data_16953 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/3'GGAU ; _BMRB_accession_number 16953 _BMRB_flat_file_name bmr16953.str _Entry_type new _Submission_date 2010-05-25 _Accession_date 2010-05-25 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Tandem AG pairs with UG closing pairs: r(GGUAGGCCA)2' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hammond Nicholas B. . 2 Kennedy Scott D. . 3 Turner Douglas H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 81 "13C chemical shifts" 19 "31P chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-09 update BMRB 'complete entry citation' 2010-07-02 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16950 GACAAGUGUCA 16951 GACGAGCGUCA 16952 GACUAGAGUCA stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20481618 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hammond Nicholas B. . 2 Tolbert Blanton S. . 3 Kierzek Ryszard . . 4 Turner Douglas H. . 5 Kennedy Scott D. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 49 _Journal_issue 27 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5817 _Page_last 5827 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-R(*GP*AP*CP*AP*AP*GP*UP*GP*UP*CP*A)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')_1' $RNA_(5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3') 'RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')_2' $RNA_(5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3') 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_RNA_(5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3') _Molecular_mass 3530.203 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence GGUAGGCCA loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 U 4 A 5 G 6 G 7 C 8 C 9 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 $RNA_(5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3') . . . . . . 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 _Details $RNA_(5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3') 'obtained from a vendor' . . . . . Dharmacon 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 $RNA_(5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3') 1 mM 'natural abundance' 'sodium chloride' 80 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3') 1 mM 'natural abundance' 'sodium chloride' 80 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.12 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1C loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement 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-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-31P_HETCOR_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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 temperature 274 . K pH 6.1 . pH pressure 1 . atm 'ionic strength' 0.1 . M 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 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_ _Software_label $SPARKY stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-1H TOCSY' '2D DQF-COSY' '2D 1H-31P HETCOR' 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 'RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')_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 G H1 H 12.330 0.003 1 2 1 1 G H1' H 5.922 0.001 . 