data_4745 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Conformation of a Bulged Adenosine in an RNA Duplex by Relaxation Matrix Refinement ; _BMRB_accession_number 4745 _BMRB_flat_file_name bmr4745.str _Entry_type original _Submission_date 2000-05-22 _Accession_date 2000-05-23 _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 Thiviyanathan Varatharasa . . 2 Guliaev Anton . . 3 Leontis Neocles B . 4 Gorenstein David G . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 164 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-12-18 original author . stop_ _Original_release_date 2000-12-18 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Conformation of a Bulged Adenosine in an RNA Duplex by Relaxation Matrix Refinement ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 20366237 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Thiviyanathan Varatharasa . . 2 Guliaev Anton . . 3 Leontis Neocles B . 4 Gorenstein David G . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume 300 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1143 _Page_last 1154 _Year 2000 _Details . save_ ################################## # Molecular system description # ################################## save_RNA _Saveframe_category molecular_system _Mol_system_name 'Bulged RNA' _Abbreviation_common RNA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'bulged RNA, duplex 1' $RNA_1 'bulged RNA, duplex 2' $RNA_2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RNA_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA _Abbreviation_common RNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence GGCAGAGUGCCGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 C 4 4 A 5 5 G 6 6 A 7 7 G 8 8 U 9 9 G 10 10 C 11 11 C 12 12 G 13 13 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_RNA_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA _Abbreviation_common RNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence GCGGCACCUGCC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 14 G 2 15 C 3 16 G 4 17 G 5 18 C 6 19 A 7 20 C 8 21 C 9 22 U 10 23 G 11 24 C 12 25 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_1 'E. coli' 562 Eubacteria . Escherichia coli 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_1 'enzymatic semisynthesis' . . . . . 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_1 1.0 mM . $RNA_2 1.0 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model VXR _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 600 _Details . save_ ####################### # Sample conditions # ####################### save_conditions _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . n/a temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 HOD H 1 . ppm 4.76 internal direct spherical . . 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_RNA_1_shifts _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $conditions _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'bulged RNA, duplex 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 G H1 H 12.43 0.01 1 2 . 1 G H8 H 8.19 0.01 1 3 . 1 G H1' H 5.84 0.01 1 4 . 1 G H2' H 4.84 0.01 1 5 . 1 G H3' H 4.66 0.01 1 6 . 1 G H4' H 4.53 0.01 1 7 . 1 G H5' H 4.09 0.01 2 8 . 1 G H5'' H 4.31 0.01 2 9 . 2 G H1 H 13.05 0.01 1 10 . 2 G H8 H 7.41 0.01 1 11 . 2 G H1' H 5.80 0.01 1 12 . 2 G H2' H 4.51 0.01 1 13 . 2 G H3' H 4.54 0.01 1 14 . 2 G H4' H 4.85 0.01 1 15 . 2 G H5' H 4.13 0.01 2 16 . 2 G H5'' H 4.34 0.01 2 17 . 3 C H41 H 8.37 0.01 2 18 . 3 C H42 H 6.84 0.01 2 19 . 3 C H5 H 5.21 0.01 1 20 . 3 C H6 H 7.63 0.01 1 21 . 3 C H1' H 5.48 0.01 1 22 . 3 C H2' H 4.61 0.01 1 23 . 3 C H3' H 4.49 0.01 1 24 . 4 A H2 H 6.89 0.01 1 25 . 4 A H8 H 7.89 0.01 1 26 . 4 A H1' H 5.86 0.01 1 27 . 4 A H2' H 4.50 0.01 1 28 . 4 A H3' H 4.61 0.01 1 29 . 4 A H4' H 4.12 0.01 1 30 . 5 G H1 H 12.90 0.01 1 31 . 5 G H8 H 7.34 0.01 1 32 . 