1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Popovic, M. Greenbaum, N.L. 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 y URIDINE-5'-MONOPHOSPHATE RNA linking UK Rna RNARFU 2122 1355-8382 20 24 35 10.1261/rna.039701.113 24243113 Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5' splice site. 2014 10.2210/pdb2m12/pdb pdb_00002m12 7443.480 RNA (5'-R(*GP*GP*GP*UP*GP*UP*AP*UP*UP*GP*GP*AP*AP*AP*UP*GP*AP*GP*CP*AP*CP*CP*C)-3') 1 syn polymer no no GGGUGUAUUGGAAAUGAGCACCC GGGUGUAUUGGAAAUGAGCACCC 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 RNA stem loop 16.713 1 19 A 1 A 23 -4.772 A_G1:C23_A 1 23.023 -0.134 -0.298 -0.234 4.243 1 19 A 2 A 22 -4.313 A_G2:C22_A 2 -11.576 -0.042 0.646 -0.248 -0.079 1 19 A 3 A 21 -2.005 A_G3:C21_A 3 -9.923 -0.101 0.110 -0.183 0.585 1 20 A 4 A 20 -4.059 A_U4:A20_A 4 -9.636 -0.041 -0.221 -0.072 -2.248 1 19 A 5 A 19 -2.907 A_G5:C19_A 5 -8.696 -0.041 0.184 -0.175 -8.467 1 28 A 6 A 18 -4.437 A_U6:G18_A 6 0.196 1.997 0.421 -0.391 -17.049 1 A 9 A 17 22.952 A_U9:A17_A 7 3.242 1.283 1.912 -0.672 -5.962 A 11 A 13 -8.194 A_G11:A13_A 8 -31.384 4.473 -2.491 -1.821 3.485 32.786 A A 1 2 17.700 A A 23 22 4.029 9.676 -0.737 -1.361 AA_G1G2:C22C23_AA 1 -10.413 19.048 29.621 -4.427 -0.862 3.086 31.591 A A 2 3 15.982 A A 22 21 3.649 8.594 0.051 -1.622 AA_G2G3:C21C22_AA 2 1.314 -2.443 30.400 -4.652 0.161 2.752 31.632 A A 3 4 18.380 A A 21 20 3.410 9.857 -0.104 -1.606 AA_G3U4:A20C21_AA 3 1.334 -2.488 30.066 -4.709 0.430 2.778 31.544 A A 4 5 19.803 A A 20 19 3.516 10.561 0.140 -1.616 AA_U4G5:C19A20_AA 4 -1.935 3.629 29.705 -4.923 -0.614 3.546 37.497 A A 5 6 18.641 A A 19 18 4.234 11.776 0.449 -1.678 AA_G5U6:G18C19_AA 5 3.632 -5.750 35.483 -4.499 -0.116 database_2 pdbx_database_status pdbx_nmr_software pdbx_nmr_spectrometer repository Initial release Database references Data collection Database references Other 1 0 2013-10-23 1 1 2014-02-05 1 2 2023-06-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model BMRB Y RCSB 2012-11-13 REL REL REL REL 287 130 26 99 structures with the least restraint violations 100 10 2D 1H-1H NOESY 2D 1H-1H TOCSY 2D DQF-COSY 2D 1H-15N HSQC 2D 1H-13C HSQC 2D 1H-13C HSQC aliphatic 2D 1H-13C HSQC aromatic 3D 1H-15N NOESY 3D HCCH-COSY 3D HCCH-TOCSY 2D 1H-1H NOESY 0.03-0.9 mM 60 mM 0.3-0.9 mM 60 mM 0.3-0.5 mM [U-100% 13C; U-100% 15N] 60 mM 0.3-0.5 mM [U-100% 13C; U-100% 15N] 60 mM 0.06 6.4 ambient 277 K 0.06 6.4 ambient 303 K torsion angle dynamics 1 fewest violations 0.03-0.9 mM ID3, 60 mM sodium chloride, 90% H2O/10% D2O 90% H2O/10% D2O 0.3-0.9 mM ID3, 60 mM sodium chloride, 100% D2O 100% D2O 0.3-0.5 mM [U-100% 13C; U-100% 15N] ID3, 60 mM sodium chloride, 90% H2O/10% D2O 90% H2O/10% D2O 0.3-0.5 mM [U-100% 13C; U-100% 15N] ID3, 60 mM potassium chloride, 100% D2O 100% D2O CCPN chemical shift assignment CCPN