1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Leeper, T.C. Schmidt, F.J. Van Doren, S.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 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 Nat.Struct.Biol. NSBIEW 2024 1072-8368 9 397 403 11927952 Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action. 2002 10.2210/pdb1jp0/pdb pdb_00001jp0 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 PL5.1 HAIRPIN FROM RNASE P RNA 6776.060 5'-R(*GP*GP*CP*GP*GP*UP*GP*CP*UP*GP*AP*GP*AP*UP*GP*CP*CP*CP*GP*UP*C)-3' 1 syn polymer no no GGCGGUGCUGAGAUGCCCGUC GGCGGUGCUGAGAUGCCCGUC A polyribonucleotide n n n n n n n n n n n n n n n n n n n n n 0.135 1 19 A 1 A 21 7.767 A_G1:C21_A 1 -4.796 -1.390 -0.120 -0.448 0.604 28 A 2 A 20 -11.429 A_G2:U20_A 2 -9.245 -1.249 0.077 -0.292 4.030 1 19 A 3 A 19 2.724 A_C3:G19_A 3 2.058 0.109 -0.166 -0.194 -0.898 1 19 A 4 A 18 2.490 A_G4:C18_A 4 -7.837 -0.799 -0.130 -0.571 4.427 1 19 A 5 A 17 -5.800 A_G5:C17_A 5 6.517 -0.402 -0.521 -0.614 8.472 A 7 A 16 -11.967 A_G7:C16_A 6 -2.976 0.104 0.207 0.212 3.991 1 19 A 8 A 15 -2.714 A_C8:G15_A 7 -4.962 0.549 0.043 -0.371 3.555 28.538 A A 1 2 -18.027 A A 21 20 3.072 -8.748 -0.993 -2.014 AA_G1G2:U20C21_AA 1 -0.578 1.191 27.185 -2.017 1.878 3.725 36.065 A A 2 3 -18.234 A A 20 19 3.340 -11.106 0.743 -2.016 AA_G2C3:G19U20_AA 2 -2.750 4.514 34.259 -1.509 -1.633 2.610 26.931 A A 3 4 11.022 A A 19 18 3.030 5.083 -0.853 -2.493 AA_C3G4:C18G19_AA 3 -4.221 9.153 26.123 -6.492 0.884 2.581 44.115 A A 4 5 39.469 A A 18 17 2.772 27.548 -2.513 0.178 AA_G4G5:C17C18_AA 4 -5.241 7.508 34.404 -2.176 2.887 3.159 34.939 A A 5 7 3.610 A A 17 16 3.031 2.110 -1.180 -1.464 AA_G5G7:C16C17_AA 5 -13.845 23.686 32.090 -2.754 -0.107 2.153 30.979 A A 7 8 24.529 A A 16 15 3.134 12.724 -0.376 -1.819 AA_G7C8:G15C16_AA 6 -1.799 3.468 28.248 -5.487 0.409 database_2 pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2002-05-01 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession NMR structure of the LP5.1 hairpin from Bacillus RNase P RNA refined WITH residual dipolar couplings. RCSB Y RCSB 2001-07-31 REL REL IN VITRO TRANSCRIPTION sample structures with the lowest energy 100 28 13C-separated-NOESY (Mixing times of 200 and 250 ms) NOESY (Mixing times of 80 and 140 ms) HCCH-TOCSY HCCH-COSY 13C-Hetero-TOCSY 20 mM Sodium Phosphate 5.5 ambient 298 K 20 mM Sodium Phosphate 5.5 ambient 277 K 20 mM Sodium Phosphate 5.5 ambient 298 K 20 mM Sodium Phosphate 5.5 ambient 298 K 20 mM Sodium Phosphate 5.5 ambient 277 K residual dipolar coupling refinement were NOT used for this structure, see 1JOX. torsion angle