data_30268 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop ; _BMRB_accession_number 30268 _BMRB_flat_file_name bmr30268.str _Entry_type original _Submission_date 2017-03-06 _Accession_date 2017-03-06 _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 Kauffmann A. D. . 2 Kennedy S. D. . 3 Turner D. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 152 "31P chemical shifts" 13 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-11-22 update BMRB 'update entry citation' 2017-07-20 original author 'original release' stop_ _Original_release_date 2017-06-20 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Nuclear Magnetic Resonance Structure of an 8 x 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28700212 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kauffmann Andrew D. . 2 Kennedy Scott D. . 3 Zhao Jianbo . . 4 Turner Douglas H. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 56 _Journal_issue 29 _Journal_ISSN 1520-4995 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3733 _Page_last 3744 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-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 'not present' _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*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3')" _Molecular_mass 4878.018 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence ; CCAGAAACGGAUGGA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 C 2 2 C 3 3 A 4 4 G 5 5 A 6 6 A 7 7 A 8 8 C 9 9 G 10 10 G 11 11 A 12 12 U 13 13 G 14 14 G 15 15 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_1 . 32630 . . . . 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 "3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'), 95% H2O/5% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 3.1 mM None stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details "3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3'), 100% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 3.1 mM None 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 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name AMBER _Version 14 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'data analysis' refinement stop_ _Details . save_ save_software_3 _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_ save_software_4 _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_5 _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_6 _Saveframe_category software _Name VNMR _Version 6.1C loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection 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-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_31P-1H_COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 31P-1H COSY' _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' 0.1 . M pH 6.2 . pH pressure 1 . atm temperature 273 . 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' 0.1 . M pH 6.2 . pH pressure 1 . atm temperature 283 . 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 H 1 'methyl protons' ppm 0.000 internal direct . . . 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-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _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 5.585 0.001 1 2 1 1 C H2' H 4.494 0.001 1 3 1 1 C H3' H 4.433 0.001 1 4 1 1 C H4' H 4.371 0.002 1 5 1 1 C H5 H 5.984 0.001 1 6 1 1 C H5' H 4.097 0.004 2 7 1 1 C H5'' H 3.916 0.003 2 8 1 1 C H6 H 8.122 0.002 1 9 2 2 C H1' H 5.446 0.001 1 10 2 2 C H2' H 4.692 0.002 1 11 2 2 C H3' H 4.572 0.002 1 12 2 2 C H4' H 4.4 0.004 1 13 2 2 C H5 H 5.442 0.002 1 14 2 2 C H5'' H 4.12 0 2 15 2 2 C H6 H 7.767 0.003 1 16 2 2 C P P -4.094 0 1 17 3 3 A H1' H 5.783 0.001 1 18 3 3 A H2 H 7.318 0.001 1 19 3 3 A H2' H 4.66 0.001 1 20 3 3 A H3' H 4.343 0.002 1 21 3 3 A H4' H 4.492 0.003 1 22 3 3 A H5'' H 4.137 0 2 23 3 3 A H8 H 7.763 0.003 1 24 3 3 A P P -3.605 0 1 25 4 4 G H1' H 5.178 0.003 1 26 4 4 G H2' H 4.37 0.003 1 27 4 4 G H3' H 4.783 0.002 1 28 4 4 G H4' H 4.547 0.002 1 29 4 4 G H8 H 7.654 0.002 1 30 4 4 G P P -4.097 0 1 31 5 5 A H1' H 5.567 