1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Dallas, A. Moore, P.B. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking UK Structure STRUE6 2005 0969-2126 5 1639 1653 10.1016/S0969-2126(97)00311-0 9438864 The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. 1997 10.2210/pdb1a4d/pdb pdb_00001a4d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 6857.093 RNA (5'-R(*GP*GP*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*GP*UP*C)-3') LOOP D/LOOP E ARM 1 man polymer 6397.871 RNA (5'-R(P*UP*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*GP*CP*C)-3') LOOP D/LOOP E ARM 1 man polymer no no GGCCGAUGGUAGUGUGGGGUC GGCCGAUGGUAGUGUGGGGUC A polyribonucleotide no no UCCCCAUGCGAGAGUAGGCC UCCCCAUGCGAGAGUAGGCC B 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 Escherichia Escherichia sample CYTOPLASM 562 Escherichia coli 562 Escherichia coli JM101 PAD3 Escherichia Escherichia sample CYTOPLASM 562 Escherichia coli 562 Escherichia coli JM101 PAD3 -0.591 1 19 A 68 B 108 0.408 A_G68:C108_B 1 -3.453 -0.394 0.044 -0.250 -2.016 1 19 A 69 B 107 0.789 A_G69:C107_B 2 0.238 -0.891 -0.115 -0.446 3.121 1 19 A 70 B 106 -0.450 A_C70:G106_B 3 -0.027 0.743 -0.219 -0.371 -5.044 1 19 A 71 B 105 2.343 A_C71:G105_B 4 -5.772 0.235 -0.278 -0.248 4.084 10 11 A 72 B 104 -4.152 A_G72:A104_B 5 -1.328 6.909 0.188 -3.932 2.893 4 24 A 73 B 103 -108.004 A_A73:U103_B 6 -10.183 -3.550 -0.024 -0.999 -4.940 2 A 74 B 102 -93.929 A_U74:G102_B 7 -7.970 -4.202 -0.426 0.991 -1.294 A 75 B 101 -70.254 A_G75:A101_B 8 -2.028 -2.011 -0.091 2.182 2.719 A 76 B 100 -95.070 A_G76:G100_B 9 0.235 4.433 -0.314 0.927 2.902 4 24 A 77 B 99 -94.507 A_U77:A99_B 10 -6.526 3.991 -0.476 -1.669 3.285 9 11 A 78 B 98 0.732 A_A78:G98_B 11 -0.231 -6.756 -0.148 -4.333 -2.523 1 19 A 79 B 97 1.692 A_G79:C97_B 12 -6.682 -0.821 -0.254 -0.440 3.373 1 28 A 80 B 96 -4.522 A_U80:G96_B 13 -7.611 1.531 0.450 -0.379 -10.735 1 28 A 81 B 95 -5.652 A_G81:U95_B 14 -8.759 -1.089 -1.078 -0.736 1.555 1 20 A 82 B 94 0.644 A_U82:A94_B 15 -6.520 0.062 0.077 -0.244 5.085 1 19 A 83 B 93 -8.429 A_G83:C93_B 16 -16.711 -0.397 0.888 -0.751 -0.547 1 19 A 84 B 92 -0.045 A_G84:C92_B 17 -9.958 -0.344 -0.065 -0.263 -6.985 1 19 A 85 B 91 1.452 A_G85:C91_B 18 -5.107 -0.979 -0.046 -0.450 -10.354 1 A 86 B 90 53.777 A_G86:C90_B 19 6.472 0.842 -1.196 2.197 2.297 40.553 A A 68 69 21.834 B B 108 107 3.083 14.809 0.173 -1.655 AA_G68G69:C107C108_BB 1 -1.261 1.859 37.839 -3.798 -0.370 2.505 39.013 A A 69 70 29.856 B B 107 106 3.111 19.135 -0.072 -0.480 AA_G69C70:G106C107_BB 2 0.938 -1.463 34.145 -2.849 0.212 2.491 37.523 A A 70 71 20.531 B B 106 105 3.312 12.950 0.205 -1.903 AA_C70C71:G105G106_BB 3 1.589 -2.518 35.259 -4.510 -0.128 3.053 60.092 A A 71 72 8.776 B B 105 104 3.078 8.763 -0.457 0.038 AA_C71G72:A104G105_BB 4 0.344 -0.345 59.508 -0.369 0.472 -1.285 -14.665 A A 72 73 11.322 B B 104 103 2.889 -2.700 -6.189 -0.634 AA_G72A73:U103A104_BB 5 -8.307 -34.839 -11.791 3.123 -26.214 2.759 57.445 A A 73 74 9.758 B B 103 102 3.276 