data_15780 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of adenosine bulged RNA duplex with C:G-A triple ; _BMRB_accession_number 15780 _BMRB_flat_file_name bmr15780.str _Entry_type original _Submission_date 2008-05-26 _Accession_date 2008-05-26 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Popenda Lukasz . . 2 Bielecki Lukasz . . 3 Gdaniec Zofia . . 4 Adamiak Ryszard W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 72 "13C chemical shifts" 52 "31P chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-05-16 update BMRB 'update entry citation' 2008-09-02 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 15781 5'-R(*GP*UP*CP*GP*UP*GP*CP*UP*G)-3' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Bulged adenosine influence on the RNA duplex conformation in solution.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 18399645 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Popenda Lukasz . . 2 Adamiak Ryszard W. . 3 Gdaniec Zofia . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 47 _Journal_issue 18 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5059 _Page_last 5067 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3')' $RNA_(5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3')_ 'RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')' $RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-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*UP*CP*GP*AP*GP*CP*UP*G)-3')_ _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3')_ _Molecular_mass 2887.786 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence GUCGAGCUG loop_ _Residue_seq_code _Residue_label 1 G 2 U 3 C 4 G 5 A 6 G 7 C 8 U 9 G stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_ _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_ _Molecular_mass 2524.609 _Mol_thiol_state 'not present' _Details . _Residue_count 8 _Mol_residue_sequence CAGCCGAC loop_ _Residue_seq_code _Residue_label 1 C 2 A 3 G 4 C 5 C 6 G 7 A 8 C 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*UP*CP*GP*AP*GP*CP*UP*G)-3')_ . . . . . . $RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-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 $RNA_(5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3')_ 'chemical synthesis' . . . . . $RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_ 'chemical synthesis' . . . . . 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*UP*CP*GP*AP*GP*CP*UP*G)-3')_ 1 mM 'natural abundance' $RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_ 1 mM 'natural abundance' NaCl 50 mM . 'phosphate buffer' 10 mM . EDTA 0.1 mM . D2O 100 % . 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*UP*CP*GP*AP*GP*CP*UP*G)-3')_ 1 mM 'natural abundance' $RNA_(5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')_ 1 mM 'natural abundance' NaCl 50 mM . 'phosphate buffer' 10 mM . EDTA 0.1 mM . H2O 90 % 'natural abundance' D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_Felix _Saveframe_category software _Name FELIX _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_CURVES _Saveframe_category software _Name CURVES _Version . loop_ _Vendor _Address _Electronic_address 'Lavery and Sklenar' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-31P_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HSQC' _Sample_label $sample_1 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 '50 mM NaCl, 10 mM phosphate buffer, 0.1 mM EDTA' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 60 . mM pH 6.8 . pH pressure 1 . atm temperature 298 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details '50 mM NaCl, 10 mM phosphate buffer, 0.1 mM EDTA' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 60 . mM pH 6.8 . pH pressure 1 . atm temperature 283 . K 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 C 13 'methyl carbons' ppm 0 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0 na direct . . . 