data_25414 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural features of a 3' splice site influenza A: 11-nt hairpin ; _BMRB_accession_number 25414 _BMRB_flat_file_name bmr25414.str _Entry_type original _Submission_date 2015-01-06 _Accession_date 2015-01-06 _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 Turner Douglas H. . 2 Kennedy Scott D. . 3 Chen Jonathan L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 97 "31P chemical shifts" 10 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-02-18 update BMRB 'update entry citation' 2015-05-04 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 25415 '3 splice site influenza A: 19-nt duplex' 25416 "3' splice site in influenza A: 39-nt hairpin" stop_ _Original_release_date 2015-05-04 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural features of a 3' splice site in influenza A ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 25909229 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chen Jonathan L. . 2 Kennedy Scott D. . 3 Turner Douglas H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 54 _Journal_issue 21 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3269 _Page_last 3285 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "3' splice site influenza A: 11-nt hairpin" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(11-MER) _Molecular_mass 3552.259 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence ; CCAGAAACGGA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 16 C 2 17 C 3 18 A 4 19 G 5 20 A 6 21 A 7 22 A 8 23 C 9 24 G 10 25 G 11 26 A 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 $entity . . . . . . 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 $entity 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '11-nt hairpin' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 1.0 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '11-nt hairpin' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 4.0 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection 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 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_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_2 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-31P_HETCOR_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $sample_2 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' 101.12 . mM pH 6.0 . pH pressure 1 . atm temperature 293.15 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 101.12 . mM pH 6.0 . pH pressure 1 . atm temperature 275.15 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 101.12 . mM pH 6.0 . pH pressure 1 . atm temperature 272.15 . K stop_ save_ save_sample_conditions_4 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 101.12 . mM pH 6.0 . pH pressure 1 . atm temperature 271.15 . 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 H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS P 31 'methyl protons' ppm 0.00 na indirect . . . 