dynamics 1 closest to the average 1.0 mM PL5.1 hairpin RNA U-15N,13C, 20mM phosphate buffer NA, 100% D2O 100% D2O 1.0 mM PL5.1 hairpin RNA U-15N,13C, 20mM phosphate buffer NA, 8% H2O 92% D2O 8% H2O 92% D2O 2.5 mM PL5.1 hairpin RNA U-15N,13C U and A residues only, 20mM phosphate buffer NA, 100% D2O 100% D2O 1.8 mM PL5.1 hairpin RNA U-15N,13C A, C, and G residues only, 20mM phosphate buffer NA, 100% D2O 100% D2O 1.8 mM PL5.1 hairpin RNA U-15N,13C A, C, and G residues only, 20mM phosphate buffer NA, 8% H2O 92% D2O 8% H2O 92% D2O Brunger et. al refinement CNS 1.0 Brunger et. al structure solution CNS 1.0 500 Bruker DRX 600 Varian INOVA G 1 n 1 G 1 A G 2 n 2 G 2 A C 3 n 3 C 3 A G 4 n 4 G 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A U 9 n 9 U 9 A G 10 n 10 G 10 A A 11 n 11 A 11 A G 12 n 12 G 12 A A 13 n 13 A 13 A U 14 n 14 U 14 A G 15 n 15 G 15 A C 16 n 16 C 16 A C 17 n 17 C 17 A C 18 n 18 C 18 A G 19 n 19 G 19 A U 20 n 20 U 20 A C 21 n 21 C 21 A author_defined_assembly 1 monomeric 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 H2' O4' U G 14 15 1.34 1 A A HO2' O5' G U 5 6 1.38 1 A A HO2' O5' G A 12 13 1.40 1 A A N7 H5'' A A 11 13 1.49 1 A A HO2' O5' G G 4 5 1.52 1 A A H21 O2 G C 4 18 1.55 1 A A O2 H21 C G 3 19 1.56 2 A A H2' O4' U G 14 15 1.42 2 A A H21 O2 G C 4 18 1.53 2 A A HO2' O4 U U 9 14 1.55 2 A A O2 H21 C G 3 19 1.57 2 A A H21 O2 G C 5 17 1.58 2 A A O2' HO2' U A 9 13 1.60 2 A A O2 H21 C G 8 15 1.60 3 A A H2' O4' U G 14 15 1.39 3 A A HO2' O4 U U 9 14 1.51 3 A A H21 O2 G C 4 18 1.55 3 A A O2 H21 C G 3 19 1.57 4 A A HO2' O5' G U 5 6 1.35 4 A A H2' O4' U G 14 15 1.37 4 A A H2' O4' C U 8 9 1.52 4 A A HO2' O5' G A 12 13 1.54 4 A A O2 H21 C G 3 19 1.54 4 A A H21 O2 G C 4 18 1.55 5 A A H2' O4' U G 14 15 1.37 5 A A HO2' O5' G U 5 6 1.40 5 A A H2' O4' C U 8 9 1.48 5 A A HO2' O5' G G 4 5 1.48 5 A A H21 O2 G C 4 18 1.55 5 A A O2 H21 C G 3 19 1.57 5 A A HO2' O5' G A 12 13 1.57 6 A A H2' O4' U G 14 15 1.40 6 A A H21 O2 G C 4 18 1.55 6 A A O2 H21 C G 3 19 1.56 6 A A HO2' O5' G G 4 5 1.57 6 A A O6 H41 G C 5 17 1.60 7 A A H2' O4' U G 14 15 1.35 7 A A HO2' O4 U U 9 14 1.42 7 A A H2' O4' C U 8 9 1.49 7 A A H21 O2 G C 4 18 1.55 7 A A O2 H21 C G 3 19 1.55 7 A A H21 O2 G C 5 17 1.56 8 A A H2' O4' U G 14 15 1.45 8 A A HO2' O5' G G 4 5 1.52 8 A A H21 O2 G C 4 18 1.53 8 A A H4' O5' G U 5 6 1.55 8 A A O2 H21 C G 3 19 1.57 8 A A HO2' O4 U U 9 14 1.58 9 A A H2' O4' U G 14 15 1.38 9 A A H2' O4' C U 8 9 1.46 9 A A HO2' O5' G G 4 5 1.49 9 A A H4' O5' G U 5 6 1.54 9 A A H21 O2 G C 4 18 1.55 9 A A O2 H21 C G 3 19 1.59 10 A A HO2' O5' G U 5 6 1.32 10 A A