data_18240 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Mutant of the sub-genomic promoter from Brome Mosaic Virus ; _BMRB_accession_number 18240 _BMRB_flat_file_name bmr18240.str _Entry_type original _Submission_date 2012-02-06 _Accession_date 2012-02-06 _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 Skov Joan . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 100 "31P chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-06-14 update BMRB 'update entry citation' 2012-03-13 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 18239 'Pseudo-triloop from the sub-genomic promoter of Brome Mosaic Virus' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22393035 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Skov Joan . . 2 Gaudin Mathieu . . 3 Podbevsek Peter . . 4 Olsthoorn Rene C.L. . 5 Petersen Michael . . stop_ _Journal_abbreviation RNA _Journal_name_full 'RNA (New York, N.Y.)' _Journal_volume 18 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 992 _Page_last 1000 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Mutant of the sub-genomic promoter from Brome Mosaic Virus' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*UP*CP*UP*UP*C)-3')' $delA_RNA 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_delA_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*UP*CP*UP*UP*C)-3')_ _Molecular_mass 4792.932 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence GAGGACAUAGUCUUC loop_ _Residue_seq_code _Residue_label 1 G 2 A 3 G 4 G 5 A 6 C 7 A 8 U 9 A 10 G 11 U 12 C 13 U 14 U 15 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 $delA_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 $delA_RNA 'obtained from a vendor' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '2 mM RNA, 10 mM sodium phosphate buffer (pH 7), 50 mM NaCl, 2 mM EDTA' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $delA_RNA 2 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' EDTA 2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.851 loop_ _Vendor _Address _Electronic_address Brunger . . 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 500 _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_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7 . pH pressure 1 . atm 'ionic strength' 65 . 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 water H 1 protons ppm 4.78 internal direct . . . 1.0 'phosphoric acid (85%)' P 31 protons ppm 0.00 external indirect . . . . 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' 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(*GP*AP*GP*GP*AP*CP*AP*UP*AP*GP*UP*CP*UP*UP*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 G H1 H 12.50 0.01 . 2 1 1 G H1' H 5.75 0.01 . 3 1 1 G H2' H 4.86 0.01 . 4 1 1 G H3' H 4.67 0.01 . 5 1 1 G H4' H 4.40 0.01 . 6 1 1 G H8 H 8.08 0.01 . 7 2 2 A H1' H 6.18 0.01 . 8 2 2 A H2 H 7.63 0.01 . 9 2 2 A H2' H 4.78 0.01 . 10 2 2 A H3' H 4.79 0.01 . 