data_16980 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RDC and RCSA refinement of an A-form RNA: Improvements in Major Groove Width ; _BMRB_accession_number 16980 _BMRB_flat_file_name bmr16980.str _Entry_type original _Submission_date 2010-06-07 _Accession_date 2010-06-07 _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 Tolbert Blanton S. . 2 Summers Michael F. . 3 Miyazaki Yasuyuki . . 4 Barton Shawn . . 5 Kinde Benyam . . 6 Stark Patrice . . 7 Singh Rashmi . . 8 Bax Ad . . 9 Case David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 77 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-26 original author . stop_ _Original_release_date 2010-07-26 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20549304 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tolbert Blanton S. . 2 Miyazaki Yasuyuki . . 3 Barton Shawn . . 4 Kinde Benyam . . 5 Starck Patrice . . 6 Singh Rashmi . . 7 Bax Ad . . 8 Case David A. . 9 Summers Michael F. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 47 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 205 _Page_last 219 _Year 2010 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3')_1' $RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') 'RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3')_2' $RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-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(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; GCGGUACUAGUUAGCUAACU AGCUUUGUA ; loop_ _Residue_seq_code _Residue_label 1 G 2 C 3 G 4 G 5 U 6 A 7 C 8 U 9 A 10 G 11 U 12 U 13 A 14 G 15 C 16 U 17 A 18 A 19 C 20 U 21 A 22 G 23 C 24 U 25 U 26 U 27 G 28 U 29 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 _ICTVdb_decimal_code _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') 'Murine leukemia virus' 00.061.1.02.001. 11786 . . Gammaretrovirus . 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 $RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') 'cell free synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_slb1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') . mM 0.25 1 'natural abundance' $RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') 0.25 mM . . '[U-100% 13C], [C-100% 13C]' $RNA_(5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') 0.25 mM . . '[G-100% 13C], [A-100% 13C]' 'sodium chloride' 150 mM . . 'natural abundance' TRIS 10 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 Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _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 $slb1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $slb1 save_ save_2D_1H-13C_HMQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC' _Sample_label $slb1 save_ save_2D_Tr_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D Tr 1H-13C HSQC' _Sample_label $slb1 save_ save_2D_Tr_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D Tr 1H-13C HSQC' _Sample_label $slb1 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' 0.15 . M pH 6.5 . pH pressure 1 . atm temperature 303 . 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 $entry_citation $entry_citation 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 $slb1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-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 1 277 1 G H1' H 5.87 . . 2 278 2 C H1' H 5.67 . . 3 278 2 C H5 H 5.59 . 1 4 278 2 C H6 H 7.72 . 1 5 279 3 G H1' H 5.79 . . 6 279 3 G H8 H 7.58 . 1 7 280 4 G H1' H 5.75 . . 8 280 4 G H8 H 7.25 . 1 9 281 5 U H1' H 5.64 . . 10 281 5 U H5 H 5.45 . 1 11 281 5 U H6 H 7.53 . 1 12 282 6 A H1' H 6.04 . . 13 282 6 A H2 H 8.04 . 1 14 282 6 A H8 H 8.27 . 1 15 283 7 C H1' H 5.15 . . 16 283 7 C H5 H 5.48 . 1 17 283 7 C H6 H 7.45 . 1 18 284 8 U H1' H 5.55 . . 19 284 8 U H5 H 5.43 . 1 20 284 8 U H6 H 7.89 . 1 21 285 9 A H1' H 6.01 . . 22 285 9 A H2 H 6.78 . 1 23 285 9 A H8 H 8.15 . 1 24 286 10 G H1' H 5.53 . . 25 286 10 G H8 H 7.18 . 1 26 287 11 U H1' H 5.51 . . 27 287 11 U H5 H 4.97 . 1 28 287 11 U H6 H 7.69 . 1 29 288 12 U H1' H 5.64 . . 30 288 12 U H5 H 5.59 . 1 31 288 12 U H6 H 7.97 . 1 32 289 13 A H1' H 5.95 . . 33 289 13 A H2 H 6.69 . 1 34 289 13 A H8 H 8.13 . 1 35 290 14 G H1' H 5.54 . . 36 290 14 G H8 H 7.24 . 1 37 291 15 C H1' H 5.45 . . 38 291 15 C H5 H 5.13 . 1 39 291 15 C H6 H 7.56 . 1 40 292 16 U H1' H 5.5 . . 41 292 16 U H5 H 5.4 . 1 42 292 16 U H6 H 7.85 . 1 43 293 17 A H1' H 5.91 . . 44 293 17 A H2 H 6.43 . 1 45 293 17 A H8 H 8.12 . 1 46 294 18 A H1' H 5.84 . . 47 294 18 A H2 H 7.62 . 1 48 294 18 A H8 H 7.86 . 1 49 295 19 C H1' H 5.31 . . 50 295 19 C H5 H 5.16 . 1 51 295 19 C H6 H 7.41 . 1 52 296 20 U H1' H 5.52 . . 53 296 20 U H5 H 5.35 . 1 54 296 20 U H6 H 7.82 . 1 55 297 21 A H1' H 5.97 . . 56 297 21 A H2 H 6.78 . 1 57 297 21 A H8 H 8.08 . 1 58 298 22 G H1' H 5.53 . . 59 298 22 G H8 H 7.09 . 1 60 299 23 C H1' H 5.59 . . 61 299 23 C H5 H 5.51 . 1 62 299 23 C H6 H 7.71 . 1 63 300 24 U H1' H 5.36 . . 64 300 24 U H5 H 5.76 . 1 65 300 24 U H6 H 7.9 . 1 66 301 25 U H5 H 5.75 . 1 67 301 25 U H6 H 7.81 . 1 68 302 26 U H1' H 5.71 . . 69 302 26 U H5 H 5.75 . 1 70 302 26 U H6 H 7.81 . 1 71 303 27 G H1' H 5.79 . . 72 303 27 G H8 H 7.91 . 1 73 304 28 U H1' H 5.64 . . 74 304 28 U H5 H 5.53 . 1 75 304 28 U H6 H 7.66 . 1 76 305 29 A H1' H 6.03 . . 77 305 29 A H8 H 8.29 . 1 stop_ save_