data_18872 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; ID3 stem ; _BMRB_accession_number 18872 _BMRB_flat_file_name bmr18872.str _Entry_type original _Submission_date 2012-12-03 _Accession_date 2012-12-03 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'RNA duplex' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Popovic Milena . . 2 Greenbaum Nancy L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 73 "13C chemical shifts" 59 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-12-13 original author . stop_ _Original_release_date 2012-12-13 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'ID3 stem' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Popovic Milena . . 2 Greenbaum Nancy . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'ID3 stem' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label GGGUGUA $RNA_GGGUGUA AGCACCC $RNA_AGCACCC 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_GGGUGUA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_GGGUGUA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence GGGUGUA loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 G 4 U 5 G 6 U 7 A stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_RNA_AGCACCC _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_AGCACCC _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 7 _Mol_residue_sequence AGCACCC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 17 A 2 18 G 3 19 C 4 20 A 5 21 C 6 22 C 7 23 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_GGGUGUA 'baker's yeast' 4932 Eukaryota Fungi Saccharomyces cerevisiae $RNA_AGCACCC 'baker's yeast' 4932 Eukaryota Fungi Saccharomyces cerevisiae 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_GGGUGUA 'enzymatic semisynthesis' . Saccharomyces cerevisiae . . $RNA_AGCACCC 'enzymatic semisynthesis' . Saccharomyces cerevisiae . . 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_GGGUGUA 1 mM 'natural abundance' $RNA_AGCACCC 1 mM 'natural abundance' 'sodium chloride' 80 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 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 'structure solution' stop_ _Details . save_ save_CCPN _Saveframe_category software _Name CCPN _Version . loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_600 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_aliphatic_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.08 . M pH 6.4 . pH pressure 1 . atm temperature 288 . 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 protons' ppm 0.00 na indirect . . . 0.251449530 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' '2D 1H-1H NOESY' 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 GGGUGUA _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 C1' C 92.646 0.1 1 2 1 1 G C2' C 75.178 0.1 1 3 1 1 G C3' C 72.283 0.1 1 4 1 1 G C4' C 84.545 0.1 1 5 1 1 G C5' C 62.435 0.1 1 6 1 1 G C8 C 138.671 0.1 1 7 1 1 G H1' H 5.765 0.01 1 8 1 1 G H2' H 4.903 0.01 1 9 1 1 G H3' H 4.588 0.01 1 10 1 1 G H4' H 4.339 0.01 1 11 1 1 G H5' H 3.919 0.01 1 12 1 1 G H5'' H 4.019 0.01 1 13 1 1 G H8 H 8.033 0.01 1 14 2 2 G C1' C 92.874 0.1 1 15 2 2 G C2' C 75.278 0.1 1 16 2 2 G C8 C 136.587 0.1 1 17 2 2 G H1' H 5.939 0.01 1 18 2 2 G H2' H 4.773 0.01 1 19 2 2 G H3' H 4.684 0.01 1 20 2 2 G H4' H 4.185 0.01 1 21 2 2 G H8 H 7.517 0.01 1 22 3 3 G C1' C 