H2' O4' U G 14 15 1.34 10 A A HO2' O5' G G 4 5 1.53 10 A A H21 O2 G C 4 18 1.54 10 A A HO2' O4 U U 9 14 1.57 10 A A O2 H21 C G 3 19 1.57 10 A A N7 H5'' A A 11 13 1.58 11 A A H2' O4' U G 14 15 1.36 11 A A O2' H8 G G 5 7 1.44 11 A A H21 O2 G C 4 18 1.51 11 A A O2' H5' C G 3 4 1.54 11 A A O2 H21 C G 3 19 1.56 11 A A HO2' O5' G A 12 13 1.56 11 A A H2' O4' C U 8 9 1.59 12 A A HO2' O5' G A 12 13 1.39 12 A A HO2' O5' G G 4 5 1.47 12 A A H21 O2 G C 4 18 1.53 12 A A H2' O4' U G 14 15 1.54 12 A A O2 H21 C G 3 19 1.56 12 A A H2' O4' C U 8 9 1.58 13 A A H2' O4' U G 14 15 1.35 13 A A HO2' O5' G G 4 5 1.39 13 A A O2' H3' G U 5 6 1.47 13 A A HO2' O5' G U 5 6 1.50 13 A A H2' O4' C U 8 9 1.55 13 A A H21 O2 G C 4 18 1.55 13 A A H21 O2 G C 5 17 1.57 14 A A H2' O4' U G 14 15 1.31 14 A A H21 O2 G C 4 18 1.54 14 A A HO2' O5' G U 5 6 1.56 14 A A O2 H21 C G 8 15 1.57 15 A A H2' O4' U G 14 15 1.46 15 A A H21 O2 G C 4 18 1.54 15 A A O2 H21 C G 8 15 1.57 15 A A O2 H21 C G 3 19 1.59 16 A A H2' O4' U G 14 15 1.39 16 A A HO2' O5' G A 12 13 1.42 16 A A H2' O4' C U 8 9 1.52 16 A A HO2' O4 U U 9 14 1.52 16 A A N7 H5'' A A 11 13 1.53 16 A A H21 O2 G C 4 18 1.53 16 A A O2' H5' C G 3 4 1.54 16 A A HO2' O5' U G 6 7 1.55 16 A A O2 H21 C G 3 19 1.56 16 A A O6 H41 G C 5 17 1.60 17 A A H2' O4' U G 14 15 1.40 17 A A O2' H5' C G 3 4 1.45 17 A A H21 O2 G C 4 18 1.53 17 A A H2' O4' C U 8 9 1.56 17 A A O2 H21 C G 3 19 1.56 17 A A H2' O4' C C 17 18 1.58 17 A A N7 H5'' A A 11 13 1.58 18 A A H2' O4' U G 14 15 1.38 18 A A HO2' O4 U U 9 14 1.42 18 A A H2' O4' C U 8 9 1.51 18 A A H21 O2 G C 4 18 1.52 18 A A HO2' O5' G U 5 6 1.58 18 A A HO2' O5' C U 8 9 1.60 19 A A H2' O4' U G 14 15 1.33 19 A A H21 O2 G C 4 18 1.54 19 A A O2 H21 C G 3 19 1.56 19 A A O2 H21 C G 8 15 1.56 20 A A H2' O4' U G 14 15 1.37 20 A A HO2' O5' G U 5 6 1.40 20 A A O2' H3' G U 5 6 1.54 20 A A H21 O2 G C 4 18 1.54 20 A A H2' O4' C U 8 9 1.55 20 A A H2' O4' G C 15 16 1.56 20 A A HO2' O5' G A 12 13 1.57 20 A A HO2' O5' U G 6 7 1.58 20 A A O2 H21 C G 3 19 1.60 21 A A H2' O4' U G 14 15 1.37 21 A A O2' H5' C G 3 4 1.46 21 A A HO2' O5' G U 5 6 1.48 21 A A H2' O4' C U 8 9 1.50 21 A A H21 O2 G C 4 18 1.53 21 A A O2 H21 C G 3 19 1.54 21 A A H21 O2 G C 5 17 1.54 21 A A H21 O2 G C 1 21 1.58 22 A A H2' O4' U G 14 15 1.35 22 A A O2' H5' C G 3 4 1.45 22 A A H21 O2 G C 4 18 1.53 22 A A O4' H6 G U 5 6 1.56 22 A A O2 H21 C G 3 19 1.56 22 A A H2' N7 G G 4 5 1.58 23 A A H2' O4' U G 14 15 1.42 23 A A H2' O4' C U 8 9 1.50 23 A A H21 O2 G C 4 18 1.55 23 A A N7 H5'' A A 11 13 1.55 23 A A O2 H21 C G 3 19 1.57 23 A A H2' O4' C C 17 18 1.58 23 A A H4' O5' G