data_16952 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGA/3'AGAU ; _BMRB_accession_number 16952 _BMRB_flat_file_name bmr16952.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 UA closing pairs: r(GACUAGAGUCA)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" 95 "13C chemical shifts" 29 "15N chemical shifts" 5 "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 16951 GACGAGCGUCA 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*UP*AP*GP*AP*GP*UP*CP*A)-3')_1' $RNA_(5'-R(*GP*AP*CP*UP*AP*GP*AP*GP*UP*CP*A)-3') 'RNA (5'-R(*GP*AP*CP*UP*AP*GP*AP*GP*UP*CP*A)-3')_2' $RNA_(5'-R(*GP*AP*CP*UP*AP*GP*AP*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*UP*AP*GP*AP*GP*UP*CP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*GP*AP*CP*UP*AP*GP*AP*GP*UP*CP*A)-3') _Molecular_mass 3530.203 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence GACUAGAGUCA loop_ _Residue_seq_code _Residue_label 1 G 2 A 3 C 4 U 5 A 6 G 7 A 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*UP*AP*GP*AP*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*UP*AP*GP*AP*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*UP*AP*GP*AP*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*UP*AP*GP*AP*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_ save_2D_1H-15N_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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 274 . 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 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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-1H TOCSY' '2D DQF-COSY' '2D 1H-31P HETCOR' '2D 1H-15N HSQC' '2D 1H-13C HSQC' 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*UP*AP*GP*AP*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 12.000 0.002 1 2 1 1 G H1' H 5.849 0.001 . 3 1 1 G H2' H 4.850 0.001 . 4 1 1 G H3' H 4.648 0.001 . 5 1 1 G H4' H 4.447 0.002 . 6 1 1 G H5' H 4.113 0.001 . 7 1 1 G H5'' H 3.973 0.001 2 8 1 1 G H8 H 8.113 0.002 1 9 1 1 G H22 H 6.150 0.000 2 10 1 1 G C1' C 93.078 0.000 . 11 1 1 G C8 C 138.764 0.000 1 12 1 1 G N1 N 147.276 0.000 1 13 2 2 A H1' H 6.001 0.002 . 14 2 2 A H2 H 7.724 0.001 1 15 2 2 A H2' H 4.650 0.001 . 16 2 2 A H3' H 4.713 0.002 . 17 2 2 A H4' H 4.544 0.001 . 18 2 2 A H5' H 4.641 0.001 . 19 2 2 A H5'' H 4.216 0.000 2 20 2 2 A H8 H 8.047 0.002 1 21 2 2 A C1' C 92.995 0.000 . 22 2 2 A C2 C 154.025 0.000 1 23 2 2 A C8 C 139.731 0.000 1 24 2 2 A P P -3.981 0.000 1 25 3 3 C H1' H 5.336 0.002 . 26 3 3 C H2' H 4.163 0.002 . 27 3 3 C H3' H 4.353 0.002 . 28 3 3 C H4' H 4.416 0.003 . 29 3 3 C H5 H 5.249 0.001 1 30 3 3 C H5' H 4.518 0.002 . 31 3 3 C H5'' H 4.069 0.001 2 32 3 3 C H6 H 7.499 0.003 1 33 3 3 C C1' C 93.974 0.000 . 34 3 3 C C5 C 97.222 0.000 1 35 3 3 C C6 C 140.675 0.000 1 36 3 3 C P P -4.114 0.000 1 37 4 4 U H1' H 5.465 0.002 . 38 4 4 U H2' H 4.199 0.001 . 39 4 4 U H3 H 12.721 0.003 1 40 4 4 U H3' H 4.675 0.002 . 41 4 4 U H4' H 4.362 0.003 . 