -8.165 2.087 0.134 -0.582 -6.795 1 20 A 38 A 68 4.613 A_U38:A68_A 8 -9.445 0.353 0.567 -0.045 -0.012 1 19 A 43 A 66 1.259 A_G43:C66_A 9 -2.060 -0.732 -0.125 -0.192 -6.507 1 19 A 44 A 65 -0.024 A_G44:C65_A 10 -10.547 0.125 -0.052 -0.109 -4.324 1 28 A 45 A 64 4.099 A_U45:G64_A 11 -4.440 1.965 0.096 -0.572 1.310 6 A 46 A 63 -21.379 A_C46:A63_A 12 -8.844 6.134 0.654 -4.675 1.160 4 25 A 47 A 62 -85.633 A_A47:C62_A 13 -1.218 -2.817 0.001 -0.616 4.374 A 48 A 61 -18.635 A_G48:G61_A 14 -9.848 -6.967 0.717 -2.593 8.697 8 A 49 A 60 -13.183 A_G49:A60_A 15 -8.319 -0.526 -0.106 1.433 15.035 1 20 A 50 A 59 -2.650 A_U50:A59_A 16 -8.684 -0.617 0.064 -0.217 9.258 1 19 A 51 A 58 2.004 A_C51:G58_A 17 -4.855 -0.651 -0.102 -0.156 2.227 1 19 A 52 A 57 1.910 A_C52:G57_A 18 -9.075 0.724 -0.069 -0.404 -5.500 9 11 A 53 A 56 -6.386 A_G53:A56_A 19 -8.266 6.399 -0.162 -3.747 17.406 9 11 A 54 A 55 13.660 A_G54:A55_A 20 6.587 6.232 0.677 -4.144 -17.406 9 11 A 55 A 54 13.660 A_A55:G54_A 21 6.587 -6.232 0.677 -4.144 5.500 9 11 A 56 A 53 -6.386 A_A56:G53_A 22 -8.266 -6.399 -0.162 -3.747 -2.227 1 19 A 57 A 52 1.910 A_G57:C52_A 23 -9.075 -0.724 -0.069 -0.404 -9.258 1 19 A 58 A 51 2.004 A_G58:C51_A 24 -4.855 0.651 -0.102 -0.156 -15.035 1 20 A 59 A 50 -2.650 A_A59:U50_A 25 -8.684 0.617 0.064 -0.217 -8.697 8 A 60 A 49 -13.183 A_A60:G49_A 26 -8.319 0.526 -0.106 1.433 -4.374 A 61 A 48 -18.635 A_G61:G48_A 27 -9.847 6.967 0.717 -2.593 -1.160 4 25 A 62 A 47 -85.633 A_C62:A47_A 28 -1.218 2.817 0.001 -0.616 -1.310 6 A 63 A 46 -21.379 A_A63:C46_A 29 -8.844 -6.134 0.654 -4.675 4.324 1 28 A 64 A 45 4.099 A_G64:U45_A 30 -4.440 -1.965 0.096 -0.572 6.507 1 19 A 65 A 44 -0.024 A_C65:G44_A 31 -10.547 -0.125 -0.052 -0.109 0.012 1 19 A 66 A 43 1.259 A_C66:G43_A 32 -2.060 0.732 -0.125 -0.192 6.795 1 20 A 68 A 38 4.613 A_A68:U38_A 33 -9.445 -0.353 0.567 -0.045 5.645 1 28 A 69 A 37 2.583 A_G69:U37_A 34 -8.165 -2.087 0.134 -0.582 -0.363 1 28 A 70 A 36 3.557 A_G70:U36_A 35 -7.213 -1.988 0.561 -0.384 -6.409 1 A 71 A 35 9.821 A_C71:G35_A 36 -7.541 -0.339 1.035 0.088 -5.243 1 20 A 72 A 34 10.563 A_A72:U34_A 37 -0.181 -0.090 -0.205 -0.089 0.876 1 19 A 73 A 33 0.198 A_G73:C33_A 38 -9.775 -0.330 0.294 -0.321 -1.281 1 20 A 74 A 32 4.093 A_A74:U32_A 39 -16.429 0.039 0.276 -0.305 -10.286 1 19 A 75 A 31 1.428 A_PGP75:C31_A 40 -13.615 -0.569 -0.156 -0.528 1.992 35.970 A A 31 32 28.901 A A 75 74 3.199 17.133 0.236 -1.722 AA_C31U32:A74PGP75_AA 1 -3.713 6.264 