5 G H1' H 5.66 0.01 1 33 . 5 G H2' H 4.15 0.01 1 34 . 5 G H3' H 4.67 0.01 1 35 . 5 G H4' H 4.28 0.01 1 36 . 6 A H2 H 7.95 0.01 1 37 . 6 A H61 H 8.31 0.01 2 38 . 6 A H62 H 6.79 0.01 2 39 . 6 A H8 H 8.12 0.01 1 40 . 6 A H1' H 6.03 0.01 1 41 . 6 A H2' H 4.60 0.01 1 42 . 6 A H3' H 4.70 0.01 1 43 . 6 A H4' H 4.49 0.01 1 44 . 7 G H1 H 12.87 0.01 1 45 . 7 G H8 H 7.52 0.01 1 46 . 7 G H1' H 5.44 0.01 1 47 . 7 G H2' H 4.55 0.01 1 48 . 7 G H3' H 4.12 0.01 1 49 . 8 U H3 H 13.52 0.01 1 50 . 8 U H5 H 5.01 0.01 1 51 . 8 U H6 H 7.72 0.01 1 52 . 8 U H1' H 5.58 0.01 1 53 . 8 U H2' H 4.63 0.01 1 54 . 8 U H3' H 4.47 0.01 1 55 . 8 U H4' H 4.50 0.01 1 56 . 9 G H1 H 13.13 0.01 1 57 . 9 G H8 H 7.73 0.01 1 58 . 9 G H1' H 5.82 0.01 1 59 . 9 G H2' H 4.46 0.01 1 60 . 9 G H3' H 4.58 0.01 1 61 . 9 G H4' H 4.63 0.01 1 62 . 10 C H41 H 8.48 0.01 2 63 . 10 C H42 H 7.67 0.01 2 64 . 10 C H5 H 5.23 0.01 1 65 . 10 C H6 H 7.67 0.01 1 66 . 10 C H1' H 5.45 0.01 1 67 . 10 C H2' H 4.30 0.01 1 68 . 10 C H3' H 4.06 0.01 1 69 . 11 C H41 H 8.41 0.01 2 70 . 11 C H42 H 6.72 0.01 2 71 . 11 C H5 H 5.42 0.01 1 72 . 11 C H6 H 7.57 0.01 1 73 . 11 C H1' H 5.46 0.01 1 74 . 11 C H2' H 4.36 0.01 1 75 . 11 C H3' H 4.55 0.01 1 76 . 11 C H4' H 4.24 0.01 1 77 . 12 G H1 H 12.95 0.01 1 78 . 12 G H8 H 7.44 0.01 1 79 . 12 G H1' H 5.67 0.01 1 80 . 12 G H2' H 4.28 0.01 1 81 . 12 G H3' H 4.37 0.01 1 82 . 12 G H4' H 4.21 0.01 1 83 . 13 C H41 H 8.38 0.01 2 84 . 13 C H42 H 6.95 0.01 2 85 . 13 C H5 H 5.35 0.01 1 86 . 13 C H6 H 7.54 0.01 1 87 . 13 C H1' H 5.58 0.01 1 88 . 13 C H2' H 3.92 0.01 1 89 . 13 C H3' H 4.09 0.01 1 90 . 13 C H4' H 4.31 0.01 1 stop_ save_ save_RNA_2_shifts _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $conditions _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'bulged RNA, duplex 2' _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 G H8 H 8.14 0.01 1 2 . 1 G H1' H 5.74 0.01 1 3 . 1 G H2' H 4.80 0.01 1 4 . 1 G H3' H 4.71 0.01 1 5 . 1 G H4' H 4.22 0.01 1 6 . 1 G H5' H 4.30 0.01 2 7 . 1 G H5'' H 4.01 0.01 2 8 . 2 C H5 H 5.34 0.01 1 9 . 2 C H6 H 7.82 0.01 1 10 . 2 C H1' H 5.66 0.01 1 11 . 2 C H2' H 4.70 0.01 1 12 . 2 C H3' H 4.66 0.01 1 13 . 3 G H1 H 12.48 0.01 1 14 . 3 G H8 H 7.53 0.01 1 15 . 3 G H1' H 5.75 0.01 1 16 . 3 G H2' H 4.61 0.01 1 17 . 3 G H3' H 4.52 0.01 1 18 . 4 G H1 H 12.47 0.01 1 19 . 4 G H8 H 7.30 0.01 1 20 . 4 G H1' H 5.72 0.01 1 21 . 4 G H2' H 4.43 0.01 1 22 . 4 G H3' H 4.52 0.01 1 23 . 5 C H41 H 8.48 0.01 2 24 . 5 C H42 H 6.87 0.01 2 25 . 5 C H5 H 5.18 0.01 1 26 . 5 C H6 H 7.65 0.01 1 27 . 5 C H1' H 5.46 0.01 1 28 . 5 C H2' H 4.45 0.01 1 29 . 5 C H3' H 4.08 0.01 1 30 . 6 A H2 H 7.45 0.01 1 31 . 6 A H8 H 8.05 0.01 1 32 . 6 A H1' H 5.95 0.01 1 33 . 6 A H2' H 4.55 0.01 1 34 . 6 A H3' H 4.67 0.01 1 35 . 6 A H4' H 4.49 0.01 1 36 . 7 C H41 H 8.18 0.01 2 37 . 7 C H42 H 7.19 0.01 2 38 . 7 C H5 H 5.35 0.01 1 39 . 7 C H6 H 7.41 0.01 1 40 . 7 C H1' H 5.47 0.01 1 41 . 7 C H2' H 4.21 0.01 1 42 . 7 C H3' H 4.34 0.01 1 43 . 7 C H4' H 4.36 0.01 1 44 . 8 C H5 H 5.63 0.01 1 45 . 8 C H6 H 7.87 0.01 1 46 . 8 C H1' H 5.46 0.01 1 47 . 8 C H2' H 4.35 0.01 1 48 . 8 C H3' H 4.47 0.01 1 49 . 9 U H3 H 13.81 0.01 1 50 . 9 U H5 H 5.52 0.01 1 51 . 9 U H6 H 7.95 0.01 1 52 . 9 U H1' H 5.32 0.01 1 53 . 9 U H2' H 4.45 0.01 1 54 . 9 U H3' H 4.35 0.01 1 55 . 10 G H1 H 12.47 0.01 1 56 . 10 G H8 H 7.74 0.01 1 57 . 10 G H1' H 5.16 0.01 1 58 . 10 G H2' H 4.37 0.01 1 59 . 10 G H3' H 4.41 0.01 1 60 . 10 G H4' H 4.29 0.01 1 61 . 11 C H41 H 8.35 0.01 2 62 . 11 C H42 H 6.86 0.01 2 63 . 11 C H5 H 5.41 0.01 1 64 . 11 C H6 H 7.58 0.01 1 65 . 11 C H1' H 5.71 0.01 1 66 . 11 C H2' H 4.39 0.01 1 67 . 11 C H3' H 4.06 0.01 1 68 . 11 C H4' H 4.15 0.01 1 69 . 12 C H5 H 5.22 0.01 1 70 . 12 C H6 H 7.49 0.01 1 71 . 12 C H1' H 5.69 0.01 1 72 . 12 C H2' H 3.96 0.01 1 73 . 12 C H3' H 4.12 0.01 1 74 . 12 C H4' H 4.33 0.01 1 stop_ save_