0.002 1 32 5 5 A H2 H 7.237 0.001 1 33 5 5 A H2' H 4.762 0.002 1 34 5 5 A H3' H 4.594 0.004 1 35 5 5 A H4' H 4.489 0.002 1 36 5 5 A H8 H 8.075 0.003 1 37 5 5 A P P -4.448 0 1 38 6 6 A H1' H 5.705 0.002 1 39 6 6 A H2 H 8.101 0.001 1 40 6 6 A H2' H 4.845 0.002 1 41 6 6 A H3' H 4.189 0.002 1 42 6 6 A H4' H 4.517 0.003 1 43 6 6 A H5'' H 4.021 0.003 2 44 6 6 A H8 H 7.089 0.001 1 45 6 6 A P P -3.407 0 1 46 7 7 A H1' H 5.014 0.003 1 47 7 7 A H2' H 4.352 0.001 1 48 7 7 A H3' H 4.19 0.002 1 49 7 7 A H4' H 4.141 0.007 1 50 7 7 A H8 H 7.236 0.001 1 51 7 7 A P P -3.936 0 1 52 8 8 C H2' H 4.075 0.001 1 53 8 8 C H3' H 4.141 0.006 1 54 8 8 C H4' H 4.18 0.003 1 55 8 8 C H5 H 5.377 0.002 1 56 8 8 C H6 H 7.288 0.002 1 57 9 9 G H1' H 5.371 0.006 1 58 9 9 G H2' H 3.423 0.002 1 59 9 9 G H3' H 4.6 0.003 1 60 9 9 G H4' H 4.28 0.003 1 61 9 9 G H8 H 7.707 0.002 1 62 9 9 G P P -4.533 0 1 63 10 10 G H1' H 5.591 0.003 1 64 10 10 G H2' H 4.98 0.003 1 65 10 10 G H3' H 4.423 0.001 1 66 10 10 G H8 H 8.066 0.002 1 67 10 10 G P P -4.977 0 1 68 11 11 A H1' H 5.047 0.002 1 69 11 11 A H2 H 8.018 0.001 1 70 11 11 A H2' H 4.576 0.003 1 71 11 11 A H3' H 4.351 0.003 1 72 11 11 A H4' H 4.351 0 1 73 11 11 A H8 H 7.765 0.001 1 74 11 11 A P P -5.96 0 1 75 12 12 U H1' H 4.022 0.001 1 76 12 12 U H2' H 4.291 0.001 1 77 12 12 U H3' H 4.259 0.003 1 78 12 12 U H4' H 4.208 0 1 79 12 12 U H5 H 5.596 0.001 1 80 12 12 U H6 H 7.371 0.001 1 81 12 12 U P P -4.516 0 1 82 13 13 G H1' H 5.747 0.001 1 83 13 13 G H2' H 4.604 0 1 84 13 13 G H3' H 4.475 0.003 1 85 13 13 G H4' H 4.416 0 1 86 13 13 G H5'' H 4.034 0 2 87 13 13 G H8 H 7.615 0.001 1 88 13 13 G P P -4.054 0 1 89 14 14 G H1' H 5.642 0 1 90 14 14 G H2' H 4.477 0.001 1 91 14 14 G H3' H 4.421 0.006 1 92 14 14 G H4' H 4.477 0.004 1 93 14 14 G H5'' H 4.025 0 2 94 14 14 G H8 H 7.108 0.001 1 95 14 14 G P P -3.876 0 1 96 15 15 A H1' H 5.934 0.001 1 97 15 15 A H2 H 7.836 0.001 1 98 15 15 A H2' H 4.03 0.002 1 99 15 15 A H3' H 4.223 0.002 1 100 15 15 A H8 H 7.741 0.001 1 101 15 15 A P P -3.962 0 1 stop_ save_ save_assigned_chemical_shifts_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 31P-1H COSY' stop_ loop_ _Sample_label $sample_2 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 5.553 0.001 1 2 1 1 C H2' H 4.464 0.002 1 3 1 1 C H5 H 5.954 0.001 1 4 1 1 C H6 H 8.098 0.002 1 5 1 1 C H41 H 8.481 0.002 1 6 1 1 C H42 H 6.999 0.001 1 7 2 2 C H1' H 5.408 0.003 1 8 2 2 C H5 H 5.408 0.001 1 9 2 2 C H6 H 7.727 0.002 1 10 2 2 C H41 H 8.156 0.001 1 11 2 2 C H42 H 6.704 0.001 1 12 3 3 A H1' H 5.752 0.001 1 13 3 3 A H2 H 7.296 0.002 1 14 3 3 A H2' H 4.662 0 1 15 3 3 A H8 H 7.741 0 1 16 4 4 G H1 H 10.023 0.002 1 17 4 4 G H1' H 5.117 0.001 1 18 4 4 G H8 H 7.617 0.001 1 19 4 4 G H21 H 7.381 0.003 1 20 4 4 G H22 H 5.305 0.002 1 21 5 5 A H1' H 5.527 0 1 22 5 5 A H2 H 7.194 0.002 1 23 5 5 A H8 H 8.071 0.002 1 24 6 6 A H1' H 5.735 0.001 1 25 6 6 A H2 H 8.123 0.001 1 26 6 6 A H2' H 4.8 0.001 1 27 6 6 A H8 H 7.028 0.001 1 28 7 7 A H1' H 4.896 0 1 29 7 7 A H8 H 7.279 0.001 1 30 8 8 C H5 H 5.371 0 1 31 8 8 C H6 H 7.302 0.001 1 32 9 9 G H1 H 10.393 0.001 1 33 9 9 G H1' H 5.163 0.005 1 34 9 9 G H2' H 3.387 0.001 1 35 9 9 G H3' H 4.563 0.001 1 36 9 9 G H8 H 7.677 0.001 1 37 10 10 G H1 H 9.394 0.002 1 38 10 10 G H1' H 5.564 0.002 1 39 10 10 G H2' H 4.961 0 1 40 10 10 G H3' H 4.891 0 1 41 10 10 G H8 H 8.032 0.004 1 42 11 11 A H1' H 5.025 0 1 43 11 11 A H2 H 8.01 0.001 1 44 11 11 A H8 H 7.733 0.001 1 45 12 12 U H1' H 3.984 0 1 46 12 12 U H3 H 13.252 0.004 1 47 12 12 U H5 H 5.562 0.002 1 48 12 12 U H6 H 7.318 0.002 1 49 13 13 G H1 H 11.712 0.001 1 50 13 13 G H1' H 5.72 0 1 51 13 13 G H2' H 4.585 0.001 1 52 13 13 G H8 H 7.589 0.001 1 53 13 13 G H21 H 6.023 0.004 1 54 13 13 G H22 H 7.961 0.002 1 55 14 14 G H1 H 12.594 0.003 1 56 14 14 G H1' H 5.614 0.001 1 57 14 14 G H2' H 4.463 0.001 1 58 14 14 G H8 H 7.074 0 1 59 14 14 G H21 H 5.874 0.021 1 60 14 14 G H22 H 8.131 0.001 1 61 15 15 A H1' H 5.902 0.001 1 62 15 15 A H2 H 7.803 0.001 1 63 15 15 A H2' H 3.996 0.001 1 64 15 15 A H8 H 7.698 0 1 stop_ save_