data_16951 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Structure of RNA Internal Loops with Tandem AG Pairs: 5'GAGC/3'CGAG ; _BMRB_accession_number 16951 _BMRB_flat_file_name bmr16951.str _Entry_type new _Submission_date 2010-05-25 _Accession_date 2010-05-25 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Tandem AG pairs with GC closing pairs: r(GACGAGCGUCA)2' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hammond Nicholas B. . 2 Kennedy Scott D. . 3 Turner Douglas H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 107 "13C chemical shifts" 50 "31P chemical shifts" 10 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-09 update BMRB 'complete entry citation' 2010-07-02 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16950 GACAAGUGUCA 16952 GACUAGAGUCA 16953 GGUAGGCCA stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20481618 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hammond Nicholas B. . 2 Tolbert Blanton S. . 3 Kierzek Ryszard . . 4 Turner Douglas H. . 5 Kennedy Scott D. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 49 _Journal_issue 27 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5817 _Page_last 5827 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_1' $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_2' $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') _Molecular_mass 3530.203 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence GACGAGCGUCA loop_ _Residue_seq_code _Residue_label 1 G 2 A 3 C 4 G 5 A 6 G 7 C 8 G 9 U 10 C 11 A stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name _Details $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 'obtained from a vendor' . . . . . Dharmacon stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 1 mM 'natural abundance' 'sodium chloride' 80 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3') 1 mM 'natural abundance' 'sodium chloride' 80 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.12 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1C loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-31P_HETCOR_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 6.1 . pH pressure 1 . atm 'ionic strength' 0.1 . M stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 288 . K pH 6.1 . pH pressure 1 . atm 'ionic strength' 0.1 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS P 31 'methyl protons' ppm 0.00 na indirect . . . 0.404808636 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-1H TOCSY' '2D DQF-COSY' '2D 1H-31P HETCOR' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(*GP*AP*CP*GP*AP*GP*CP*GP*UP*CP*A)-3')_1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 G H1 H 12.006 0.002 1 2 1 1 G H1' H 5.845 0.001 . 3 1 1 G H2' H 4.818 0.000 . 4 1 1 G H3' H 4.647 0.001 . 5 1 1 G H4' H 4.445 0.001 . 6 1 1 G H5' H 4.112 0.002 . 7 1 1 G H5'' H 3.974 0.001 2 8 1 1 G H8 H 8.115 0.001 1 9 1 1 G H21 H 7.745 0.000 2 10 1 1 G H22 H 6.160 0.002 2 11 1 1 G C1' C 93.112 0.000 . 12 1 1 G C2' C 75.152 0.000 . 13 1 1 G C3' C 74.017 0.000 . 14 1 1 G C4' C 84.751 0.000 . 15 1 1 G C8 C 138.786 0.000 1 16 2 2 A H1' H 6.004 0.001 . 17 2 2 A H2 H 7.699 0.001 1 18 2 2 A H2' H 4.628 0.001 . 19 2 2 A H3' H 4.725 0.001 . 20 2 2 A H4' H 4.538 0.002 . 21 2 2 A H5' H 4.651 0.001 . 22 2 2 A H5'' H 4.212 0.001 2 23 2 2 A H8 H 8.066 0.000 1 24 2 2 A H61 H 7.898 0.000 2 25 2 2 A H62 H 6.494 0.000 2 26 2 2 A HO2' H 6.918 0.000 . 27 2 2 A C1' C 92.814 0.000 . 28 2 2 A C2 C 154.042 0.000 1 29 2 2 A C2' C 75.554 0.000 . 30 2 2 A C3' C 72.527 0.000 . 31 2 2 A C4' C 82.244 0.000 . 32 2 2 A C8 C 139.685 0.000 1 33 2 2 A P P -4.012 0.000 1 34 3 3 C H1' H 5.306 0.001 . 35 3 3 C H2' H 4.215 0.000 . 36 3 3 C H3' H 4.395 0.004 . 37 3 3 C H4' H 4.371 0.002 . 38 3 3 C H5 H 5.243 0.001 1 39 3 3 C H5' H 4.492 0.002 . 