9.343 0.836 -3.323 AA_A73U74:G102U103_BB 6 1.206 -1.259 56.732 -3.928 -0.809 3.080 39.558 A A 74 75 -1.451 B B 102 101 3.015 -0.982 1.252 -2.253 AA_U74G75:A101G102_BB 7 0.414 -0.611 39.545 -3.222 -1.804 3.247 59.722 A A 75 76 0.584 B B 101 100 3.277 0.582 -0.551 -2.712 AA_G75G76:G100A101_BB 8 0.684 -0.686 59.716 -2.753 0.588 3.378 46.043 A A 76 77 -5.261 B B 100 99 3.128 -4.102 -0.775 -2.322 AA_G76U77:A99G100_BB 9 -5.289 6.784 45.580 -2.616 0.536 3.466 -18.664 A A 77 78 -6.764 B B 99 98 3.134 2.188 5.491 -0.933 AA_U77A78:G98A99_BB 10 -0.850 -2.629 -18.517 1.688 16.472 3.166 66.009 A A 78 79 6.608 B B 98 97 3.250 7.182 -0.202 -0.777 AA_A78G79:C97G98_BB 11 -4.862 4.473 65.501 -0.999 -0.008 3.086 43.556 A A 79 80 2.900 B B 97 96 3.117 2.151 -0.366 -0.659 AA_G79U80:G96C97_BB 12 -0.393 0.530 43.503 -1.084 0.457 4.080 20.093 A A 80 81 -15.964 B B 96 95 4.025 -5.390 -0.418 -2.192 AA_U80G81:U95G96_BB 13 6.803 -20.149 18.139 -3.037 5.296 2.953 40.962 A A 81 82 -9.041 B B 95 94 2.976 -6.271 0.374 -0.822 AA_G81U82:A94U95_BB 14 -7.467 10.765 39.833 -0.543 -1.285 3.014 29.988 A A 82 83 -1.116 B B 94 93 2.933 -0.576 -0.620 -1.524 AA_U82G83:C93A94_BB 15 -3.710 7.189 29.757 -2.837 0.500 3.910 33.906 A A 83 84 -14.058 B B 93 92 3.637 -8.108 0.415 -1.501 AA_G83G84:C92C93_BB 16 3.638 -6.307 32.754 -1.043 -0.026 4.036 29.150 A A 84 85 -17.966 B B 92 91 3.695 -8.887 0.275 -1.872 AA_G84G85:C91C92_BB 17 -3.079 6.224 27.622 -1.362 -1.363 3.514 34.895 A A 85 86 10.933 B B 91 90 3.463 6.503 2.655 -1.076 AA_G85G86:C90C91_BB 18 4.462 -7.502 34.019 -2.860 -3.697 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1998-04-29 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site ENSEMBLE OF 9 STRUCTURES Y BNL 1998-01-29 REL REL NO NOE, DIHEDRAL VIOLATIONS, LOW OVERALL ENERGY STRUCTURES, GOOD LOCAL GEOMETRY 60 1 7.2 283 K 5.5 283 K FOR REFINEMENT DETAILS, SEE JRNL REFERENCE ABOVE. TORSION ANGLE MOLECULAR DYNAMICS BRUNGER refinement X-PLOR structure solution X-PLOR 500 Varian UNITY 600 GE UNITYPLUS 600 GE OMEGA G 68 n 1 G 68 A G 69 n 2 G 69 A C 70 n 3 C 70 A C 71 n 4 C 71 A G 72 n 5 G 72 A A 73 n 6 A 73 A U 74 n 7 U 74 A G 75 n 8 G 75 A G 76 n 9 G 76 A U 77 n 10 U 77 A A 78 n 11 A 78 A G 79 n 12 G 79 A U 80 n 13 U 80 A G 81 n 14 G 81 A U 82 n 15 U 82 A G 83 n 16 G 83 A G 84 n 17 G 84 A G 85 n 18 G 85 A G 86 n 19 G 86 A U 87 n 20 U 87 A C 88 n 21 C 88 A U 89 n 1 U 89 B C 90 n 2 C 90 B C 91 n 3 C 91 B C 92 n 4 C 92 B C 93 n 5 C 93 B A 94 n 6 A 94 B U 95 n 7 U 95 B G 96 n 8 G 96 B C 97 n 9 C 97 B G 98 n 10 G 98 B A 99 n 11 A 99 B G 100 n 12 G 100 B A 101 n 13 A 101 B G 102 n 14 G 102 B U 103 n 15 U 103 B A 104 n 16 A 104 B G 105 n 17 G 105 B G 106 n 18 G 106 B C 107 n 19 C 107 B C 108 n 20 C 108 B author_defined_assembly 2 dimeric 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 1 A B O4 H1 U G 74 102 1.39 1 A B O3' P C U 88 89 1.61 model building X-PLOR refinement X-PLOR phasing X-PLOR LOOP D/LOOP E ARM OF ESCHERICHIA COLI 5S RRNA, NMR, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N