data_19887 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; oligonucleotide model of miR-21 pre-element ; _BMRB_accession_number 19887 _BMRB_flat_file_name bmr19887.str _Entry_type original _Submission_date 2014-04-02 _Accession_date 2014-04-02 _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 Chirayil Sara . . 2 Wu Qiong . . 3 Amezcua Carlos . . 4 Luebke Kevin . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 100 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-09-29 original author . stop_ _Original_release_date 2014-09-29 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR Characterization of an Oligonucleotide Model of the MiR-21 Pre-Element' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25250627 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chirayil Sara . . 2 Wu Qiong . . 3 Amezcua Carlos . . 4 Luebke Kevin . . stop_ _Journal_abbreviation 'PLOS ONE' _Journal_volume 9 _Journal_issue 9 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first e108231 _Page_last e108231 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Oligonucleotide Model of the MiR-21 Pre-Element' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'miR-21 pre-element' $miR-21_pre-element 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_miR-21_pre-element _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common miR-21_pre-element _Molecular_mass 111.103 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; GGGUUGACCGUUGAAUCUCA CGGCAACCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -6 G 2 -5 G 3 -4 G 4 -3 U 5 -2 U 6 -1 G 7 0 A 8 1 C 9 2 C 10 3 G 11 4 U 12 5 U 13 6 G 14 7 A 15 8 A 16 9 U 17 10 C 18 11 U 19 12 C 20 13 A 21 14 C 22 15 G 23 16 G 24 17 C 25 18 A 26 19 A 27 20 C 28 21 C 29 22 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 $miR-21_pre-element Human 9606 Eukaryota Metazoa Homo sapiens 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 $miR-21_pre-element 'obtained from a vendor' . . . . . 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 $miR-21_pre-element 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.3 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' 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 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 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 6.7 . pH pressure 1 . atm 'ionic strength' 10 . mM 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 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 DQF-COSY' '2D 1H-1H NOESY' '2D 1H-13C 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 'miR-21 pre-element' _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 8 C H1' H 5.45 0.01 . 2 1 8 C H2' H 4.24 0.01 . 3 1 8 C H3' H 3.98 0.01 . 4 1 8 C H4' H 4.16 0.01 . 5 1 8 C H5 H 5.56 0.01 . 6 1 8 C H6 H 7.73 0.01 . 7 2 9 C H1' H 5.49 0.01 . 8 2 9 C H2' H 4.48 0.01 . 9 2 9 C H3' H 4.56 0.01 . 10 2 9 C H4' H 4.40 0.01 . 11 2 9 C H5 H 5.46 0.01 . 12 2 9 C H6 H 7.74 0.01 . 13 3 10 G H1 H 12.64 0.01 . 14 3 10 G H1' H 5.74 0.01 . 15 3 10 G H2' H 4.45 0.01 . 16 3 10 G H3' H 4.60 0.01 . 17 3 10 G H4' H 4.50 0.01 . 18 3 10 G H8 H 7.62 0.01 . 19 3 10 G H21 H 8.25 0.01 . 20 3 10 G H22 H 6.71 0.01 . 21 4 11 U H1' H 5.91 0.01 . 22 4 11 U H2' H 4.41 0.01 . 23 4 11 U H3 H 14.34 0.01 . 24 4 11 U H3' H 4.71 0.01 . 25 4 11 U H4' H 4.46 0.01 . 26 4 11 U H5 H 5.41 0.01 . 27 4 11 U H6 H 7.78 0.01 . 28 5 12 U H1' H 5.80 0.01 . 29 5 12 U H2' H 4.41 0.01 . 30 5 12 U H3' H 4.64 0.01 . 31 5 12 U H4' H 4.48 0.01 . 32 5 12 U H5 H 5.68 0.01 . 33 5 12 U H6 H 7.85 0.01 . 34 6 13 G H1 H 12.76 0.01 . 35 6 13 G H1' H 5.72 0.01 . 36 6 13 G H2' H 4.73 0.01 . 37 6 13 G H4' H 4.48 0.01 . 38 6 13 G H8 H 7.85 0.01 . 39 7 14 A H1' H 5.87 0.01 . 40 7 14 A H2 H 7.66 0.01 . 41 7 14 A H2' H 4.58 0.01 . 42 7 14 A H3' H 4.53 0.01 . 43 7 14 A H4' H 4.50 0.01 . 44 7 14 A H8 H 7.75 0.01 . 45 8 15 A H1' H 5.54 0.01 . 46 8 15 A H2 H 7.66 0.01 . 47 8 15 A H2' H 4.46 0.01 . 48 8 15 A H3' H 4.41 0.01 . 49 8 15 A H8 H 7.78 0.01 . 50 9 16 U H1' H 5.61 0.01 . 51 9 16 U H2' H 4.12 0.01 . 52 9 16 U H3' H 4.29 0.01 . 53 9 16 U H4' H 4.61 0.01 . 54 9 16 U H5 H 5.47 0.01 . 55 9 16 U H6 H 7.53 0.01 . 56 10 17 C H1' H 5.95 0.01 . 57 10 17 C H2' H 4.36 0.01 . 58 10 17 C H3' H 4.66 0.01 . 59 10 17 C H4' H 4.53 0.01 . 60 10 17 C H5 H 5.98 0.01 . 61 10 17 C H6 H 7.74 0.01 . 62 11 18 U H1' H 5.82 0.01 . 63 11 18 U H2' H 4.23 0.01 . 64 11 18 U H3 H 11.53 0.01 . 65 11 18 U H3' H 4.50 0.01 . 66 11 18 U H4' H 4.58 0.01 . 67 11 18 U H5 H 5.88 0.01 . 68 11 18 U H6 H 7.85 0.01 . 69 12 19 C H1' H 5.54 0.01 . 70 12 19 C H2' H 4.62 0.01 . 71 12 19 C H3' H 4.30 0.01 . 72 12 19 C H5 H 5.68 0.01 . 73 12 19 C H6 H 7.69 0.01 . 74 13 20 A H1' H 5.84 0.01 . 75 13 20 A H2 H 7.22 0.01 . 76 13 20 A H2' H 4.55 0.01 . 77 13 20 A H3' H 4.45 0.01 . 78 13 20 A H4' H 4.48 0.01 . 79 13 20 A H8 H 7.95 0.01 . 80 14 21 C H1' H 5.20 0.01 . 81 14 21 C H2' H 4.39 0.01 . 82 14 21 C H3' H 4.31 0.01 . 83 14 21 C H4' H 4.47 0.01 . 84 14 21 C H5 H 5.20 0.01 . 85 14 21 C H6 H 7.39 0.01 . 86 15 22 G H1 H 12.52 0.01 . 87 15 22 G H1' H 5.64 0.01 . 88 15 22 G H2' H 4.42 0.01 . 89 15 22 G H3' H 4.62 0.01 . 90 15 22 G H8 H 7.38 0.01 . 91 15 22 G H21 H 8.13 0.01 . 92 15 22 G H22 H 6.48 0.01 . 93 16 23 G H1 H 13.12 0.01 . 94 16 23 G H1' H 5.65 0.01 . 95 16 23 G H2' H 4.60 0.01 . 96 16 23 G H3' H 4.34 0.01 . 97 16 23 G H4' H 4.65 0.01 . 98 16 23 G H8 H 7.03 0.01 . 99 16 23 G H21 H 8.03 0.01 . 100 16 23 G H22 H 6.99 0.01 . stop_ save_