data_30547 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RNA Duplex containing the internal loop 5'-GCAU/3'-UACG ; _BMRB_accession_number 30547 _BMRB_flat_file_name bmr30547.str _Entry_type original _Submission_date 2018-11-29 _Accession_date 2018-11-29 _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 Berger K. D. . 2 Kennedy S. D. . 3 Turner D. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 88 "13C chemical shifts" 18 "31P chemical shifts" 5 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-07-09 update BMRB 'update entry citation' 2019-02-08 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30546 "RNA Duplex containing the internal loop 5'-GCUU/3'-UUCG" 30548 "RNA Duplex containing the internal loop 5'-UUCG/3'-GCUU" stop_ _Original_release_date 2018-12-13 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30702283 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Berger K. D. . 2 Kennedy S. D. . 3 Turner D. H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 58 _Journal_issue 8 _Journal_ASTM BICHAW _Journal_ISSN 0006-2960 _Journal_CSD 0033 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1094 _Page_last 1108 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "RNA (5'-R(*CP*GP*GP*GP*CP*AP*UP*CP*CP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common "RNA (5'-R(*CP*GP*GP*GP*CP*AP*UP*CP*CP*G)-3')" _Molecular_mass 3191.964 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; CGGGCAUCCG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 C 2 2 G 3 3 G 4 4 G 5 5 C 6 6 A 7 7 U 8 8 C 9 9 C 10 10 G 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_1 . 32644 . . . . 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_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details "1 mM RNA (5'-R(*CP*GP*GP*GP*CP*AP*UP*CP*CP*G)-3'), 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM none 'sodium chloride' 80 mM 'natural abundance' 'sodium phosphate' 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _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 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_software_3 _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_software_4 _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _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-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_HETCOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name HETCOR _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 'ionic strength' 130 . mM pH 6.2 . pH pressure 1 . atm temperature 288 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 0.000 internal indirect . . . 0.25144953 DSS H 1 'methyl protons' ppm 0.000 internal indirect . . . 