31.534 -4.864 -0.831 3.209 38.107 A A 32 33 0.065 A A 74 73 3.204 0.042 -0.222 -1.421 AA_U32C33:G73A74_AA 2 -1.535 2.351 38.077 -2.181 0.150 3.199 27.716 A A 33 34 -0.271 A A 73 72 3.195 -0.130 -0.149 -1.557 AA_C33U34:A72G73_AA 3 0.497 -1.038 27.711 -3.219 0.429 2.431 34.426 A A 34 35 14.520 A A 72 71 2.981 8.427 -0.180 -1.763 AA_U34G35:C71A72_AA 4 -8.355 14.396 32.374 -4.101 -0.809 3.234 38.466 A A 35 36 1.260 A A 71 70 3.296 0.828 -0.141 -1.421 AA_G35U36:G70C71_AA 5 4.114 -6.257 38.245 -2.259 0.725 2.614 37.013 A A 36 37 10.759 A A 70 69 3.048 6.736 0.283 -2.106 AA_U36U37:G69G70_AA 6 8.568 -13.686 35.426 -4.120 0.575 1.145 27.692 A A 37 38 36.165 A A 69 68 3.009 16.236 -0.871 -2.286 AA_U37U38:A68G69_AA 7 -0.448 0.999 22.504 -7.542 1.744 5.505 79.614 A A 38 43 12.601 A A 68 66 6.092 16.050 -1.271 -2.525 AA_U38G43:C66A68_AA 8 4.766 -3.742 78.121 -2.745 1.222 3.026 37.641 A A 43 44 8.399 A A 66 65 3.349 5.399 -0.131 -2.114 AA_G43G44:C65C66_AA 9 -1.910 2.971 37.218 -3.964 -0.040 3.222 35.792 A A 44 45 -0.752 A A 65 64 3.197 -0.462 0.246 -1.632 AA_G44U45:G64C65_AA 10 0.888 -1.445 35.778 -2.590 -0.275 2.934 55.061 A A 45 46 9.564 A A 64 63 3.233 8.799 -0.763 -1.280 AA_U45C46:A63G64_AA 11 4.962 -5.394 54.197 -1.880 1.105 3.973 7.291 A A 46 47 26.079 A A 63 62 2.855 3.130 -4.712 -0.110 AA_C46A47:C62A63_AA 12 -2.539 21.153 6.077 -13.423 26.867 2.724 29.327 A A 47 48 13.822 A A 62 61 2.797 6.928 4.977 -1.480 AA_A47G48:G61C62_AA 13 2.123 -4.236 28.436 -4.204 -9.438 3.166 53.621 A A 48 49 4.817 A A 61 60 3.275 4.341 0.229 -1.402 AA_G48G49:A60G61_AA 14 1.775 -1.970 53.430 -1.822 -0.144 2.630 26.297 A A 49 50 5.604 A A 60 59 2.940 2.530 0.232 -2.074 AA_G49U50:A59A60_AA 15 -5.164 11.439 25.672 -5.144 -1.706 2.883 33.893 A A 50 51 12.577 A A 59 58 3.407 7.266 0.472 -1.861 AA_U50C51:G58A59_AA 16 -3.371 5.835 32.960 -4.333 -1.338 3.282 39.621 A A 51 52 5.326 A A 58 57 3.473 3.605 0.263 -2.036 AA_C51C52:G57G58_AA 17 0.082 -0.122 39.464 -3.440 -0.379 3.488 54.847 A A 52 53 4.948 A A 57 56 3.588 4.550 -0.276 -0.882 AA_C52G53:A56G57_AA 18 3.494 -3.799 54.569 -1.252 0.526 2.770 33.565 A A 53 54 14.498 A A 56 55 2.861 8.213 1.280 -0.942 AA_G53G54:A55A56_AA 19 7.980 -14.086 31.604 -2.828 -1.053 -0.722 -10.157 A A 54 55 68.697 A A 55 54 4.165 -9.461 0.000 -2.406 AA_G54A55:G54A55_AA 20 0.000 0.000 -3.699 26.862 0.000 2.770 33.565 A A 55 56 14.498 A A 54 53 2.861 8.213 -1.280 -0.942 AA_A55A56:G53G54_AA 21 -7.980 14.085 31.604 -2.828 1.053 3.488 54.847 A A 56 57 4.948 A A 53 52 3.588 4.550 0.276 -0.882 AA_A56G57:C52G53_AA 22 -3.494 3.799 54.569 -1.252 -0.526 3.282 39.621 A A 57 58 5.326 A A 52 51 3.473 3.605 -0.263 -2.036 AA_G57G58:C51C52_AA 23 -0.082 0.122 39.464 -3.440 0.379 2.883 33.893 A A 58 59 12.577 A A 51 50 3.407 7.266 -0.472 -1.861 AA_G58A59:U50C51_AA 24 3.371 -5.835 32.960 -4.333 1.338 2.630 26.297 A A 59 60 5.604 A A 50 49 2.940 2.530 -0.232 -2.074 AA_A59A60:G49U50_AA 25 5.164 -11.439 25.672 -5.144 1.706 3.166 53.620 A A 60 61 4.817 A A 49 48 3.275 4.341 -0.229 -1.402 AA_A60G61:G48G49_AA 26 -1.775 1.970 53.430 -1.822 0.144 2.724 29.327 A A 61 62 13.822 A A 48 47 2.797 6.928 -4.977 -1.480 AA_G61C62:A47G48_AA 27 -2.123 4.236 28.436 -4.204 9.438 3.973 7.291 A A 62 63 26.079 A A 47 46 2.855 3.130 4.712 -0.110 AA_C62A63:C46A47_AA 28 2.539 -21.153 6.077 -13.424 -26.867 2.934 55.061 A A 63 64 9.564 A A 46 45 3.233 8.799 0.763 -1.280 AA_A63G64:U45C46_AA 29 -4.962 5.394 54.197 -1.880 -1.105 3.222 35.792 A A 64 65 -0.752 A A 45 44 3.197 -0.462 -0.246 -1.632 AA_G64C65:G44U45_AA 30 -0.888 1.445 35.778 -2.590 0.275 3.026 37.641 A A 65 66 8.399 A A 44 43 3.349 5.399 0.131 -2.114 AA_C65C66:G43G44_AA 31 1.910 -2.971 37.218 -3.964 0.040 5.505 79.614 A A 66 68 12.601 A A 43 38 6.092 16.050 1.271 -2.525 AA_C66A68:U38G43_AA 32 -4.766 3.742 78.121 -2.745 -1.222 1.145 27.692 A A 68 69 36.165 A A 38 37 3.009 16.236 0.871 -2.286 AA_A68G69:U37U38_AA 33 0.448 -0.999 22.504 -7.542 -1.744 2.614 37.013 A A 69 70 10.759 A A 37 36 3.048 6.736 -0.283 -2.106 AA_G69G70:U36U37_AA 34 -8.568 13.686 35.426 -4.120 -0.575 3.234 38.466 A A 70 71 1.260 A A 36 35 3.296 0.828 0.141 -1.421 AA_G70C71:G35U36_AA 35 -4.114 6.257 38.245 -2.259 -0.725 2.431 34.426 A A 71 72 14.520 A A 35 34 2.981 8.427 0.180 -1.763 AA_C71A72:U34G35_AA 36 8.355 -14.396 32.374 -4.101 0.809 3.199 27.716 A A 72 73 -0.271 A A 34 33 3.195 -0.130 0.149 -1.557 AA_A72G73:C33U34_AA 37 -0.497 1.038 27.711 -3.219 -0.429 3.209 38.107 A A 73 74 0.065 A A 33 32 3.204 0.042 0.222 -1.421 AA_G73A74:U32C33_AA 38 1.535 -2.351 38.077 -2.181 -0.150 1.992 35.970 A A 74 75 28.901 A A 32 31 3.199 17.133 -0.236 -1.722 AA_A74PGP75:C31U32_AA 39 3.713 -6.264 31.534 -4.864 0.831 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_conn_type struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2000-05-08 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2000-01-17 