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/pdb1f6z/pdb pdb_00001f6z 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 8634.127 RNASE P RNA RIBOZYME, P4 DOMAIN MUTANT P4 STEM C70U 1 syn polymer no no GGAAGUUCGGUCUUCGGACCGGCUUCC GGAAGUUCGGUCUUCGGACCGGCUUCC 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 60.648 1 19 A 1 A 27 -3.522 A_G1:C27_A 1 18.925 -0.056 -0.009 -0.141 18.692 1 19 A 2 A 26 -10.549 A_G2:C26_A 2 1.795 -0.053 1.590 -0.562 13.278 1 20 A 3 A 25 -7.827 A_A3:U25_A 3 -17.077 -0.026 0.094 -0.159 2.460 1 20 A 4 A 24 -0.112 A_A4:U24_A 4 -13.001 0.003 -0.720 -0.125 -6.799 1 19 A 5 A 23 -1.792 A_G5:C23_A 5 -29.002 -0.206 -0.158 -0.256 -16.733 28 A 6 A 22 -7.820 A_U6:G22_A 6 3.955 2.075 1.081 -0.671 -26.763 1 19 A 8 A 21 -10.282 A_C8:G21_A 7 14.205 -0.064 -1.154 -0.898 3.058 1 19 A 9 A 20 -4.729 A_G9:C20_A 8 -2.272 0.054 1.457 -0.751 -2.253 1 19 A 10 A 19 8.102 A_G10:C19_A 9 -26.447 -0.397 -0.791 -0.460 -0.775 1 20 A 11 A 18 -10.453 A_U11:A18_A 10 -1.209 -0.110 -1.587 -0.769 -7.798 1 19 A 12 A 17 0.267 A_C12:G17_A 11 -7.953 0.513 -0.400 -0.302 27.077 6 A 13 A 16 -75.546 A_U13:G16_A 12 -6.454 1.320 -0.436 -5.494 4.186 29.596 A A 1 2 35.649 A A 27 26 5.881 16.824 -1.331 -1.347 AA_G1G2:C26C27_AA 1 -8.848 18.747 22.790 -8.869 -0.672 2.594 42.302 A A 2 3 24.725 A A 26 25 3.640 17.228 -0.050 -1.679 AA_G2A3:U25C26_AA 2 9.017 -12.940 37.751 -4.114 1.005 4.785 35.221 A A 3 4 -17.333 A A 25 24 4.708 -10.317 0.989 -0.661 AA_A3A4:U24U25_AA 3 4.365 -7.334 33.445 1.196 -0.666 4.005 31.638 A A 4 5 3.479 A A 24 23 4.076 1.896 0.199 -1.054 AA_A4G5:C23U24_AA 4 -0.263 0.483 31.581 -2.367 -0.426 2.677 50.784 A A 5 6 32.241 A A 23 22 3.718 26.403 0.445 -0.997 AA_G5U6:G22C23_AA 5 -5.089 6.214 43.488 -3.141 -0.901 1.716 44.968 A A 6 8 54.773 A A 22 21 4.643 35.397 0.633 -1.267 AA_U6C8:G21G22_AA 6 15.200 -23.520 23.652 -5.855 0.976 1.754 34.385 A A 8 9 14.840 A A 21 20 2.550 8.536 0.821 -1.382 AA_C8G9:C20G21_AA 7 -10.968 19.068 31.529 -3.256 -2.567 3.911 35.446 A A 9 10 12.004 A A 20 19 4.063 7.018 1.000 -0.522 AA_G9G10:C19C20_AA 8 15.696 -26.847 31.114 -2.201 1.364 3.699 30.100 A A 10 11 11.985 A A 19 18 3.875 6.182 -1.365 -0.583 AA_G10U11:A18C19_AA 9 -0.467 0.904 29.469 -2.603 2.516 2.325 42.333 A A 11 12 40.143 A A 18 17 3.801 26.878 0.083 -1.032 AA_U11C12:G17A18_AA 10 -3.950 5.900 32.778 -4.369 -0.547 3.233 105.621 A A 12 13 1.214 A A 17 16 3.610 1.928 2.307 -1.610 AA_C12U13:G16G17_AA 11 -20.798 13.096 104.149 -1.038 -1.749 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 1F6X shows the structure of the wildtype P4 stem oligoribonucleotide; in the wildtype the universally conserved U69 occupies the bulged position found for U70 in the mutant RCSB Y RCSB 2000-06-24 REL REL synthesized from DNA oligonucleotide template by T7 RNA polymerase sample This structure was determined using standard 2D homonuclear techniques as well as 13C and 31P heteronuclear experiments at natural isotope 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 17 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.9 Angstrom. A total of 268 NOE derived distance constraints, 171 dihedral restraints and 49 distance restraints from hydrogen bonds were used for refinement restrained molecular dynamics and simulated annealing 1 minimized average structure 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O 99.96% D2O 2 mM P4m RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O 90% H2O/10% D2O 2 mM P4m 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 3.84 Brunger refinement X-PLOR 2.84 600 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 U 7 n 7 U 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 1 A A O6 H41 G C 1 27 1.60 minimized average SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT 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 TYPE_28_PAIR A U 6 A N3 U 6 1_555 A G 22 A O6 G 22 1_555 hydrog TYPE_28_PAIR A U 6 A O2 U 6 1_555 A G 22 A N1 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, C70U MUTANT, METAL BINDING SITE, RNA 1F6Z PDB 1 1F6Z 1 27 1F6Z 1 27 1F6Z A 1 1 27 1 P 1