1.0 DSS P 31 'methyl protons' ppm 0.000 internal 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' HETCOR stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 1' _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 C H1' H 5.550 0.005 1 2 1 1 C H2' H 4.556 0.005 1 3 1 1 C H3' H 4.547 0.005 1 4 1 1 C H4' H 4.312 0.005 1 5 1 1 C H5 H 5.970 0.005 1 6 1 1 C H5' H 4.020 0.005 2 7 1 1 C H5'' H 3.906 0.005 2 8 1 1 C H6 H 8.056 0.005 1 9 1 1 C H41 H 8.122 0.005 1 10 1 1 C H42 H 7.087 0.005 1 11 1 1 C C1' C 93.865 0.2 1 12 1 1 C C5 C 98.898 0.2 1 13 1 1 C C6 C 142.733 0.2 1 14 1 1 C P P -3.649 0.02 1 15 2 2 G H1 H 12.670 0.005 1 16 2 2 G H1' H 5.822 0.005 1 17 2 2 G H2' H 4.735 0.005 1 18 2 2 G H3' H 4.735 0.005 1 19 2 2 G H4' H 4.497 0.005 1 20 2 2 G H5' H 4.505 0.005 2 21 2 2 G H5'' H 4.179 0.005 2 22 2 2 G H8 H 7.794 0.005 1 23 2 2 G C1' C 92.405 0.2 1 24 2 2 G C8 C 136.561 0.2 1 25 2 2 G P P -3.581 0.02 1 26 3 3 G H1 H 12.740 0.005 1 27 3 3 G H1' H 5.775 0.005 1 28 3 3 G H2' H 4.560 0.005 1 29 3 3 G H3' H 4.490 0.005 1 30 3 3 G H4' H 4.491 0.005 1 31 3 3 G H5' H 4.494 0.005 2 32 3 3 G H5'' H 4.109 0.005 2 33 3 3 G H8 H 7.317 0.005 1 34 3 3 G C1' C 92.596 0.2 1 35 3 3 G C8 C 136.075 0.2 1 36 4 4 G H1 H 11.090 0.005 1 37 4 4 G H1' H 5.735 0.005 1 38 4 4 G H2' H 4.409 0.005 1 39 4 4 G H3' H 4.370 0.005 1 40 4 4 G H4' H 4.481 0.005 1 41 4 4 G H5' H 4.394 0.005 2 42 4 4 G H5'' H 4.008 0.005 2 43 4 4 G H8 H 7.213 0.005 1 44 4 4 G P P -4.443 0.02 1 45 5 5 C H1' H 5.662 0.005 1 46 5 5 C H2' H 4.717 0.005 1 47 5 5 C H3' H 4.484 0.005 1 48 5 5 C H4' H 4.389 0.005 1 49 5 5 C H5 H 5.063 0.005 1 50 5 5 C H5' H 4.547 0.005 2 51 5 5 C H5'' H 4.104 0.005 2 52 5 5 C H6 H 7.620 0.005 1 53 5 5 C H41 H 7.305 0.005 1 54 5 5 C H42 H 6.757 0.005 1 55 5 5 C C1' C 93.505 0.2 1 56 5 5 C C5 C 95.662 0.2 1 57 6 6 A H1' H 5.929 0.005 1 58 6 6 A H2 H 7.920 0.005 1 59 6 6 A H2' H 4.685 0.005 1 60 6 6 A H3' H 4.264 0.005 1 61 6 6 A H4' H 4.549 0.005 1 62 6 6 A H5' H 4.371 0.005 2 63 6 6 A H5'' H 4.153 0.005 2 64 6 6 A H8 H 7.909 0.005 1 65 6 6 A C1' C 93.547 0.2 1 66 6 6 A P P -4.456 0.02 1 67 7 7 U H1' H 5.410 0.005 1 68 7 7 U H2' H 4.019 0.005 1 69 7 7 U H3 H 11.980 0.005 1 70 7 7 U H3' H 4.450 0.005 1 71 7 7 U H4' H 4.387 0.005 1 72 7 7 U H5 H 5.209 0.005 1 73 7 7 U H5' H 4.495 0.005 2 74 7 7 U H5'' H 4.033 0.005 2 75 7 7 U H6 H 7.530 0.005 1 76 7 7 U C1' C 93.674 0.2 1 77 7 7 U C5 C 103.487 0.2 1 78 8 8 C H1' H 5.530 0.005 1 79 8 8 C H2' H 4.306 0.005 1 80 8 8 C H3' H 4.467 0.005 1 81 8 8 C H4' H 4.331 0.005 1 82 8 8 C H5 H 5.573 0.005 1 83 8 8 C H5' H 4.501 0.005 2 84 8 8 C H5'' H 4.037 0.005 2 85 8 8 C H6 H 7.943 0.005 1 86 8 8 C H41 H 8.486 0.005 1 87 8 8 C H42 H 6.872 0.005 1 88 8 8 C C1' C 93.505 0.2 1 89 8 8 C C5 C 97.291 0.2 1 90 8 8 C P P -4.068 0.02 1 91 9 9 C H1' H 5.427 0.005 1 92 9 9 C H2' H 4.323 0.005 1 93 9 9 C H3' H 4.451 0.005 1 94 9 9 C H4' H 4.351 0.005 1 95 9 9 C H5 H 5.477 0.005 1 96 9 9 C H5' H 4.496 0.005 2 97 9 9 C H5'' H 4.038 0.005 2 98 9 9 C H6 H 7.665 0.005 1 99 9 9 C H41 H 8.369 0.005 1 100 9 9 C H42 H 6.827 0.005 1 101 9 9 C C1' C 93.970 0.2 1 102 9 9 C C5 C 97.925 0.2 1 103 9 9 C C6 C 140.896 0.2 1 104 10 10 G H1' H 5.802 0.005 1 105 10 10 G H2' H 4.073 0.005 1 106 10 10 G H3' H 4.266 0.005 1 107 10 10 G H4' H 4.205 0.005 1 108 10 10 G H5' H 4.436 0.005 2 109 10 10 G H5'' H 4.016 0.005 2 110 10 10 G H8 H 7.580 0.005 1 111 10 10 G C1' C 91.284 0.2 1 stop_ save_