REL REL LU LUTETIUM (III) ION MG MAGNESIUM ION SO4 SULFATE ION HOH water RNA SEQUENCE TAKEN FROM ESCHERICHIA COLI 4.5S RNA. THE RNA WAS PRODUCED BY T7 RNA POLYMERASE IN VITRO TRANSCRIPTION USING RIBOZYME TECHNOLOGY sample LU 1 2 LU LU 1 A MG 2 3 MG MG 2 A SO4 3 4 SO4 SO4 3 A SO4 4 4 SO4 SO4 4 A HOH 1 5 HOH HOH 101 A HOH 2 5 HOH HOH 102 A HOH 3 5 HOH HOH 103 A HOH 4 5 HOH HOH 104 A HOH 5 5 HOH HOH 105 A HOH 6 5 HOH HOH 106 A C 31 n 1 C 31 A U 32 n 2 U 32 A C 33 n 3 C 33 A U 34 n 4 U 34 A G 35 n 5 G 35 A U 36 n 6 U 36 A U 37 n 7 U 37 A U 38 n 8 U 38 A A 39 n 9 A 39 A C 40 n 10 C 40 A C 41 n 11 C 41 A A 42 n 12 A 42 A G 43 n 13 G 43 A G 44 n 14 G 44 A U 45 n 15 U 45 A C 46 n 16 C 46 A A 47 n 17 A 47 A G 48 n 18 G 48 A G 49 n 19 G 49 A U 50 n 20 U 50 A C 51 n 21 C 51 A C 52 n 22 C 52 A G 53 n 23 G 53 A G 54 n 24 G 54 A A 55 n 25 A 55 A A 56 n 26 A 56 A G 57 n 27 G 57 A G 58 n 28 G 58 A A 59 n 29 A 59 A A 60 n 30 A 60 A G 61 n 31 G 61 A C 62 n 32 C 62 A A 63 n 33 A 63 A G 64 n 34 G 64 A C 65 n 35 C 65 A C 66 n 36 C 66 A A 67 n 37 A 67 A A 68 n 38 A 68 A G 69 n 39 G 69 A G 70 n 40 G 70 A C 71 n 41 C 71 A A 72 n 42 A 72 A G 73 n 43 G 73 A A 74 n 44 A 74 A PGP 75 n 45 PGP 75 A author_defined_assembly 2 dimeric A A 59 A O3' A 29 1_555 A MG 2 C MG MG 1_555 A A 60 A OP1 A 30 1_555 62.1 A PGP 75 GUANOSINE-3',5'-DIPHOSPHATE A PGP 45 G 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 0.8660254038 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 4_555 y,x,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 DNA_RNA_REP+.PARAM DNA_RNA+.TOP ION_REP+.PARAM ION+.TOP WATER_REP.PARA WATER.TOP 80.6 26.51 21.46 0.00 26.51 0.00 -53.03 A LOW RESOLUTION LIMIT OF 8.0 A WAS USED FOR INITIAL B FACTOR AND BULK SOLVENT CORRECTIONS. NUCLEOTIDE A39 WAS REFINED WITH OCCUPANCY OF 0.5 TO ACCOUNT FOR ITS ALTERNATIVELY ORDERED AND DISORDERED CONFORMATION IN ADJACENT MOLECULES WITHIN THE CRYSTAL. THE APPARENT DISCREPANCY BETWEEN DATA COMPLETENESS IN SCALING AND REFINEMENT IS DUE TO THE VERY HIGH ANISOTROPY OF THE CRYSTAL DIFFRACTION, SO THAT, ALTHOUGH DATA COVERAGE WAS COMPLETE UP TO 2.70 A RESOLUTION, A SIGNIFICANT PROPORTION OF REFLECTIONS AT HIGH RESOLUTION WERE EXTINCT. THIS RESULTS IN THE HIGH R SYM IN THE OUTER SHELL, AND THE LOWER EFFECTIVE DATA COMPLETENESS DURING REFINEMENT (EXTINCT REFLECTIONS WERE OMITTED BY CNS). 