1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Znosko, B.M. Kennedy, S.D. Wille, P.C. Krugh, T.R. Turner, D.H. 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 US Biochemistry BICHAW 0033 0006-2960 43 15822 15837 10.1021/bi049256y 15595837 Structural Features and Thermodynamics of the J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns. 2004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 3648.282 5'-R(*GP*AP*GP*GP*AP*AP*GP*GP*CP*GP*A)-3' 1 syn polymer 3405.034 5'-R(*UP*CP*GP*UP*UP*AP*AP*UP*CP*UP*C)-3' 1 syn polymer no no GAGGAAGGCGA GAGGAAGGCGA A polyribonucleotide no no UCGUUAAUCUC UCGUUAAUCUC B polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n -22.809 1 19 A 1 B 21 -0.467 A_G1:C21_B 1 -10.764 -0.445 -0.737 -0.077 -19.421 1 20 A 2 B 20 -0.293 A_A2:U20_B 2 -5.777 0.198 -0.391 0.096 -2.562 1 19 A 3 B 19 0.162 A_G3:C19_B 3 -4.666 -0.403 -0.134 -0.083 1.716 1 28 A 4 B 18 -1.528 A_G4:U18_B 4 -20.242 -1.967 0.328 -0.386 3.621 10 A 5 B 17 -14.589 A_A5:A17_B 5 -16.119 6.483 -0.073 -4.541 -7.921 10 A 6 B 16 -13.754 A_A6:A16_B 6 4.069 -6.487 0.034 -4.215 -0.482 28 A 7 B 15 4.948 A_G7:U15_B 7 -13.869 -2.659 -0.297 -0.442 4.245 1 28 A 8 B 14 1.831 A_G8:U14_B 8 -13.558 -2.218 0.243 -0.328 7.907 1 19 A 9 B 13 0.458 A_C9:G13_B 9 -19.629 0.243 0.001 -0.068 -1.428 1 19 A 10 B 12 0.009 A_G10:C12_B 10 -17.927 -0.443 -0.016 -0.108 -4.994 1 20 A 11 B B 11 -1.655 A_A11:U11B_B 11 -23.613 0.182 -0.368 0.008 2.825 35.197 A A 1 2 15.245 B B 21 20 3.218 9.119 0.364 -1.121 AA_G1A2:U20C21_BB 1 -0.745 1.245 34.023 -3.130 -0.706 2.891 27.681 A A 2 3 4.337 B B 20 19 2.992 2.073 0.413 -1.421 AA_A2G3:C19U20_BB 2 0.890 -1.862 27.591 -3.423 -0.669 1.699 25.291 A A 3 4 22.197 B B 19 18 2.949 9.438 0.422 -2.507 AA_G3G4:U18C19_BB 3 -4.405 10.360 23.078 -7.767 -1.917 3.565 70.036 A A 4 5 -2.184 B B 18 17 3.527 -2.506 -2.085 -0.865 AA_G4A5:A17U18_BB 4 -0.514 0.448 69.995 -0.658 1.797 3.651 -16.983 A A 5 6 -4.749 B B 17 16 3.581 1.398 0.203 -1.455 AA_A5A6:A16A17_BB 5 1.697 5.763 -16.841 3.923 1.906 2.950 43.759 A A 6 7 8.064 B B 16 15 3.157 5.993 2.311 -1.447 AA_A6G7:U15A16_BB 6 0.190 -0.255 43.366 -2.478 -3.083 3.275 30.637 A A 7 8 -2.039 B B 15 14 3.244 -1.070 -0.152 -1.846 AA_G7G8:U14U15_BB 7 -5.935 11.302 30.052 -3.281 -0.890 3.247 41.811 A A 8 9 -0.162 B B 14 13 3.244 -0.115 -0.374 -1.503 AA_G8C9:G13U14_BB 8 0.069 -0.097 41.810 -2.093 0.531 2.356 35.250 A A 9 10 27.270 B B 13 12 3.329 15.939 -0.571 -1.497 AA_C9G10:C12G13_BB 9 -2.150 3.679 31.471 -4.655 0.648 3.091 37.360 A A 10 11 13.450 B B B 12 11 3.338 8.542 -0.411 -0.654 AA_G10A11:U11BC12_BB 10 1.549 -2.439 36.372 -2.144 0.845 repository Initial release Version format compliance Version format compliance 1 0 2004-12-28 1 1 2008-04-30 1 2 2011-07-13 RCSB Y RCSB 2004-06-25 REL REL closest to average 50 1 2D NOESY 2D NOESY 80 mM NaCl, 3 mM cobalt hexamine 6.1 ambient 298 K 80 mM NaCl, 3 mM cobalt hexamine 6.1 ambient 298 K The structures are based on a total of 217 NMR-derived interproton distance restraints (108 intranucleotide and 109 internucleotide). Hydrogn bond restraints were used for the six WC pairs and for the G8-U14 wobble pair. On the basis of NMR data that is consistent with the formation of tandem sheared AA pairs, two artificial