1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Schmitz, M. Tinoco Jr., I. 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 RNA RNARFU 2122 1355-8382 6 1212 1225 10.1017/S1355838200000881 10999599 Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA. 2000 10.2210/pdb1f6x/pdb pdb_00001f6x 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 8633.143 RNASE P RNA RIBOZYME, P4 DOMAIN P4 STEM 1 syn polymer no no GGAAGUCCGGUCUUCGGACCGGCUUCC GGAAGUCCGGUCUUCGGACCGGCUUCC 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 45.429 1 19 A 1 A 27 -1.594 A_G1:C27_A 1 13.442 -0.073 -0.447 -0.357 3.832 1 19 A 2 A 26 -7.953 A_G2:C26_A 2 -13.694 -0.263 0.367 -0.318 -3.680 1 20 A 3 A 25 -6.315 A_A3:U25_A 3 -27.087 0.057 -0.288 -0.218 1.189 1 20 A 4 A 24 -3.277 A_A4:U24_A 4 -3.902 0.035 -0.544 -0.032 3.569 1 19 A 5 A 23 -3.362 A_G5:C23_A 5 -2.771 -0.265 -0.717 -0.288 -7.523 1 19 A 7 A 22 -1.490 A_C7:G22_A 6 22.793 0.184 0.301 -0.041 -16.224 1 19 A 8 A 21 -7.479 A_C8:G21_A 7 6.319 -0.044 -0.566 -0.331 5.116 1 19 A 9 A 20 -3.282 A_G9:C20_A 8 -1.410 -0.074 -0.448 -0.255 1.824 1 19 A 10 A 19 9.722 A_G10:C19_A 9 -17.560 -0.374 -1.213 -0.693 5.860 1 20 A 11 A 18 -3.791 A_U11:A18_A 10 -4.862 -0.257 -0.598 0.012 -31.562 1 19 A 12 A 17 -3.886 A_C12:G17_A 11 18.315 0.241 1.929 -0.605 37.427 2 A 13 A 16 -64.645 A_U13:G16_A 12 9.967 1.250 0.239 -5.438 4.050 35.173 A A 1 2 40.347 A A 27 26 5.665 22.491 -0.958 -0.674 AA_G1G2:C26C27_AA 1 -4.437 7.960 26.857 -6.821 0.459 3.129 36.654 A A 2 3 19.695 A A 26 25 3.733 12.142 0.162 -1.249 AA_G2A3:U25C26_AA 2 4.011 -6.506 34.423 -3.792 0.338 3.863 33.718 A A 3 4 -10.768 A A 25 24 3.743 -6.212 0.597 -1.035 AA_A3A4:U24U25_AA 3 -0.252 0.437 33.156 -0.600 -1.078 2.490 30.279 A A 4 5 31.348 A A 24 23 3.689 15.617 -0.131 -1.356 AA_A4G5:C23U24_AA 4 0.521 -1.046 26.017 -5.816 0.358 3.364 60.484 A A 5 7 30.664 A A 23 22 3.603 29.516 -2.212 -0.493 AA_G5C7:G22C23_AA 5 -13.860 14.399 51.657 -2.173 1.405 3.830 35.118 A A 7 8 20.123 A A 22 21 4.641 11.874 -1.184 -1.031 AA_C7C8:G21G22_AA 6 5.054 -8.566 32.730 -4.096 2.979 2.980 26.741 A A 8 9 13.308 A A 21 20 3.234 6.102 0.247 -0.745 AA_C8G9:C20G21_AA 7 -0.487 1.063 26.043 -3.138 -0.657 3.683 31.387 A A 9 10 21.151 A A 20 19 4.056 11.146 0.777 -0.544 AA_G9G10:C19C20_AA 8 5.395 -10.237 28.898 -3.592 -0.184 2.170 39.219 A A 10 11 34.776 A A 19 18 3.195 21.998 -0.892 -1.081 AA_G10U11:A18C19_AA 9 -5.280 8.347 32.248 -3.999 0.755 2.346 40.921 A A 11 12 33.511 A A 18 17 4.397 21.301 -0.618 -2.238 AA_U11C12:G17A18_AA 10 -19.217 30.231 29.493 -6.041 -1.679 2.124 99.581 A A 12 13 -0.381 A A 17 16 2.498 -0.579 2.012 -2.103 AA_C12U13:G16G17_AA 11 -22.973 15.115 97.585 -1.371 -1.579 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2000-10-09 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name THE WILDTYPE P4 STEM OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMMINE THE C70U MUTANT P4 STEM OLIGORIBONUCLEOTIDE RCSB Y RCSB 2000-06-23 REL REL synthesized from DNA oligonucleotide template by T7 RNA polymerase sample This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance 1 2D NOESY 2D NOESY 2D NOESY 2D NOESY DQF-COSY 31P-1H-COSY 13C-1H-HMQC 100 mM Na 6.5 ambient 288 K 100 mM Na 6.5 ambient 288 K 100 mM Na, 10 mM Mg 6.5 ambient 288 K 100 mM Na, 3 mM Co(NH3)6 6.5 ambient 288 K The average structure is based on superposition of nine converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.8 Angstrom. A