40 3 3 C H5'' H 4.075 0.004 2 41 3 3 C H6 H 7.388 0.001 1 42 3 3 C H41 H 8.150 0.000 2 43 3 3 C H42 H 6.892 0.001 2 44 3 3 C C2' C 75.511 0.000 . 45 3 3 C C3' C 72.292 0.000 . 46 3 3 C C4' C 81.821 0.000 . 47 3 3 C C5 C 97.700 0.000 1 48 3 3 C C6 C 139.843 0.000 1 49 3 3 C P P -3.925 0.000 1 50 4 4 G H1 H 12.444 0.003 1 51 4 4 G H1' H 5.584 0.001 . 52 4 4 G H2' H 3.973 0.001 . 53 4 4 G H3' H 4.808 0.002 . 54 4 4 G H4' H 4.354 0.000 . 55 4 4 G H5' H 4.573 0.000 . 56 4 4 G H5'' H 4.099 0.000 2 57 4 4 G H8 H 7.570 0.001 1 58 4 4 G H21 H 7.301 0.004 2 59 4 4 G H22 H 5.444 0.001 2 60 4 4 G C1' C 92.658 0.000 . 61 4 4 G C2' C 75.726 0.000 . 62 4 4 G C3' C 72.617 0.000 . 63 4 4 G C4' C 81.893 0.000 . 64 4 4 G C8 C 136.651 0.000 1 65 4 4 G P P -4.021 0.000 1 66 5 5 A H1' H 6.119 0.001 . 67 5 5 A H2 H 7.763 0.001 1 68 5 5 A H2' H 4.812 0.000 . 69 5 5 A H3' H 4.813 0.001 . 70 5 5 A H4' H 4.489 0.002 . 71 5 5 A H5' H 4.572 0.000 . 72 5 5 A H5'' H 4.172 0.000 2 73 5 5 A H8 H 8.226 0.001 1 74 5 5 A H61 H 7.668 0.000 2 75 5 5 A H62 H 7.668 0.000 2 76 5 5 A C1' C 91.071 0.000 . 77 5 5 A C2 C 153.981 0.000 1 78 5 5 A C2' C 76.229 0.000 . 79 5 5 A C8 C 140.094 0.000 1 80 5 5 A P P -4.301 0.000 1 81 6 6 G H1 H 12.831 0.002 1 82 6 6 G H1' H 5.559 0.001 . 83 6 6 G H2' H 4.573 0.000 . 84 6 6 G H3' H 4.102 0.006 . 85 6 6 G H4' H 4.529 0.000 . 86 6 6 G H5' H 4.276 0.001 . 87 6 6 G H5'' H 4.116 0.000 2 88 6 6 G H8 H 7.104 0.001 1 89 6 6 G H21 H 5.753 0.003 2 90 6 6 G H22 H 5.753 0.003 2 91 6 6 G C2' C 75.367 0.000 . 92 6 6 G P P -3.530 0.001 1 93 7 7 C H1' H 5.563 0.001 . 94 7 7 C H2' H 4.463 0.000 . 95 7 7 C H3' H 4.507 0.002 . 96 7 7 C H4' H 4.425 0.000 . 97 7 7 C H5 H 5.170 0.001 1 98 7 7 C H6 H 7.451 0.001 1 99 7 7 C H41 H 8.397 0.000 2 100 7 7 C H42 H 6.828 0.002 2 101 7 7 C C2' C 75.090 0.000 . 102 7 7 C C3' C 71.892 0.000 . 103 7 7 C C4' C 81.903 0.000 . 104 7 7 C C5 C 98.039 0.000 1 105 7 7 C C6 C 140.142 0.000 1 106 7 7 C P P -4.403 0.000 1 107 8 8 G H1 H 13.173 0.001 1 108 8 8 G H1' H 5.604 0.001 . 109 8 8 G H2' H 4.363 0.001 . 110 8 8 G H3' H 4.589 0.001 . 111 8 8 G H4' H 4.421 0.003 . 112 8 8 G H5' H 4.516 0.002 . 113 8 8 G H5'' H 4.067 0.004 2 114 8 8 G H8 H 7.549 0.000 1 115 8 8 G H21 H 8.147 0.006 2 116 8 8 G H22 H 5.854 0.001 2 117 8 8 G C2' C 75.464 0.000 . 118 8 8 G C3' C 72.364 0.000 . 119 8 8 G C4' C 82.163 0.000 . 120 8 8 G C8 C 135.933 0.000 1 121 8 8 G P P -3.965 0.000 1 122 9 9 U H1' H 5.452 0.001 . 123 9 9 U H2' H 4.395 0.000 . 124 9 9 U H3 H 14.348 0.002 1 125 9 9 U H3' H 4.440 0.002 . 126 9 9 U H4' H 4.380 0.000 . 127 9 9 U H5 H 5.046 0.001 1 128 9 9 U H5' H 4.536 0.001 . 129 9 9 U H5'' H 4.049 0.000 2 130 9 9 U H6 H 7.726 0.001 1 131 9 9 U C1' C 93.542 0.000 . 132 9 9 U C2' C 75.383 0.000 . 133 9 9 U C3' C 72.227 0.000 . 134 9 9 U C4' C 81.602 0.000 . 135 9 9 U C5 C 102.613 0.000 1 136 9 9 U C6 C 141.404 0.000 1 137 9 9 U P P -4.510 0.000 1 138 10 10 C H1' H 5.543 0.001 . 139 10 10 C H2' H 4.381 0.000 . 140 10 10 C H3' H 4.442 0.002 . 141 10 10 C H4' H 4.381 0.000 . 142 10 10 C H5 H 5.521 0.001 1 143 10 10 C H5' H 4.498 0.000 . 144 10 10 C H5'' H 4.075 0.000 2 145 10 10 C H6 H 7.737 0.002 1 146 10 10 C H41 H 8.201 0.001 2 147 10 10 C H42 H 7.000 0.002 2 148 10 10 C C2' C 75.240 0.000 . 149 10 10 C C5 C 97.729 0.000 1 150 10 10 C C6 C 140.942 0.000 1 151 10 10 C P P -4.074 0.000 1 152 11 11 A H1' H 5.924 0.001 . 153 11 11 A H2 H 7.324 0.001 1 154 11 11 A H2' H 4.022 0.001 . 155 11 11 A H3' H 4.284 0.002 . 156 11 11 A H4' H 4.223 0.002 . 157 11 11 A H5' H 4.445 0.000 . 158 11 11 A H5'' H 4.046 0.001 2 159 11 11 A H8 H 8.037 0.000 1 160 11 11 A H61 H 6.526 0.003 2 161 11 11 A C1' C 91.720 0.000 . 162 11 11 A C2 C 154.336 0.000 1 163 11 11 A C2' C 77.965 0.000 . 164 11 11 A C3' C 70.301 0.000 . 165 11 11 A C4' C 83.921 0.000 . 166 11 11 A C8 C 140.130 0.000 1 167 11 11 A P P -3.801 0.000 1 stop_ save_