0.2450000 0.008 0.2300000 0.2710000 0.2440000 2.70 22.50 909 12560 10539 8.6 83.9 RANDOM 1101782.89 0.00 1 RESTRAINED THROUGHOUT 0.0 0.0 MAD PARKINSON ET AL. FLAT MODEL 36.81 0.266 0.53 0.50 5.00 0.90 0.92 2.70 22.50 6 988 12 970 0 0.006 1.0 15.6 1.24 0.5310000 0.057 0.5310000 2.82 86 858 8 5.5 60.0 0.4370000 0.042 0.4370000 2.97 106 1022 8 6.8 72.3 0.3640000 0.033 0.3630000 3.16 119 1150 8 7.5 80.4 0.3120000 0.029 0.3120000 3.40 117 1292 8 7.5 89.7 0.2510000 0.024 0.2510000 3.74 108 1287 8 7.0 89.9 0.2290000 0.020 0.2290000 4.29 132 1295 8 8.4 91.1 0.1760000 0.016 0.1760000 5.40 114 1417 8 7.2 97.0 0.1540000 0.014 0.1550000 60.36 125 1300 8 8.0 90.6 100.3 2.70 22.50 1DUH 12371 12371 0 0 0.0760000 1 14.5 4.2 98.5 0.5930000 2.70 2.80 2.1 4.1 100.0 refinement CNS data reduction DENZO data scaling SCALEPACK phasing CNS CRYSTAL STRUCTURE OF THE CONSERVED DOMAIN IV OF E. COLI 4.5S RNA 1 N N 2 N N 3 N N 4 N N 4 N N 5 N N covale 1.607 both A A 74 A O3' A 44 1_555 A PGP 75 A P PGP 45 1_555 metalc 1.918 A MG 2 C MG MG 1_555 A A 59 A O3' A 29 1_555 metalc 2.738 A MG 2 C MG MG 1_555 A A 60 A OP1 A 30 1_555 hydrog WATSON-CRICK A C 31 A N3 C 1 1_555 A PGP 75 A N1 PGP 45 4_555 hydrog WATSON-CRICK A C 31 A N4 C 1 1_555 A PGP 75 A O6 PGP 45 4_555 hydrog WATSON-CRICK A C 31 A O2 C 1 1_555 A PGP 75 A N2 PGP 45 4_555 hydrog WATSON-CRICK A U 32 A N3 U 2 1_555 A A 74 A N1 A 44 4_555 hydrog WATSON-CRICK A U 32 A O4 U 2 1_555 A A 74 A N6 A 44 4_555 hydrog WATSON-CRICK A C 33 A N3 C 3 1_555 A G 73 A N1 G 43 4_555 hydrog WATSON-CRICK A C 33 A N4 C 3 1_555 A G 73 A O6 G 43 4_555 hydrog WATSON-CRICK A C 33 A O2 C 3 1_555 A G 73 A N2 G 43 4_555 hydrog WATSON-CRICK A U 34 A N3 U 4 1_555 A A 72 A N1 A 42 4_555 hydrog WATSON-CRICK A U 34 A O4 U 4 1_555 A A 72 A N6 A 42 4_555 hydrog G-C PAIR A G 35 A N1 G 5 1_555 A C 71 A N3 C 41 4_555 hydrog TYPE_28_PAIR A U 36 A N3 U 6 1_555 A G 70 A O6 G 40 4_555 hydrog TYPE_28_PAIR A U 36 A O2 U 6 1_555 A G 70 A N1 G 40 4_555 hydrog TYPE_28_PAIR A U 37 A N3 U 7 1_555 A G 69 A O6 G 39 4_555 hydrog TYPE_28_PAIR A U 37 A O2 U 7 1_555 A G 69 A N1 G 39 4_555 hydrog WATSON-CRICK A U 38 A N3 U 8 1_555 A A 68 A N1 A 38 4_555 hydrog WATSON-CRICK A U 38 A O4 U 8 1_555 A A 68 A N6 A 38 4_555 hydrog WATSON-CRICK A G 43 A N1 G 13 1_555 A C 66 A N3 C 36 4_555 hydrog WATSON-CRICK A G 43 A N2 G 13 1_555 A C 66 A O2 C 36 4_555 hydrog WATSON-CRICK A G 43 A O6 G 13 1_555 A C 66 A N4 C 36 4_555 hydrog WATSON-CRICK A G 44 A N1 G 14 1_555 A C 65 A N3 C 35 4_555 hydrog WATSON-CRICK