1.0 TMP P 31 phosphorus ppm 0 na indirect . . . 0.404808688 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_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' '2D 1H-31P HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3')' _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 C H1' H 5.52 0.01 1 2 1 1 C H2' H 4.52 0.01 1 3 1 1 C H3' H 4.58 0.01 1 4 1 1 C H4' H 4.33 0.01 1 5 1 1 C H5 H 5.99 0.01 1 6 1 1 C H5' H 4.04 0.01 2 7 1 1 C H5'' H 3.94 0.01 2 8 1 1 C H6 H 8.07 0.01 1 9 1 1 C H41 H 8.30 0.01 2 10 1 1 C H42 H 7.03 0.01 2 11 1 1 C C1' C 93.96 0.05 1 12 1 1 C C2' C 75.47 0.05 1 13 1 1 C C3' C 73.69 0.05 1 14 1 1 C C4' C 84.44 0.05 1 15 1 1 C C5 C 98.85 0.05 1 16 1 1 C C5' C 62.04 0.05 1 17 1 1 C C6 C 143.05 0.05 1 18 2 2 A H1' H 5.99 0.01 1 19 2 2 A H2 H 7.32 0.01 1 20 2 2 A H2' H 4.76 0.01 1 21 2 2 A H3' H 4.84 0.01 1 22 2 2 A H4' H 4.54 0.01 1 23 2 2 A H5' H 4.55 0.01 2 24 2 2 A H5'' H 4.25 0.01 2 25 2 2 A H8 H 8.23 0.01 1 26 2 2 A C1' C 92.45 0.05 1 27 2 2 A C2 C 153.02 0.05 1 28 2 2 A C2' C 75.82 0.05 1 29 2 2 A C3' C 73.24 0.05 1 30 2 2 A C4' C 82.31 0.05 1 31 2 2 A C5' C 65.56 0.05 1 32 2 2 A C8 C 140.07 0.05 1 33 2 2 A P P -3.89 0.01 1 34 3 3 G H1 H 13.51 0.01 1 35 3 3 G H1' H 5.63 0.01 1 36 3 3 G H2' H 4.48 0.01 1 37 3 3 G H3' H 4.41 0.01 1 38 3 3 G H4' H 4.48 0.01 1 39 3 3 G H5' H 4.47 0.01 2 40 3 3 G H5'' H 4.14 0.01 2 41 3 3 G H8 H 7.30 0.01 1 42 3 3 G C1' C 92.63 0.05 1 43 3 3 G C2' C 75.42 0.10 1 44 3 3 G C3' C 73.10 0.05 1 45 3 3 G C4' C 82.12 0.05 1 46 3 3 G C5' C 66.17 0.05 1 47 3 3 G C8 C 135.69 0.05 1 48 3 3 G P P -3.95 0.01 1 49 4 4 C H1' H 5.47 0.01 1 50 4 4 C H2' H 4.43 0.01 1 51 4 4 C H3' H 4.32 0.01 1 52 4 4 C H4' H 4.38 0.01 1 53 4 4 C H5 H 5.22 0.01 1 54 4 4 C H5' H 4.50 0.01 2 55 4 4 C H5'' H 4.05 0.01 2 56 4 4 C H6 H 7.37 0.01 1 57 4 4 C H41 H 8.21 0.01 2 58 4 4 C H42 H 6.86 0.01 2 59 4 4 C C1' C 94.35 0.05 1 60 4 4 C C2' C 75.59 0.05 1 61 4 4 C C3' C 72.34 0.05 1 62 4 4 C C4' C 82.10 0.05 1 63 4 4 C C5 C 97.63 0.05 1 64 4 4 C C5' C 64.73 0.05 1 65 4 4 C C6 C 140.47 0.05 1 66 4 4 C P P -4.28 0.01 1 67 5 5 C H1' H 5.51 0.01 1 68 5 5 C H2' H 4.57 0.01 1 69 5 5 C H3' H 4.58 0.01 1 70 5 5 C H4' H 4.37 0.01 1 71 5 5 C H5 H 5.62 0.01 1 72 5 5 C H5' H 4.49 0.01 2 73 5 5 C H5'' H 4.10 0.01 2 74 5 5 C H6 H 7.86 0.01 1 75 5 5 C H41 H 8.39 0.01 2 76 5 5 C H42 H 6.88 0.01 2 77 5 5 C C1' C 93.69 0.05 1 78 5 5 C C2' C 75.40 0.05 1 79 5 5 C C3' C 72.40 0.05 1 80 5 5 C C4' C 81.87 0.05 1 81 5 5 C C5 C 98.43 0.05 1 82 5 5 C C5' C 64.39 0.05 1 83 5 5 C C6 C 140.98 0.05 1 84 5 5 C P P -4.45 0.01 1 85 6 6 G H1 H 12.47 0.01 1 86 6 6 G H1' H 5.53 0.01 1 87 6 6 G H2' H 4.49 0.01 1 88 6 6 G H3' H 4.57 0.01 1 89 6 6 G H4' H 4.44 0.01 1 90 6 6 G H5' H 4.46 0.01 2 91 6 6 G H5'' H 4.12 0.01 2 92 6 6 G H8 H 7.56 0.01 1 93 6 6 G C1' C 92.72 0.05 1 94 6 6 G C2' C 75.46 0.10 1 95 6 6 G C3' C 73.16 0.05 1 96 6 6 G C5' C 65.98 0.05 1 97 6 6 G C8 C 136.29 0.05 1 98 6 6 G P P -3.89 0.01 1 99 7 7 A H1' H 5.91 0.01 1 100 7 7 A H2 H 7.86 0.01 1 101 7 7 A H2' H 4.40 0.01 1 102 7 7 A H3' H 4.62 0.01 1 103 7 7 A H4' H 4.44 0.01 1 104 7 7 A H5' H 4.57 0.01 2 105 7 7 A H5'' H 4.09 0.01 2 106 7 7 A H8 H 7.83 0.01 1 107 7 7 A C1' C 93.07 0.05 1 108 7 7 A C2 C 154.29 0.05 1 109 7 7 A C2' C 75.72 0.05 1 110 7 7 A C3' C 72.37 0.05 1 111 7 7 A C5' C 64.62 0.05 1 112 7 7 A C8 C 139.37 0.05 1 113 7 7 A P P -4.26 0.01 1 114 8 8 C H1' H 5.66 0.01 1 115 8 8 C H2' H 3.90 0.01 1 116 8 8 C H3' H 4.07 0.01 1 117 8 8 C H4' H 4.14 0.01 1 118 8 8 C H5 H 5.20 0.01 1 119 8 8 C H5' H 4.45 0.01 2 120 8 8 C H5'' H 3.99 0.01 2 121 8 8 C H6 H 7.33 0.01 1 122 8 8 C H41 H 8.14 0.01 2 123 8 8 C H42 H 7.04 0.01 2 124 8 8 C C1' C 92.67 0.05 1 125 8 8 C C2' C 77.55 0.05 1 126 8 8 C C3' C 69.85 0.05 1 127 8 8 C C4' C 83.38 0.05 1 128 8 8 C C5 C 97.72 0.05 1 129 8 8 C C5' C 65.18 0.05 1 130 8 8 C C6 C 141.12 0.05 1 131 8 8 C P P -4.16 0.01 1 stop_ save_