1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Jiang, J. Aduri, R. Chow, C.S. Santalucia, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 n PSEUDOURIDINE-5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking UK Nucleic Acids Res. NARHAD 0389 0305-1048 42 3971 3981 10.1093/nar/gkt1329 24371282 Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations. 2014 6077.673 RNA_(5'-R(P*GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3') 1 syn polymer no yes GGCCG(PSU)AAC(PSU)A(PSU)AACGGUC GGCCGUAACUAUAACGGUC A polyribonucleotide n n n n n n n n n n n n n n n n n n n 2.359 1 19 A 1 A 19 -8.118 A_G1:C19_A 1 1.988 0.290 0.015 -0.242 1.806 1 28 A 2 A 18 -1.392 A_G2:U18_A 2 -1.428 -2.020 -0.076 -0.292 1.759 1 19 A 3 A 17 1.839 A_C3:G17_A 3 -2.505 -0.232 -0.047 -0.121 6.787 1 19 A 4 A 16 0.669 A_C4:G16_A 4 4.416 0.016 -0.321 -0.244 -1.109 1 19 A 5 A 15 -5.546 A_G5:C15_A 5 0.386 -0.225 -0.193 -0.176 -0.458 1 21 A 6 A 14 -12.254 A_PSU6:A14_A 6 -4.209 -0.271 0.036 -0.265 30.204 1 A 8 A 12 37.321 A_A8:PSU12_A 7 -3.382 0.064 2.091 0.660 3.789 21.088 A A 1 2 -9.222 A A 19 18 3.498 -3.361 0.276 -2.111 AA_G1G2:U18C19_AA 1 0.200 -0.549 20.820 -4.190 -0.660 4.205 37.124 A A 2 3 -11.336 A A 18 17 4.051 -7.174 0.134 -1.200 AA_G2C3:G17U18_AA 2 0.486 -0.767 36.445 -0.664 -0.129 4.072 36.259 A A 3 4 -12.528 A A 17 16 3.965 -7.731 0.800 -0.673 AA_C3C4:G16G17_AA 3 3.198 -5.182 35.313 0.269 -0.728 4.552 27.689 A A 4 5 -18.033 A A 16 15 4.460 -8.494 -1.166 -1.168 AA_C4G5:C15G16_AA 4 1.172 -2.489 26.353 0.466 2.838 3.778 25.060 A A 5 6 -2.115 A A 15 14 3.767 -0.914 0.042 -1.839 AA_G5PSU6:A14C15_AA 5 -3.938 9.113 24.737 -3.923 -1.451 repository Initial release Database references Database references 1 0 2014-01-01 1 1 2014-01-15 1 2 2014-04-16 BMRB Y RCSB 2013-09-26 REL REL REL CONVERGED LOWEST ENERGY STRUCTURES 100 10 2D 1H-13C NATURAL ABUNDANCE HMQC 2D 1H-1H NOESY 2D DQF-COSY 3D 1H-1H-1H TOCSY-NOESY 2D 1H-31P HETCOR 1D 31P 2D 1H-1H NOESY 1.0 mM 10 mM 50 mM 0.1 mM 1.0 mM 10 mM 50 mM 0.1 mM 70 7.3 ambient 310.2 K 70 7.3 ambient 283.2 K simulated annealing, molecular dynamics, torsion angle dynamics 1 lowest energy 1.0 mM RNA (5'-P(GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 100% D2O 100% D2O 1.0 mM RNA (5'-P(GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 90% H2O/10% D2O 90% H2O/10% D2O Goddard chemical shift assignment SPARKY Goddard data analysis SPARKY Brunger, Adams, Clore, Gros, Nilges and Read structure solution CNS 1.2 Brunger, Adams, Clore, Gros, Nilges and Read refinement CNS 1.2 Bruker Biospin collection TOPSPIN Bruker Biospin processing TOPSPIN 700 Bruker Avance Bruker Avance 400 Varian Mercury Varian Mercury G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A C 4 n 4 C 4 A G 5 n 5 G 5 A PSU 