A G 44 A N2 G 14 1_555 A C 65 A O2 C 35 4_555 hydrog WATSON-CRICK A G 44 A O6 G 14 1_555 A C 65 A N4 C 35 4_555 hydrog TYPE_28_PAIR A U 45 A N3 U 15 1_555 A G 64 A O6 G 34 4_555 hydrog TYPE_28_PAIR A U 45 A O2 U 15 1_555 A G 64 A N1 G 34 4_555 hydrog C-A MISPAIR A C 46 A O2 C 16 1_555 A A 63 A N6 A 33 4_555 hydrog TYPE_25_PAIR A A 47 A N6 A 17 1_555 A C 62 A N3 C 32 4_555 hydrog TYPE_25_PAIR A A 47 A N7 A 17 1_555 A C 62 A N4 C 32 4_555 hydrog G-G MISPAIR A G 48 A O6 G 18 1_555 A G 61 A N2 G 31 4_555 hydrog TYPE_8_PAIR A G 49 A N1 G 19 1_555 A A 60 A N1 A 30 4_555 hydrog TYPE_8_PAIR A G 49 A O6 G 19 1_555 A A 60 A N6 A 30 4_555 hydrog WATSON-CRICK A U 50 A N3 U 20 1_555 A A 59 A N1 A 29 4_555 hydrog WATSON-CRICK A U 50 A O4 U 20 1_555 A A 59 A N6 A 29 4_555 hydrog WATSON-CRICK A C 51 A N3 C 21 1_555 A G 58 A N1 G 28 4_555 hydrog WATSON-CRICK A C 51 A N4 C 21 1_555 A G 58 A O6 G 28 4_555 hydrog WATSON-CRICK A C 51 A O2 C 21 1_555 A G 58 A N2 G 28 4_555 hydrog WATSON-CRICK A C 52 A N3 C 22 1_555 A G 57 A N1 G 27 4_555 hydrog WATSON-CRICK A C 52 A N4 C 22 1_555 A G 57 A O6 G 27 4_555 hydrog WATSON-CRICK A C 52 A O2 C 22 1_555 A G 57 A N2 G 27 4_555 hydrog TYPE_11_PAIR A G 53 A N2 G 23 1_555 A A 56 A N7 A 26 4_555 hydrog TYPE_11_PAIR A G 53 A N3 G 23 1_555 A A 56 A N6 A 26 4_555 hydrog TYPE_11_PAIR A G 54 A N2 G 24 1_555 A A 55 A N7 A 25 4_555 hydrog TYPE_11_PAIR A G 54 A N3 G 24 1_555 A A 55 A N6 A 25 4_555 hydrog TYPE_11_PAIR A A 55 A N6 A 25 1_555 A G 54 A N3 G 24 4_555 hydrog TYPE_11_PAIR A A 55 A N7 A 25 1_555 A G 54 A N2 G 24 4_555 hydrog TYPE_11_PAIR A A 56 A N6 A 26 1_555 A G 53 A N3 G 23 4_555 hydrog TYPE_11_PAIR A A 56 A N7 A 26 1_555 A G 53 A N2 G 23 4_555 hydrog WATSON-CRICK A G 57 A N1 G 27 1_555 A C 52 A N3 C 22 4_555 hydrog WATSON-CRICK A G 57 A N2 G 27 1_555 A C 52 A O2 C 22 4_555 hydrog WATSON-CRICK A G 57 A O6 G 27 1_555 A C 52 A N4 C 22 4_555 hydrog WATSON-CRICK A G 58 A N1 G 28 1_555 A C 51 A N3 C 21 4_555 hydrog WATSON-CRICK A G 58 A N2 G 28 1_555 A C 51 A O2 C 21 4_555 hydrog WATSON-CRICK A G 58 A O6 G 28 1_555 A C 51 A N4 C 21 4_555 hydrog WATSON-CRICK A A 59 A N1 A 29 1_555 A U 50 A N3 U 20 4_555 hydrog WATSON-CRICK A A 59 A N6 A 29 1_555 A U 50 A O4 U 20 4_555 hydrog TYPE_8_PAIR A A 60 A N1 A 30 1_555 A G 49 A N1 G 19 4_555 hydrog TYPE_8_PAIR A A 60 A N6 A 30 1_555 A G 49 A O6 G 19 4_555 hydrog G-G MISPAIR A G 61 A N2 G 31 1_555 A G 48 A O6 G 18 4_555 hydrog