0.404808636 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 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name entity _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 16 1 C H1' H 5.620 0.005 1 2 16 1 C H2' H 4.495 0.005 1 3 16 1 C H3' H 4.460 0.005 1 4 16 1 C H4' H 4.395 0.01 1 5 16 1 C H5 H 6.040 0.01 1 6 16 1 C H5' H 4.120 0.005 4 7 16 1 C H5'' H 3.935 0.005 4 8 16 1 C H6 H 8.130 0.005 1 9 16 1 C H41 H 8.550 0.005 1 10 16 1 C H42 H 7.102 0.005 1 11 17 2 C H1' H 5.433 0.005 1 12 17 2 C H2' H 4.279 0.005 1 13 17 2 C H3' H 4.675 0.005 1 14 17 2 C H4' H 4.407 0.01 1 15 17 2 C H5 H 5.526 0.01 1 16 17 2 C H5' H 4.575 0.005 4 17 17 2 C H5'' H 4.155 0.005 4 18 17 2 C H6 H 7.820 0.005 1 19 17 2 C H41 H 8.493 0.005 1 20 17 2 C H42 H 6.933 0.005 1 21 17 2 C P P -4.101 0.01 1 22 18 3 A H1' H 5.980 0.005 1 23 18 3 A H2 H 7.670 0.005 1 24 18 3 A H2' H 4.474 0.005 1 25 18 3 A H3' H 4.848 0.005 1 26 18 3 A H4' H 4.423 0.005 1 27 18 3 A H5' H 4.520 0.005 4 28 18 3 A H5'' H 4.183 0.005 4 29 18 3 A H8 H 8.184 0.005 1 30 18 3 A P P -3.980 0.01 1 31 19 4 G H1 H 10.492 0.01 1 32 19 4 G H1' H 5.563 0.005 1 33 19 4 G H2' H 4.352 0.01 1 34 19 4 G H3' H 4.607 0.005 1 35 19 4 G H4' H 4.366 0.005 1 36 19 4 G H5' H 4.415 0.005 4 37 19 4 G H5'' H 4.107 0.005 4 38 19 4 G H8 H 7.335 0.005 1 39 19 4 G H21 H 7.160 0.005 1 40 19 4 G P P -3.467 0.01 1 41 20 5 A H1' H 5.681 0.005 1 42 20 5 A H2 H 7.726 0.005 1 43 20 5 A H2' H 4.680 0.005 1 44 20 5 A H3' H 4.475 0.005 1 45 20 5 A H4' H 4.250 0.005 1 46 20 5 A H5' H 4.255 0.005 4 47 20 5 A H5'' H 3.953 0.005 4 48 20 5 A H8 H 8.210 0.005 1 49 20 5 A P P -2.118 0.01 1 50 21 6 A H1' H 5.515 0.005 1 51 21 6 A H2 H 7.610 0.005 1 52 21 6 A H2' H 4.558 0.005 1 53 21 6 A H3' H 4.655 0.005 1 54 21 6 A H4' H 4.410 0.005 1 55 21 6 A H5' H 4.298 0.005 4 56 21 6 A H5'' H 4.016 0.005 4 57 21 6 A H8 H 7.888 0.005 1 58 21 6 A P P -3.210 0.01 1 59 22 7 A H1' H 5.850 0.005 1 60 22 7 A H2 H 8.082 0.005 1 61 22 7 A H2' H 4.675 0.005 1 62 22 7 A H3' H 4.620 0.005 1 63 22 7 A H4' H 4.468 0.005 1 64 22 7 A H5' H 4.584 0.005 4 65 22 7 A H5'' H 4.211 0.005 4 66 22 7 A H8 H 7.930 0.005 1 67 22 7 A P P -4.163 0.01 1 68 23 8 C H1' H 4.850 0.005 1 69 23 8 C H2' H 4.414 0.005 1 70 23 8 C H3' H 4.338 0.005 1 71 23 8 C H4' H 4.300 0.01 1 72 23 8 C H5 H 5.583 0.01 1 73 23 8 C H5' H 4.357 0.005 4 74 23 8 C H5'' H 4.127 0.005 4 75 23 8 C H6 H 7.730 0.005 1 76 23 8 C H41 H 7.723 0.005 1 77 23 8 C H42 H 6.575 0.005 1 78 23 8 C P P -3.951 0.01 1 79 24 9 G H1 H 11.967 0.01 1 80 24 9 G H1' H 5.594 0.005 1 81 24 9 G H2' H 4.719 0.01 1 82 24 9 G H3' H 4.327 0.01 1 83 24 9 G H5' H 4.250 0.005 4 84 24 9 G H5'' H 4.103 0.005 4 85 24 9 G H8 H 7.578 0.005 1 86 24 9 G H21 H 5.870 0.005 1 87 24 9 G H22 H 7.385 0.005 1 88 24 9 G P P -3.563 0.01 1 89 25 10 G H1 H 12.802 0.01 1 90 25 10 G H1' H 5.685 0.005 1 91 25 10 G H2' H 4.519 0.01 1 92 25 10 G H3' H 4.573 0.005 1 93 25 10 G H4' H 4.417 0.005 1 94 25 10 G H5' H 4.500 0.005 4 95 25 10 G H5'' H 4.073 0.005 4 96 25 10 G H8 H 7.300 0.005 1 97 25 10 G H21 H 8.178 0.005 1 98 25 10 G P P -4.068 0.01 1 99 26 11 A H1' H 5.959 0.005 1 100 26 11 A H2 H 7.913 0.005 1 101 26 11 A H2' H 4.104 0.005 1 102 26 11 A H3' H 4.287 0.005 1 103 26 11 A H4' H 4.260 0.005 1 104 26 11 A H5' H 4.425 0.005 4 105 26 11 A H5'' H 4.055 0.005 4 106 26 11 A H8 H 7.853 0.005 1 107 26 11 A P P -3.856 0.01 1 stop_ save_