Bruker Biospin collection TopSpin Bruker Biospin processing TopSpin Goddard chemical shift assignment Sparky Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax processing NMRPipe Schwieters, Kuszewski, Tjandra and Clore structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore refinement X-PLOR NIH 600 Bruker AVANCE Bruker Avance GUA 1 n 1 G 1 A GUA 2 n 2 G 2 A GUA 3 n 3 G 3 A URA 4 n 4 U 4 A GUA 5 n 5 G 5 A URA 6 n 6 U 6 A ADE 7 n 7 A 7 A URA 8 n 8 U 8 A URA 9 n 9 U 9 A GUA 10 n 10 G 10 A GUA 11 n 11 G 11 A ADE 12 n 12 A 12 A ADE 13 n 13 A 13 A ADE 14 n 14 A 14 A URA 15 n 15 U 15 A GUA 16 n 16 G 16 A ADE 17 n 17 A 17 A GUA 18 n 18 G 18 A CYT 19 n 19 C 19 A ADE 20 n 20 A 20 A CYT 21 n 21 C 21 A CYT 22 n 22 C 22 A CYT 23 n 23 C 23 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 O2' H8 G G 1 2 1.50 1 A A O2' H6 A U 14 15 1.58 2 A A O2' H5'' U U 8 9 1.57 2 A A H1' O4 G U 11 15 1.57 3 A A HO2' O5' U G 15 16 1.52 4 A A H4' OP1 G G 10 11 1.59 5 A A HO2' O5' U G 15 16 1.51 5 A A HO2' O5' A U 7 8 1.53 6 A A O2' H8 G G 1 2 1.48 6 A A HO2' O5' G G 1 2 1.54 7 A A O2' H8 G G 1 2 1.47 7 A A O2' H5' U G 15 16 1.53 7 A A HO2' O5' G G 1 2 1.54 7 A A HO2' O5' A G 17 18 1.55 8 A A HO2' O4' U G 15 16 1.46 9 A A HO2' OP1 U G 9 10 1.36 9 A A HO2' O5' A U 14 15 1.53 9 A A HO2' O5' U U 8 9 1.59 10 A A HO2' O4' A U 14 15 1.29 10 A A O2' H8 G G 1 2 1.53 10 A A HO2' O5' U G 15 16 1.54 10 A A H1' OP1 G A 10 12 1.58 fewest violations, model3 Solution structure of the ID3 stem loop of domain 1 of the ai5gamma group II intron 1 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 A C 23 A N3 C 23 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 A C 23 A O2 C 23 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 A C 23 A N4 C 23 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 22 A N3 C 22 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 22 A O2 C 22 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 22 A N4 C 22 1_555 hydrog WATSON-CRICK A G 3 A N1 G 3 1_555 A C 21 A N3 C 21 1_555 hydrog WATSON-CRICK A G 3 A N2 G 3 1_555 A C 21 A O2 C 21 1_555 hydrog WATSON-CRICK A G 3 A O6 G 3 1_555 A C 21 A N4 C 21 1_555 hydrog WATSON-CRICK A U 4 A N3 U 4 1_555 A A 20 A N1 A 20 1_555 hydrog WATSON-CRICK A U 4 A O4 U 4 1_555 A A 20 A N6 A 20 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 19 A N3 C 19 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 19 A O2 C 19 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 19 A N4 C 19 1_555 hydrog TYPE_28_PAIR A U 6 A N3 U 6 1_555 A G 18 A O6 G 18 1_555 hydrog TYPE_28_PAIR A U 6 A O2 U 6 1_555 A G 18 A N1 G 18 1_555 hydrog U-A PAIR A U 9 A N3 U 9 1_555 A A 17 A N1 A 17 1_555 hydrog G-A MISPAIR A G 11 A N3 G 11 1_555 A A 13 A N6 A 13 1_555 RNA EBS1, stem loop, ID3, RNA 2M12 PDB 1 2M12 1 23 2M12 1 23 2M12 A 1 1 23