93.314 0.1 1 23 3 3 G C2' C 75.344 0.1 1 24 3 3 G C8 C 136.253 0.1 1 25 3 3 G H1' H 5.824 0.01 1 26 3 3 G H2' H 4.509 0.01 1 27 3 3 G H5'' H 4.092 0.01 1 28 3 3 G H8 H 7.274 0.01 1 29 4 4 U C1' C 93.491 0.1 1 30 4 4 U C2' C 75.315 0.1 1 31 4 4 U C5 C 103.161 0.1 1 32 4 4 U C6 C 141.233 0.1 1 33 4 4 U H1' H 5.610 0.01 1 34 4 4 U H2' H 4.697 0.01 1 35 4 4 U H3' H 4.451 0.01 1 36 4 4 U H5 H 5.144 0.01 1 37 4 4 U H6 H 7.755 0.01 1 38 5 5 G C1' C 92.873 0.1 1 39 5 5 G C2' C 75.618 0.1 1 40 5 5 G C3' C 72.939 0.1 1 41 5 5 G C8 C 136.136 0.1 1 42 5 5 G H1' H 5.848 0.01 1 43 5 5 G H2' H 4.554 0.01 1 44 5 5 G H3' H 4.483 0.01 1 45 5 5 G H8 H 7.686 0.01 1 46 6 6 U C1' C 93.165 0.1 1 47 6 6 U C2' C 75.946 0.1 1 48 6 6 U C5 C 104.331 0.1 1 49 6 6 U C6 C 140.467 0.1 1 50 6 6 U H1' H 5.546 0.01 1 51 6 6 U H2' H 4.245 0.01 1 52 6 6 U H3' H 4.474 0.01 1 53 6 6 U H4' H 4.378 0.01 1 54 6 6 U H5 H 5.436 0.01 1 55 6 6 U H6 H 7.652 0.01 1 56 7 7 A C1' C 90.450 0.1 1 57 7 7 A C2 C 154.620 0.1 1 58 7 7 A C2' C 77.599 0.1 1 59 7 7 A C3' C 71.544 0.1 1 60 7 7 A C5' C 66.673 0.1 1 61 7 7 A C8 C 141.280 0.1 1 62 7 7 A H1' H 5.978 0.01 1 63 7 7 A H2 H 7.717 0.01 1 64 7 7 A H2' H 4.287 0.01 1 65 7 7 A H3' H 4.367 0.01 1 66 7 7 A H5'' H 4.100 0.01 1 67 7 7 A H8 H 8.240 0.01 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' '2D 1H-1H NOESY' 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 AGCACCC _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 17 1 A H1' H 6.096 0.01 1 2 17 1 A H2 H 8.087 0.01 1 3 17 1 A H3' H 4.810 0.01 1 4 17 1 A H4' H 4.535 0.01 1 5 17 1 A H5' H 3.955 0.01 1 6 17 1 A H5'' H 4.015 0.01 1 7 17 1 A H8 H 8.333 0.01 1 8 17 1 A HO2' H 4.964 0.01 1 9 17 1 A C1' C 91.732 0.1 1 10 17 1 A C2 C 154.934 0.1 1 11 17 1 A C2' C 75.718 0.1 1 12 17 1 A C3' C 76.601 0.1 1 13 17 1 A C4' C 86.719 0.1 1 14 17 1 A C5' C 63.614 0.1 1 15 17 1 A C8 C 142.888 0.1 1 16 18 2 G H1' H 5.703 0.01 1 17 18 2 G H8 H 7.987 0.01 1 18 18 2 G C1' C 92.296 0.1 1 19 18 2 G C8 C 138.164 0.1 1 20 19 3 C H1' H 5.379 0.01 1 21 19 3 C H3' H 4.569 0.01 1 22 19 3 C H4' H 4.480 0.01 1 23 19 3 C H5 H 5.544 0.01 1 24 19 3 C H6 H 7.708 0.01 1 25 19 3 C HO2' H 4.367 0.01 1 26 19 3 C C1' C 93.886 0.1 1 27 19 3 C C2' C 75.311 0.1 1 28 19 3 C C5 C 98.032 0.1 1 29 19 3 C C6 C 140.671 0.1 1 30 20 4 A H1' H 5.979 0.01 1 31 20 4 A H2 H 7.521 0.01 1 32 20 4 A H8 H 8.153 0.01 1 33 20 4 A HO2' H 4.583 0.01 1 34 20 4 A C1' C 92.767 0.1 1 35 20 4 A C2 C 153.671 0.1 1 36 20 4 A C8 C 139.545 0.1 1 37 21 5 C H1' H 5.454 0.01 1 38 21 5 C H3' H 4.401 0.01 1 39 21 5 C H4' H 4.544 0.01 1 40 21 5 C H5 H 5.300 0.01 1 41 21 5 C H5'' H 4.047 0.01 1 42 21 5 C H6 H 7.627 0.01 1 43 21 5 C HO2' H 4.240 0.01 1 44 21 5 C C1' C 93.608 0.1 1 45 21 5 C C2' C 75.680 0.1 1 46 21 5 C C3' C 72.263 0.1 1 47 21 5 C C5 C 97.173 0.1 1 48 21 5 C C6 C 141.471 0.1 1 49 22 6 C H1' H 5.531 0.01 1 50 22 6 C H5 H 5.488 0.01 1 51 22 6 C H6 H 7.796 0.01 1 52 22 6 C HO2' H 4.287 0.01 1 53 22 6 C C1' C 94.310 0.1 1 54 22 6 C C2' C 75.611 0.1 1 55 22 6 C C5 C 97.612 0.1 1 56 23 7 C H1' H 5.763 0.01 1 57 23 7 C H3' H 4.195 0.01 1 58 23 7 C H5 H 5.536 0.01 1 59 23 7 C H6 H 7.698 0.01 1 60 23 7 C HO2' H 4.047 0.01 1 61 23 7 C C1' C 93.022 0.1 1 62 23 7 C C2' C 77.509 0.1 1 63 23 7 C C3' C 69.614 0.1 1 64 23 7 C C5 C 98.113 0.1 1 65 23 7 C C6 C 141.736 0.1 1 stop_ save_