hydrogen bonding restraints were used between each sheared AA pair. molecular dynamics 1 closest to the average ~~2 mM RNA, 80 mM NaCl, 3 mM KH2PO4, 7 mM K2HPO4, 0.5 mM Na2EDTA, 3 mM cobalt hexamine, pH=6.1, 90% H2O, 10% D2O 90% H2O/10% D2O ~~2 mM RNA, 80 mM NaCl, 3 mM KH2PO4, 7 mM K2HPO4, 0.5 mM Na2EDTA, 3 mM cobalt hexamine, pH=6.1, 100% D2O 100% D2O Varian collection VNMR 5.2 Felix data analysis FELIX 2000 Insight structure solution DISCOVER 95.0 Insight refinement DISCOVER 95.0 500 Varian INOVA G 1 n 1 G 1 A A 2 n 2 A 2 A G 3 n 3 G 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A G 8 n 8 G 8 A C 9 n 9 C 9 A G 10 n 10 G 10 A A 11 n 11 A 11 A U 11 n 1 B U 11 B C 12 n 2 C 12 B G 13 n 3 G 13 B U 14 n 4 U 14 B U 15 n 5 U 15 B A 16 n 6 A 16 B A 17 n 7 A 17 B U 18 n 8 U 18 B C 19 n 9 C 19 B U 20 n 10 U 20 B C 21 n 11 C 21 B 1 A A 6 0.073 SIDE CHAIN 1 A G 10 0.082 SIDE CHAIN B 1 B U 11 0.087 SIDE CHAIN 1 B A 16 0.065 SIDE CHAIN 1 B A 17 0.060 SIDE CHAIN 1 B U 18 0.080 SIDE CHAIN 1 B C 19 0.075 SIDE CHAIN 1 B U 20 0.074 SIDE CHAIN 1 4.56 0.70 108.50 113.06 A A A O4' C1' N1 C C C 9 9 9 N 1 4.46 0.70 108.50 112.96 B B B O4' C1' N1 C C C 12 12 12 N 1 4.24 0.70 108.50 112.74 B B B O4' C1' N9 G G G 13 13 13 N 1 5.30 0.70 108.50 113.80 B B B O4' C1' N1 U U U 14 14 14 N 1 5.56 0.70 108.50 114.06 B B B O4' C1' N1 U U U 15 15 15 N 1 4.51 0.70 108.50 113.01 B B B O4' C1' N1 C C C 19 19 19 N 1 4.31 0.70 108.50 112.81 B B B O4' C1' N1 U U U 20 20 20 N 5'-R(*GP*AP*GP*GP*AP*AP*GP*GP*CP*GP*A)-3' J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 21 B N3 C 11 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 21 B O2 C 11 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 21 B N4 C 11 1_555 hydrog WATSON-CRICK A A 2 A N1 A 2 1_555 B U 20 B N3 U 10 1_555 hydrog WATSON-CRICK A A 2 A N6 A 2 1_555 B U 20 B O4 U 10 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 B C 19 B N3 C 9 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 B C 19 B O2 C 9 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 B C 19 B N4 C 9 1_555 hydrog TYPE_28_PAIR A G 4 A N1 G 4 1_555 B U 18 B O2 U 8 1_555 hydrog TYPE_28_PAIR A G 4 A O6 G 4 1_555 B U 18 B N3 U 8 1_555 hydrog A-A MISPAIR A A 5 A N3 A 5 1_555 B A 17 B N6 A 7 1_555 hydrog A-A MISPAIR A A 6 A N6 A 6 1_555 B A 16 B N3 A 6 1_555 hydrog TYPE_28_PAIR A G 7 A N1 G 7 1_555 B U 15 B O2 U 5 1_555 hydrog TYPE_28_PAIR A G 7 A O6 G 7 1_555 B U 15 B N3 U 5 1_555 hydrog TYPE_28_PAIR A G 8 A N1 G 8 1_555 B U 14 B O2 U 4 1_555 hydrog TYPE_28_PAIR A G 8 A O6 G 8 1_555 B U 14 B N3 U 4 1_555 hydrog WATSON-CRICK A C 9 A N3 C 9 1_555 B G 13 B N1 G 3 1_555 hydrog WATSON-CRICK A C 9 A N4 C 9 1_555 B G 13 B O6 G 3 1_555 hydrog WATSON-CRICK A C 9 A O2 C 9 1_555 B G 13 B N2 G 3 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 B C 12 B N3 C 2 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 B C 12 B O2 C 2 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 B C 12 B N4 C 2 1_555 hydrog WATSON-CRICK B A A 11 A N1 A 11 1_555 B U 11 B N3 U 1 1_555 hydrog WATSON-CRICK B A A 11 A N6 A 11 1_555 B U 11 B O4 U 1 1_555 RNA RNA, internal loop, tandem mismatch, GU pairs, AA pairs 1TUT PDB 1 1TUT 1TUT PDB 2 1TUT 1 11 1TUT 1 11 1TUT A 1 1 11 11 21 1TUT 11 21 1TUT B B 2 1 11 1 P 1