hydrog WATSON-CRICK A G 68 A N1 G 1 1_555 B C 108 B N3 C 20 1_555 hydrog WATSON-CRICK A G 68 A N2 G 1 1_555 B C 108 B O2 C 20 1_555 hydrog WATSON-CRICK A G 68 A O6 G 1 1_555 B C 108 B N4 C 20 1_555 hydrog WATSON-CRICK A G 69 A N1 G 2 1_555 B C 107 B N3 C 19 1_555 hydrog WATSON-CRICK A G 69 A N2 G 2 1_555 B C 107 B O2 C 19 1_555 hydrog WATSON-CRICK A G 69 A O6 G 2 1_555 B C 107 B N4 C 19 1_555 hydrog WATSON-CRICK A C 70 A N3 C 3 1_555 B G 106 B N1 G 18 1_555 hydrog WATSON-CRICK A C 70 A N4 C 3 1_555 B G 106 B O6 G 18 1_555 hydrog WATSON-CRICK A C 70 A O2 C 3 1_555 B G 106 B N2 G 18 1_555 hydrog WATSON-CRICK A C 71 A N3 C 4 1_555 B G 105 B N1 G 17 1_555 hydrog WATSON-CRICK A C 71 A N4 C 4 1_555 B G 105 B O6 G 17 1_555 hydrog WATSON-CRICK A C 71 A O2 C 4 1_555 B G 105 B N2 G 17 1_555 hydrog TYPE_11_PAIR A G 72 A N2 G 5 1_555 B A 104 B N7 A 16 1_555 hydrog TYPE_11_PAIR A G 72 A N3 G 5 1_555 B A 104 B N6 A 16 1_555 hydrog REVERSED HOOGSTEEN A A 73 A N6 A 6 1_555 B U 103 B O2 U 15 1_555 hydrog REVERSED HOOGSTEEN A A 73 A N7 A 6 1_555 B U 103 B N3 U 15 1_555 hydrog U-G MISPAIR A U 74 A O4 U 7 1_555 B G 102 B N1 G 14 1_555 hydrog G-A MISPAIR A G 75 A O6 G 8 1_555 B A 101 B N6 A 13 1_555 hydrog G-G MISPAIR A G 76 A N1 G 9 1_555 B G 100 B O6 G 12 1_555 hydrog REVERSED HOOGSTEEN A U 77 A N3 U 10 1_555 B A 99 B N7 A 11 1_555 hydrog REVERSED HOOGSTEEN A U 77 A O2 U 10 1_555 B A 99 B N6 A 11 1_555 hydrog TYPE_11_PAIR A A 78 A N6 A 11 1_555 B G 98 B N3 G 10 1_555 hydrog TYPE_11_PAIR A A 78 A N7 A 11 1_555 B G 98 B N2 G 10 1_555 hydrog WATSON-CRICK A G 79 A N1 G 12 1_555 B C 97 B N3 C 9 1_555 hydrog WATSON-CRICK A G 79 A N2 G 12 1_555 B C 97 B O2 C 9 1_555 hydrog WATSON-CRICK A G 79 A O6 G 12 1_555 B C 97 B N4 C 9 1_555 hydrog TYPE_28_PAIR A U 80 A N3 U 13 1_555 B G 96 B O6 G 8 1_555 hydrog TYPE_28_PAIR A U 80 A O2 U 13 1_555 B G 96 B N1 G 8 1_555 hydrog TYPE_28_PAIR A G 81 A N1 G 14 1_555 B U 95 B O2 U 7 1_555 hydrog TYPE_28_PAIR A G 81 A O6 G 14 1_555 B U 95 B N3 U 7 1_555 hydrog WATSON-CRICK A U 82 A N3 U 15 1_555 B A 94 B N1 A 6 1_555 hydrog WATSON-CRICK A U 82 A O4 U 15 1_555 B A 94 B N6 A 6 1_555 hydrog WATSON-CRICK A G 83 A N1 G 16 1_555 B C 93 B N3 C 5 1_555 hydrog WATSON-CRICK A G 83 A N2 G 16 1_555 B C 93 B O2 C 5 1_555 hydrog WATSON-CRICK A G 83 A O6 G 16 1_555 B C 93 B N4 C 5 1_555 hydrog WATSON-CRICK A G 84 A N1 G 17 1_555 B C 92 B N3 C 4 1_555 hydrog WATSON-CRICK A G 84 A N2 G 17 1_555 B C 92 B O2 C 4 1_555 hydrog WATSON-CRICK A G 84 A O6 G 17 1_555 B C 92 B N4 C 4 1_555 hydrog WATSON-CRICK A G 85 A N1 G 18 1_555 B C 91 B N3 C 3 1_555 hydrog WATSON-CRICK A G 85 A N2 G 18 1_555 B C 91 B O2 C 3 1_555 hydrog WATSON-CRICK A G 85 A O6 G 18 1_555 B C 91 B N4 C 3 1_555 hydrog G-C PAIR A G 86 A N2 G 19 1_555 B C 90 B O2 C 2 1_555 RNA 5S RRNA, INTERNAL LOOP, CROSS-STRAND STACK, TRANSLATION, RIBOSOME, RIBOSOMAL RNA COMPLEX, RNA 1A4D PDB 1 1A4D 1A4D PDB 2 1A4D 68 88 1A4D 68 88 1A4D A 1 1 21 89 108 1A4D 89 108 1A4D B 2 1 20 1 P 1