total of 266 NOE-derived distance constraints, 164 dihedral restraints and 48 distance restraints from hydrogen bonds were used in the refinement restrained molecular dynamics; simulated annealing 1 minimized average structure 2 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O 99.96% D2O 2 mM P4 RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4 RNA; 100 mM sodium chloride; 3 mM hexammine cobalt chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O Bruker collection XwinNMR 3.1 MSI processing Felix 95.0 Brunger structure solution X-PLOR 3.841 Brunger refinement X-PLOR 3.841 600 Bruker AMX 500 Bruker DRX G 1 n 1 G 1 A G 2 n 2 G 2 A A 3 n 3 A 3 A A 4 n 4 A 4 A G 5 n 5 G 5 A U 6 n 6 U 6 A C 7 n 7 C 7 A C 8 n 8 C 8 A G 9 n 9 G 9 A G 10 n 10 G 10 A U 11 n 11 U 11 A C 12 n 12 C 12 A U 13 n 13 U 13 A U 14 n 14 U 14 A C 15 n 15 C 15 A G 16 n 16 G 16 A G 17 n 17 G 17 A A 18 n 18 A 18 A C 19 n 19 C 19 A C 20 n 20 C 20 A G 21 n 21 G 21 A G 22 n 22 G 22 A C 23 n 23 C 23 A U 24 n 24 U 24 A U 25 n 25 U 25 A C 26 n 26 C 26 A C 27 n 27 C 27 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 minimized average SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLEOTIDE 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 27 A N3 C 27 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 27 A O2 C 27 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 27 A N4 C 27 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 26 A N3 C 26 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 26 A O2 C 26 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 26 A N4 C 26 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 A U 25 A N3 U 25 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 A U 25 A O4 U 25 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 A U 24 A N3 U 24 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 A U 24 A O4 U 24 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 23 A N3 C 23 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 23 A O2 C 23 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 23 A N4 C 23 1_555 hydrog WATSON-CRICK A C 7 A N3 C 7 1_555 A G 22 A N1 G 22 1_555 hydrog WATSON-CRICK A C 7 A N4 C 7 1_555 A G 22 A O6 G 22 1_555 hydrog WATSON-CRICK A C 7 A O2 C 7 1_555 A G 22 A N2 G 22 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 A G 21 A N1 G 21 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 A G 21 A O6 G 21 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 A G 21 A N2 G 21 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 A C 20 A N3 C 20 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 A C 20 A O2 C 20 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 A C 20 A N4 C 20 1_555 hydrog WATSON-CRICK A G 10 A N1 G 10 1_555 A C 19 A N3 C 19 1_555 hydrog WATSON-CRICK A G 10 A N2 G 10 1_555 A C 19 A O2 C 19 1_555 hydrog WATSON-CRICK A G 10 A O6 G 10 1_555 A C 19 A N4 C 19 1_555 hydrog WATSON-CRICK A U 11 A N3 U 11 1_555 A A 18 A N1 A 18 1_555 hydrog WATSON-CRICK A U 11 A O4 U 11 1_555 A A 18 A N6 A 18 1_555 hydrog WATSON-CRICK A C 12 A N3 C 12 1_555 A G 17 A N1 G 17 1_555 hydrog WATSON-CRICK A C 12 A N4 C 12 1_555 A G 17 A O6 G 17 1_555 hydrog WATSON-CRICK A C 12 A O2 C 12 1_555 A G 17 A N2 G 17 1_555 hydrog U-G MISPAIR A U 13 A O2 U 13 1_555 A G 16 A N1 G 16 1_555 RNA RIBONUCLEASE P, RIBOZYME, TRANSFER RNA PROCESSING, P4 STEM, METAL BINDING SITE, RNA 1F6X PDB 1 1F6X 1 27 1F6X 1 27 1F6X A 1 1 27 1 P 1