6 n 6 PSU 6 A A 7 n 7 A 7 A A 8 n 8 A 8 A C 9 n 9 C 9 A PSU 10 n 10 PSU 10 A A 11 n 11 A 11 A PSU 12 n 12 PSU 12 A A 13 n 13 A 13 A A 14 n 14 A 14 A C 15 n 15 C 15 A G 16 n 16 G 16 A G 17 n 17 G 17 A U 18 n 18 U 18 A C 19 n 19 C 19 A author_defined_assembly 1 monomeric A PSU 6 PSEUDOURIDINE-5'-MONOPHOSPHATE A PSU 6 U A PSU 10 PSEUDOURIDINE-5'-MONOPHOSPHATE A PSU 10 U A PSU 12 PSEUDOURIDINE-5'-MONOPHOSPHATE A PSU 12 U 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 A O2 H61 PSU A 6 14 1.49 1 A A O6 H41 G C 1 19 1.52 1 A A O2 H21 C G 4 16 1.60 2 A A O6 H41 G C 1 19 1.51 3 A A O6 H41 G C 1 19 1.49 4 A A O6 H41 G C 1 19 1.51 5 A A O2 H61 PSU A 6 14 1.49 5 A A O2' O4' A PSU 11 12 1.79 6 A A O2 H61 PSU A 6 14 1.50 6 A A O6 H41 G C 1 19 1.51 6 A A O2' O4' A PSU 11 12 1.77 7 A A O6 H41 G C 1 19 1.52 8 A A O2 H61 PSU A 6 14 1.49 8 A A O6 H41 G C 1 19 1.51 8 A A O2 H21 C G 4 16 1.60 8 A A O2' O4' A PSU 11 12 1.79 9 A A O6 H41 G C 1 19 1.51 10 A A O2 H61 PSU A 6 14 1.51 10 A A O6 H41 G C 1 19 1.52 10 A A O2 H21 C G 4 16 1.60 5'-R(P*GP*GP*CP*CP*GP*(PSU)P*AP*AP*CP*(PSU)P*AP*(PSU)P*AP*AP*CP*GP*GP*UP*C)-3' lowest energy, model1 Structure of helix 69 from escherichia coli 23s ribosomal rna 1 N N covale 1.610 A G 5 A O3' G 5 1_555 A PSU 6 A P PSU 6 1_555 covale 1.607 A PSU 6 A O3' PSU 6 1_555 A A 7 A P A 7 1_555 covale 1.612 A C 9 A O3' C 9 1_555 A PSU 10 A P PSU 10 1_555 covale 1.609 A PSU 10 A O3' PSU 10 1_555 A A 11 A P A 11 1_555 covale 1.607 A A 11 A O3' A 11 1_555 A PSU 12 A P PSU 12 1_555 covale 1.609 A PSU 12 A O3' PSU 12 1_555 A A 13 A P A 13 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 19 A N3 C 19 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 19 A O2 C 19 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 19 A N4 C 19 1_555 hydrog TYPE_28_PAIR A G 2 A N1 G 2 1_555 A U 18 A O2 U 18 1_555 hydrog TYPE_28_PAIR A G 2 A O6 G 2 1_555 A U 18 A N3 U 18 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 17 A N1 G 17 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 17 A N2 G 17 1_555 hydrog WATSON-CRICK A C 4 A N3 C 4 1_555 A G 16 A N1 G 16 1_555 hydrog WATSON-CRICK A C 4 A N4 C 4 1_555 A G 16 A O6 G 16 1_555 hydrog WATSON-CRICK A C 4 A O2 C 4 1_555 A G 16 A N2 G 16 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 15 A N3 C 15 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 15 A O2 C 15 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 15 A N4 C 15 1_555 hydrog REVERSED WATSON-CRICK A PSU 6 A N3 PSU 6 1_555 A A 14 A N1 A 14 1_555 hydrog REVERSED WATSON-CRICK A PSU 6 A O2 PSU 6 1_555 A A 14 A N6 A 14 1_555 hydrog A-PSU MISPAIR A A 8 A N1 A 8 1_555 A PSU 12 A N3 PSU 12 1_555 RNA Pseudouridine, Helix 69, Ribosomal, RNA 2MER PDB 1 2MER GGCCGUAACUAUAACGGUC 1 19 2MER 1 19 2MER A 1 1 19