11 2 2 A H4' H 4.56 0.01 . 12 2 2 A H8 H 8.15 0.01 . 13 2 2 A P P -3.98 0.01 . 14 3 3 G H1 H 10.93 0.01 . 15 3 3 G H1' H 5.64 0.01 . 16 3 3 G H2' H 4.68 0.01 . 17 3 3 G H3' H 4.23 0.01 . 18 3 3 G H4' H 4.53 0.01 . 19 3 3 G H8 H 6.97 0.01 . 20 3 3 G P P -4.24 0.01 . 21 4 4 G H1 H 12.59 0.01 . 22 4 4 G H1' H 5.70 0.01 . 23 4 4 G H2' H 4.54 0.01 . 24 4 4 G H3' H 4.56 0.01 . 25 4 4 G H4' H 4.47 0.01 . 26 4 4 G H8 H 7.15 0.01 . 27 4 4 G H21 H 8.15 0.01 . 28 4 4 G H22 H 6.35 0.01 . 29 4 4 G P P -3.83 0.01 . 30 5 5 A H1' H 5.98 0.01 . 31 5 5 A H2 H 7.83 0.01 . 32 5 5 A H2' H 4.45 0.01 . 33 5 5 A H3' H 4.64 0.01 . 34 5 5 A H4' H 4.46 0.01 . 35 5 5 A H8 H 7.77 0.01 . 36 5 5 A P P -3.66 0.01 . 37 6 6 C H1' H 5.54 0.01 . 38 6 6 C H2' H 4.24 0.01 . 39 6 6 C H3' H 4.39 0.01 . 40 6 6 C H4' H 4.35 0.01 . 41 6 6 C H5 H 5.04 0.01 . 42 6 6 C H6 H 7.18 0.01 . 43 6 6 C H41 H 7.95 0.01 . 44 6 6 C H42 H 6.75 0.01 . 45 6 6 C P P -3.89 0.01 . 46 7 7 A H1' H 6.10 0.01 . 47 7 7 A H2 H 8.00 0.01 . 48 7 7 A H2' H 4.72 0.01 . 49 7 7 A H3' H 4.58 0.01 . 50 7 7 A H4' H 4.52 0.01 . 51 7 7 A H8 H 8.42 0.01 . 52 7 7 A P P -3.74 0.01 . 53 8 8 U H1' H 5.44 0.01 . 54 8 8 U H2' H 4.01 0.01 . 55 8 8 U H3' H 4.44 0.01 . 56 8 8 U H4' H 3.83 0.01 . 57 8 8 U H5 H 5.80 0.01 . 58 8 8 U H6 H 7.46 0.01 . 59 8 8 U P P -4.52 0.01 . 60 9 9 A H1' H 5.88 0.01 . 61 9 9 A H2 H 7.93 0.01 . 62 9 9 A H2' H 4.89 0.01 . 63 9 9 A H3' H 4.85 0.01 . 64 9 9 A H4' H 4.43 0.01 . 65 9 9 A H8 H 7.96 0.01 . 66 9 9 A P P -3.44 0.01 . 67 10 10 G H1 H 12.67 0.01 . 68 10 10 G H1' H 5.54 0.01 . 69 10 10 G H2' H 4.83 0.01 . 70 10 10 G H3' H 4.67 0.01 . 71 10 10 G H4' H 4.63 0.01 . 72 10 10 G H8 H 8.09 0.01 . 73 10 10 G P P -3.71 0.01 . 74 11 11 U H1' H 5.74 0.01 . 75 11 11 U H2' H 4.63 0.01 . 76 11 11 U H3 H 13.81 0.01 . 77 11 11 U H3' H 4.33 0.01 . 78 11 11 U H4' H 4.59 0.01 . 79 11 11 U H5 H 5.15 0.01 . 80 11 11 U H6 H 7.71 0.01 . 81 11 11 U P P -5.20 0.01 . 82 12 12 C H1' H 5.62 0.01 . 83 12 12 C H2' H 4.57 0.01 . 84 12 12 C H3' H 4.34 0.01 . 85 12 12 C H4' H 4.48 0.01 . 86 12 12 C H5 H 5.61 0.01 . 87 12 12 C H6 H 7.83 0.01 . 88 12 12 C H41 H 8.37 0.01 . 89 12 12 C H42 H 6.95 0.01 . 90 12 12 C P P -3.63 0.01 . 91 13 13 U H1' H 5.62 0.01 . 92 13 13 U H2' H 4.11 0.01 . 93 13 13 U H3 H 11.78 0.01 . 94 13 13 U H4' H 4.41 0.01 . 95 13 13 U H5 H 5.72 0.01 . 96 13 13 U H6 H 7.90 0.01 . 97 13 13 U P P -3.63 0.01 . 98 14 14 U H1' H 5.58 0.01 . 99 14 14 U H2' H 4.27 0.01 . 100 14 14 U H3 H 14.34 0.01 . 101 14 14 U H3' H 4.58 0.01 . 102 14 14 U H4' H 4.37 0.01 . 103 14 14 U H5 H 5.63 0.01 . 104 14 14 U H6 H 8.10 0.01 . 105 14 14 U P P -2.73 0.01 . 106 15 15 C H1' H 5.89 0.01 . 107 15 15 C H2' H 4.00 0.01 . 108 15 15 C H3' H 4.22 0.01 . 109 15 15 C H4' H 4.18 0.01 . 110 15 15 C H5 H 5.73 0.01 . 111 15 15 C H6 H 7.76 0.01 . 112 15 15 C H41 H 8.31 0.01 . 113 15 15 C H42 H 7.14 0.01 . 114 15 15 C P P -3.63 0.01 . stop_ save_