TYPE_25_PAIR A C 62 A N3 C 32 1_555 A A 47 A N6 A 17 4_555 hydrog TYPE_25_PAIR A C 62 A N4 C 32 1_555 A A 47 A N7 A 17 4_555 hydrog A-C MISPAIR A A 63 A N6 A 33 1_555 A C 46 A O2 C 16 4_555 hydrog TYPE_28_PAIR A G 64 A N1 G 34 1_555 A U 45 A O2 U 15 4_555 hydrog TYPE_28_PAIR A G 64 A O6 G 34 1_555 A U 45 A N3 U 15 4_555 hydrog WATSON-CRICK A C 65 A N3 C 35 1_555 A G 44 A N1 G 14 4_555 hydrog WATSON-CRICK A C 65 A N4 C 35 1_555 A G 44 A O6 G 14 4_555 hydrog WATSON-CRICK A C 65 A O2 C 35 1_555 A G 44 A N2 G 14 4_555 hydrog WATSON-CRICK A C 66 A N3 C 36 1_555 A G 43 A N1 G 13 4_555 hydrog WATSON-CRICK A C 66 A N4 C 36 1_555 A G 43 A O6 G 13 4_555 hydrog WATSON-CRICK A C 66 A O2 C 36 1_555 A G 43 A N2 G 13 4_555 hydrog WATSON-CRICK A A 68 A N1 A 38 1_555 A U 38 A N3 U 8 4_555 hydrog WATSON-CRICK A A 68 A N6 A 38 1_555 A U 38 A O4 U 8 4_555 hydrog TYPE_28_PAIR A G 69 A N1 G 39 1_555 A U 37 A O2 U 7 4_555 hydrog TYPE_28_PAIR A G 69 A O6 G 39 1_555 A U 37 A N3 U 7 4_555 hydrog TYPE_28_PAIR A G 70 A N1 G 40 1_555 A U 36 A O2 U 6 4_555 hydrog TYPE_28_PAIR A G 70 A O6 G 40 1_555 A U 36 A N3 U 6 4_555 hydrog C-G PAIR A C 71 A O2 C 41 1_555 A G 35 A N2 G 5 4_555 hydrog WATSON-CRICK A A 72 A N1 A 42 1_555 A U 34 A N3 U 4 4_555 hydrog WATSON-CRICK A A 72 A N6 A 42 1_555 A U 34 A O4 U 4 4_555 hydrog WATSON-CRICK A G 73 A N1 G 43 1_555 A C 33 A N3 C 3 4_555 hydrog WATSON-CRICK A G 73 A N2 G 43 1_555 A C 33 A O2 C 3 4_555 hydrog WATSON-CRICK A G 73 A O6 G 43 1_555 A C 33 A N4 C 3 4_555 hydrog WATSON-CRICK A A 74 A N1 A 44 1_555 A U 32 A N3 U 2 4_555 hydrog WATSON-CRICK A A 74 A N6 A 44 1_555 A U 32 A O4 U 2 4_555 hydrog WATSON-CRICK A PGP 75 A N1 PGP 45 1_555 A C 31 A N3 C 1 4_555 hydrog WATSON-CRICK A PGP 75 A N2 PGP 45 1_555 A C 31 A O2 C 1 4_555 hydrog WATSON-CRICK A PGP 75 A O6 PGP 45 1_555 A C 31 A N4 C 1 4_555 RNA 4.5S RNA, DOMAIN IV, HELIX 8, SIGNAL RECOGNITION PARTICLE, SRP, FFH, SRP54, ELONGATION FACTOR G, EF-G, 23S RNA, NON-CANONICAL BASE PAIRS, MISMATCH, RNA ECRNA45 EMBL 1 X01074 192 235 1DUH 31 74 X01074 A 1 1 44 BINDING SITE FOR RESIDUE LU A 1 A LU 1 Software 1 BINDING SITE FOR RESIDUE MG A 2 A MG 2 Software 2 BINDING SITE FOR RESIDUE SO4 A 3 A SO4 3 Software 1 BINDING SITE FOR RESIDUE SO4 A 4 A SO4 4 Software 3 A PGP 75 A PGP 45 1 1_555 A A 59 A A 29 2 1_555 A A 60 A A 30 2 1_555 A C 31 A C 1 1 1_555 A G 48 A G 18 3 1_555 A G 49 A G 19 3 1_555 A C 62 A C 32 3 4_555 154 trigonal P 32 2 1