3 1 1 G H2' H 4.938 0.002 . 4 1 1 G H3' H 4.551 0.003 . 5 1 1 G H4' H 4.448 0.003 . 6 1 1 G H5' H 4.123 0.002 . 7 1 1 G H5'' H 3.971 0.002 2 8 1 1 G H8 H 8.136 0.001 1 9 1 1 G H21 H 8.146 0.002 2 10 1 1 G H22 H 6.333 0.001 2 11 1 1 G C1' C 93.347 0.000 . 12 1 1 G C2' C 75.376 0.000 . 13 1 1 G C4' C 84.624 0.000 . 14 1 1 G C8 C 138.661 0.000 1 15 2 2 G H1 H 13.420 0.004 1 16 2 2 G H1' H 5.819 0.003 . 17 2 2 G H2' H 4.552 0.001 . 18 2 2 G H3' H 4.506 0.001 . 19 2 2 G H4' H 4.505 0.002 . 20 2 2 G H5' H 4.582 0.002 . 21 2 2 G H5'' H 4.132 0.002 2 22 2 2 G H8 H 7.391 0.002 1 23 2 2 G H21 H 8.366 0.004 2 24 2 2 G H22 H 6.088 0.002 2 25 2 2 G C1' C 92.962 0.000 . 26 2 2 G C4' C 82.236 0.000 . 27 2 2 G C8 C 136.125 0.000 1 28 2 2 G P P -3.795 0.000 1 29 3 3 U H1' H 5.475 0.004 . 30 3 3 U H2' H 3.778 0.003 . 31 3 3 U H3 H 11.991 0.005 1 32 3 3 U H3' H 4.690 0.001 . 33 3 3 U H4' H 4.353 0.004 . 34 3 3 U H5 H 5.522 0.006 1 35 3 3 U H5' H 4.524 0.016 . 36 3 3 U H5'' H 4.085 0.000 2 37 3 3 U H6 H 7.632 0.001 1 38 3 3 U C1' C 93.476 0.000 . 39 3 3 U C5 C 104.489 0.000 1 40 3 3 U P P -4.234 0.000 1 41 4 4 A H1' H 6.035 0.007 . 42 4 4 A H2 H 7.538 0.005 1 43 4 4 A H2' H 4.954 0.004 . 44 4 4 A H3' H 4.878 0.003 . 45 4 4 A H4' H 4.491 0.001 . 46 4 4 A H5'' H 4.193 0.000 2 47 4 4 A H8 H 8.557 0.008 1 48 4 4 A C2 C 153.175 0.000 1 49 4 4 A P P -4.326 0.000 1 50 5 5 G H1 H 11.991 0.000 1 51 5 5 G H1' H 5.699 0.002 . 52 5 5 G H2' H 4.570 0.001 . 53 5 5 G H3' H 4.303 0.004 . 54 5 5 G H8 H 7.374 0.003 1 55 5 5 G H21 H 5.720 0.000 2 56 5 5 G H22 H 5.720 0.000 2 57 5 5 G P P -3.265 0.000 1 58 6 6 G H1 H 10.290 0.004 1 59 6 6 G H1' H 5.747 0.002 . 60 6 6 G H2' H 4.559 0.001 . 61 6 6 G H3' H 4.360 0.002 . 62 6 6 G H4' H 4.437 0.002 . 63 6 6 G H5' H 4.459 0.002 . 64 6 6 G H5'' H 4.045 0.007 2 65 6 6 G H8 H 7.083 0.004 1 66 6 6 G H21 H 6.216 0.000 2 67 6 6 G H22 H 6.216 0.000 2 68 6 6 G C1' C 93.681 0.000 . 69 6 6 G C4' C 82.327 0.000 . 70 6 6 G P P -3.716 0.000 1 71 7 7 C H1' H 5.366 0.002 . 72 7 7 C H2' H 4.192 0.001 . 73 7 7 C H3' H 4.443 0.004 . 74 7 7 C H4' H 4.354 0.005 . 75 7 7 C H5 H 5.384 0.008 1 76 7 7 C H5' H 4.449 0.000 . 77 7 7 C H5'' H 4.038 0.004 2 78 7 7 C H6 H 7.699 0.003 1 79 7 7 C H41 H 6.870 0.003 2 80 7 7 C H42 H 8.286 0.003 2 81 7 7 C C1' C 93.784 0.000 . 82 7 7 C C5 C 96.967 0.000 1 83 7 7 C P P -4.629 0.000 1 84 8 8 C H1' H 5.437 0.002 . 85 8 8 C H2' H 4.413 0.000 . 86 8 8 C H3' H 4.453 0.003 . 87 8 8 C H4' H 4.335 0.003 . 88 8 8 C H5 H 5.432 0.006 1 89 8 8 C H5' H 4.443 0.000 . 90 8 8 C H5'' H 4.032 0.001 2 91 8 8 C H6 H 7.622 0.002 1 92 8 8 C H41 H 7.034 0.001 2 93 8 8 C H42 H 8.146 0.003 2 94 8 8 C C1' C 93.886 0.000 . 95 8 8 C C5 C 97.737 0.000 1 96 8 8 C P P -3.966 0.000 1 97 9 9 A H1' H 5.978 0.003 . 98 9 9 A H2 H 7.278 0.001 1 99 9 9 A H2' H 4.018 0.001 . 100 9 9 A H3' H 4.294 0.002 . 101 9 9 A H4' H 4.215 0.004 . 102 9 9 A H5' H 4.447 0.002 . 103 9 9 A H5'' H 4.034 0.000 2 104 9 9 A H8 H 7.982 0.003 1 105 9 9 A C1' C 91.755 0.000 . 106 9 9 A C2 C 154.126 0.000 1 107 9 9 A C8 C 139.894 0.000 1 108 9 9 A P P -3.696 0.000 1 stop_ save_