42 4 4 U H5 H 5.410 0.001 1 43 4 4 U H5' H 4.600 0.002 . 44 4 4 U H5'' H 4.102 0.002 2 45 4 4 U H6 H 7.882 0.003 1 46 4 4 U C1' C 93.532 0.000 . 47 4 4 U C5 C 103.396 0.000 1 48 4 4 U C6 C 142.155 0.000 1 49 4 4 U N3 N 161.026 0.000 1 50 4 4 U P P -4.491 0.000 1 51 5 5 A H1' H 6.127 0.002 . 52 5 5 A H2 H 7.315 0.002 1 53 5 5 A H2' H 4.805 0.001 . 54 5 5 A H3' H 4.516 0.001 . 55 5 5 A H4' H 4.795 0.000 . 56 5 5 A H5' H 4.529 0.001 . 57 5 5 A H5'' H 4.181 0.000 2 58 5 5 A H8 H 8.273 0.002 1 59 5 5 A C1' C 90.965 0.000 . 60 5 5 A C2 C 153.153 0.000 1 61 5 5 A C8 C 140.436 0.000 1 62 5 5 A P P -3.915 0.000 1 63 6 6 G H1 H 11.625 0.002 1 64 6 6 G H1' H 5.613 0.002 . 65 6 6 G H2' H 4.664 0.000 . 66 6 6 G H3' H 4.209 0.001 . 67 6 6 G H4' H 4.555 0.001 . 68 6 6 G H5' H 4.278 0.001 . 69 6 6 G H5'' H 4.142 0.001 2 70 6 6 G H8 H 7.149 0.001 1 71 6 6 G H21 H 7.328 0.012 2 72 6 6 G H22 H 5.414 0.000 2 73 6 6 G C1' C 93.042 0.000 . 74 6 6 G C8 C 137.188 0.000 1 75 6 6 G N1 N 148.378 0.000 1 76 6 6 G P P -3.474 0.000 1 77 7 7 A H1' H 5.905 0.001 . 78 7 7 A H2 H 6.678 0.001 1 79 7 7 A H2' H 4.627 0.001 . 80 7 7 A H3' H 4.647 0.001 . 81 7 7 A H4' H 4.486 0.001 . 82 7 7 A H5' H 4.522 0.000 . 83 7 7 A H5'' H 4.125 0.002 2 84 7 7 A H8 H 7.459 0.001 1 85 7 7 A C1' C 93.508 0.000 . 86 7 7 A C2 C 152.819 0.000 1 87 7 7 A C8 C 139.361 0.000 1 88 7 7 A P P -4.046 0.000 1 89 8 8 G H1 H 13.639 0.002 1 90 8 8 G H1' H 5.523 0.002 . 91 8 8 G H2' H 4.283 0.001 . 92 8 8 G H3' H 4.479 0.002 . 93 8 8 G H4' H 4.405 0.000 . 94 8 8 G H5' H 4.502 0.000 . 95 8 8 G H5'' H 4.035 0.000 2 96 8 8 G H8 H 7.282 0.002 1 97 8 8 G H21 H 8.369 0.003 2 98 8 8 G H22 H 6.166 0.001 2 99 8 8 G C1' C 92.577 0.000 . 100 8 8 G C8 C 135.683 0.000 1 101 8 8 G N1 N 148.932 0.000 1 102 8 8 G P P -4.127 0.000 1 103 9 9 U H1' H 5.446 0.001 . 104 9 9 U H2' H 4.372 0.001 . 105 9 9 U H3 H 14.377 0.002 1 106 9 9 U H3' H 4.414 0.002 . 107 9 9 U H5 H 5.001 0.002 1 108 9 9 U H5' H 4.498 0.002 . 109 9 9 U H5'' H 4.028 0.002 2 110 9 9 U H6 H 7.649 0.002 1 111 9 9 U C5 C 102.631 0.000 1 112 9 9 U C6 C 141.140 0.000 1 113 9 9 U N3 N 163.308 0.000 1 114 9 9 U P P -4.548 0.000 1 115 10 10 C H1' H 5.540 0.001 . 116 10 10 C H2' H 4.380 0.001 . 117 10 10 C H3' H 4.416 0.001 . 118 10 10 C H5 H 5.502 0.001 1 119 10 10 C H5' H 4.479 0.000 . 120 10 10 C H5'' H 4.070 0.001 2 121 10 10 C H6 H 7.709 0.002 1 122 10 10 C H41 H 8.175 0.000 2 123 10 10 C H42 H 6.962 0.000 2 124 10 10 C C1' C 93.890 0.000 . 125 10 10 C C5 C 97.735 0.000 1 126 10 10 C C6 C 140.878 0.000 1 127 10 10 C P P -3.821 0.000 1 128 11 11 A H1' H 5.924 0.005 . 129 11 11 A H2 H 7.324 0.000 1 130 11 11 A H2' H 4.019 0.002 . 131 11 11 A H3' H 4.282 0.000 . 132 11 11 A H4' H 4.221 0.003 . 133 11 11 A H5' H 4.440 0.005 . 134 11 11 A H5'' H 4.043 0.001 2 135 11 11 A H8 H 8.031 0.002 1 136 11 11 A C1' C 91.705 0.000 . 137 11 11 A C2 C 154.348 0.000 1 138 11 11 A C8 C 140.161 0.000 1 139 11 11 A P P -4.080 0.000 1 stop_ save_