data_5023 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoter ; _BMRB_accession_number 5023 _BMRB_flat_file_name bmr5023.str _Entry_type original _Submission_date 2001-05-21 _Accession_date 2001-05-21 _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 Tinoco I. . . 2 Kim C.-H. . . 3 Kao C. C. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 10 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2001-08-20 original author . stop_ _Original_release_date 2001-08-20 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoter ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 11273704 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tinoco I. . . 2 Kim C.-H. . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 307 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 827 _Page_last 839 _Year 2001 _Details . loop_ _Keyword BMV NMR replication RNA Stem-loop Triloop Virus stop_ save_ ################################## # Molecular system description # ################################## save_system_mutant_RNA _Saveframe_category molecular_system _Mol_system_name 5'-R(*GP*GP*UP*GP*CP*UP*UP*AP*GP*CP*AP*CP*C)-3' _Abbreviation_common 'mutant RNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*GP*GP*UP*GP*CP*UP*UP*AP*GP*CP*AP*CP*C)-3')' $mutant_RNA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_mutant_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'mutant BMV (+) strand RNA' _Abbreviation_common 'mutant RNA' _Molecular_mass . _Mol_thiol_state 'not present' _Details ; This sequence is a mutant triloop of which wild type sequence is naturally occured in BMV (+) strand RNA. ; ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence GGUGCUUAGCACC loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 U 4 G 5 C 6 U 7 U 8 A 9 G 10 C 11 A 12 C 13 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 $mutant_RNA . . . . . . 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 $mutant_RNA . . . . . . 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 $mutant_RNA 2 mM . 'sodium phosphate buffer' 5 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 95 loop_ _Task 'data analysis' stop_ _Details . save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.1 loop_ _Task refinement 'structure solution' stop_ _Details 'Brunger, A.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 5 . mM pH 6.5 . n/a pressure 1 . atm temperature 283 . 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label . H 1 . ppm . . . . . . $entry_citation $entry_citation 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'RNA (5'-R(*GP*GP*UP*GP*CP*UP*UP*AP*GP*CP*AP*CP*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 G H2' H 4.501 . . 2 . 1 G H3' H 4.353 . . 3 . 2 G H2' H 4.134 . . 4 . 2 G H3' H 4.230 . . 5 . 3 U H2' H 3.900 . . 6 . 3 U H3' H 3.705 . . 7 . 4 G H2' H 4.086 . . 8 . 4 G H3' H 3.798 . . 9 . 5 C H2' H 4.157 . . 10 . 5 C H3' H 4.387 . . stop_ save_