U 5 6 1.60 24 A A H2' O4' U G 14 15 1.40 24 A A H2' O4' C U 8 9 1.43 24 A A HO2' O5' G U 5 6 1.49 24 A A H21 O2 G C 4 18 1.53 24 A A O3' H8 G G 4 5 1.55 24 A A HO2' O5' U G 6 7 1.56 24 A A HO2' O4 U U 9 14 1.58 25 A A HO2' O5' G A 12 13 1.38 25 A A H2' O4' C U 8 9 1.46 25 A A N7 H5'' A A 11 13 1.46 25 A A HO2' O5' G U 5 6 1.46 25 A A H2' O4' U G 14 15 1.48 25 A A HO2' O5' G G 4 5 1.49 25 A A O2 H21 C G 3 19 1.56 25 A A H21 O2 G C 4 18 1.57 26 A A H2' O4' U G 14 15 1.31 26 A A H2' O4' C U 8 9 1.46 26 A A HO2' O4 U U 9 14 1.53 26 A A H21 O2 G C 4 18 1.55 26 A A H21 O2 G C 7 16 1.58 26 A A H21 O2 G C 1 21 1.59 26 A A HO2' O5' C U 8 9 1.60 27 A A H2' O4' C U 8 9 1.45 27 A A H2' O4' U G 14 15 1.51 27 A A HO2' O5' G G 4 5 1.52 27 A A H21 O2 G C 4 18 1.55 27 A A H8 O3' G A 10 13 1.60 28 A A H2' O4' U G 14 15 1.36 28 A A HO2' O5' G A 12 13 1.44 28 A A H21 O2 G C 4 18 1.52 28 A A O2 H21 C G 3 19 1.57 28 A A N7 H5'' A A 11 13 1.57 28 A A HO2' O4 U U 9 14 1.58 20 A C 21 0.068 SIDE CHAIN 21 A C 21 0.062 SIDE CHAIN 25 A G 5 0.059 SIDE CHAIN 28 A U 9 0.084 SIDE CHAIN 26 9.88 1.30 114.00 123.88 A A A N9 C1' C2' A A A 13 13 13 N NMR Structure of the LP5.1 Hairpin from Bacillus RNase P RNA Refined WITHOUT Residual Dipolar Couplings 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 21 A N3 C 21 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 21 A O2 C 21 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 21 A N4 C 21 1_555 hydrog TYPE_28_PAIR A G 2 A N1 G 2 1_555 A U 20 A O2 U 20 1_555 hydrog TYPE_28_PAIR A G 2 A O6 G 2 1_555 A U 20 A N3 U 20 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 A G 19 A N1 G 19 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 A G 19 A O6 G 19 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 A G 19 A N2 G 19 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 A C 18 A N3 C 18 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 A C 18 A O2 C 18 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 A C 18 A N4 C 18 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 17 A N3 C 17 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 17 A O2 C 17 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 17 A N4 C 17 1_555 hydrog G-C PAIR A G 7 A N1 G 7 1_555 A C 16 A N3 C 16 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 15 A N1 G 15 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 15 A O6 G 15 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 15 A N2 G 15 1_555 RNA RIBONUCLEIC ACID, RNASE P, HAIRPIN, RESIDUAL DIPOLAR COUPLING REFINEMENT, UGNRAU, RNA 1JP0 PDB 1 1JP0 1 21 1JP0 1 21 1JP0 A 1 1 21