data_15858 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of the exon/intron binding site 1 (EBS1/IBS1) of the group II intron Sc.ai5(gamma) ; _BMRB_accession_number 15858 _BMRB_flat_file_name bmr15858.str _Entry_type new _Submission_date 2008-07-04 _Accession_date 2008-07-04 _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 Kruschel Daniela . . 2 Sigel Roland 'K. O.' . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 117 "13C chemical shifts" 36 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-10-12 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 15858 'NMR data related to NMR solution structure of the exon/intron binding site 1 (EBS1/IBS1) of the group II intron Sc.ai5(gamma)' 15857 'NMR data related to NMR solution structure of the d3'-hairpin including EBS1 and IBS1 of the group II intron Sc.ai5(gamma)' 15856 'NMR data related to NMR solution structure of the d3'-hairpin including EBS1 of the group II intron Sc.ai5(gamma)' 15859 'NMR data related to NMR solution structure of the d3'-stem closed by a GAAA tetraloop of the group II intron Sc.ai5(gamma)' 5962 'NMR data related to solution structure of domain 5 from the ai5(gamma) group II intron' 6756 'NMR data related to solution structure of domain 6 from the ai5(gamma)group II intron' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution structure of the 5'-splice site of a group II intron ribozyme' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kruschel Daniela . . 2 Sigel Roland 'K. O.' . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 29-MER _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (7A-MER)' $RNA_(7A-MER) 'RNA (7B-MER)' $RNA_(7B-MER) 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_(7A-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(7A-MER) _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence GGCACUG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 G 2 14 G 3 15 C 4 16 A 5 17 C 6 18 U 7 19 G stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_RNA_(7B-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(7B-MER) _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 7 _Mol_residue_sequence CAGUGUC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 59 C 2 60 A 3 61 G 4 62 U 5 63 G 6 64 U 7 65 C 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_(7A-MER) 'Baker's yeast' 4932 Eukaryota Fungi Saccharomyces cerevisiae $RNA_(7B-MER) 'Baker's yeast' 4932 Eukaryota Fungi Saccharomyces cerevisiae 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_(7A-MER) 'chemical synthesis' . . . . . $RNA_(7B-MER) 'chemical synthesis' . . . . . 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_(7A-MER) 0.8-0.9 mM 'natural abundance' $RNA_(7B-MER) 0.8-0.9 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' EDTA 10 uM 'natural abundance' D2O 100 % '[U-100% 2H]' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(7A-MER) 0.9 mM 'natural abundance' $RNA_(7B-MER) 0.9 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' EDTA 10 uM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % '[U-100% 2H]' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version '1.3, 2.0, 2.1' loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.1 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_CNSSOLVE _Saveframe_category software _Name CNSSOLVE _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.16 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details 'equipped with a CRYO TXI (1H; 13C; 15N) with an actively shielded z-gradient coil' 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-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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 temperature 288 . K pD 6.7 . pH pressure 1 . atm 'ionic strength' 100 . mM stop_ save_ save_sample_conditions_4 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 293 . K pD 6.7 . pH pressure 1 . atm 'ionic strength' 100 . mM stop_ save_ save_sample_conditions_5 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pD 6.7 . pH pressure 1 . atm 'ionic strength' 100 . mM stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278 . K pH 6.3 . pH pressure 1 . atm 'ionic strength' 100 . mM stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 288 . K pD 6.7 . pH pressure 1 . atm 'ionic strength' 100 . mM 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 C 13 'methyl protons' ppm 0.00 n/a 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (7A-MER)' _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 13 1 G H1 H 12.301 0.005 1 2 13 1 G H1' H 5.284 0.005 1 3 13 1 G H2' H 4.240 0.005 1 4 13 1 G H3' H 4.417 0.005 1 5 13 1 G H4' H 4.005 0.005 1 6 13 1 G H5' H 3.628 0.005 1 7 13 1 G H5'' H 3.710 0.005 1 8 13 1 G H8 H 7.667 0.005 1 9 13 1 G C8 C 137.41 0.05 1 10 14 2 G H1 H 11.393 0.005 1 11 14 2 G H1' H 5.645 0.005 1 12 14 2 G H2' H 4.457 0.005 1 13 14 2 G H3' H 4.389 0.005 1 14 14 2 G H4' H 4.283 0.005 1 15 14 2 G H8 H 7.232 0.005 1 16 14 2 G H21 H 7.521 0.005 1 17 14 2 G H22 H 6.053 0.005 1 18 14 2 G C1' C 90.05 0.05 1 19 14 2 G C8 C 134.17 0.05 1 20 15 3 C H1' H 5.278 0.005 1 21 15 3 C H2' H 4.206 0.005 1 22 15 3 C H3' H 4.403 0.005 1 23 15 3 C H4' H 4.373 0.005 1 24 15 3 C H5 H 5.308 0.005 1 25 15 3 C H5'' H 3.918 0.005 1 26 15 3 C H6 H 7.533 0.005 1 27 15 3 C H41 H 8.069 0.005 1 28 15 3 C H42 H 6.679 0.005 1 29 15 3 C C1' C 90.54 0.05 1 30 15 3 C C5 C 95.44 0.05 1 31 15 3 C C6 C 137.35 0.05 1 32 16 4 A H1' H 5.732 0.005 1 33 16 4 A H2 H 7.209 0.005 1 34 16 4 A H2' H 4.375 0.005 1 35 16 4 A H3' H 4.494 0.005 1 36 16 4 A H4' H 4.300 0.005 1 37 16 4 A H5'' H 3.942 0.005 1 38 16 4 A H8 H 7.840 0.005 1 39 16 4 A H61 H 7.705 0.005 1 40 16 4 A H62 H 6.056 0.005 1 41 16 4 A C1' C 90.08 0.05 1 42 16 4 A C2 C 150.58 0.05 1 43 16 4 A C8 C 136.41 0.05 1 44 17 5 C H1' H 5.205 0.005 1 45 17 5 C H2' H 4.022 0.005 1 46 17 5 C H3' H 4.194 0.005 1 47 17 5 C H4' H 4.178 0.005 1 48 17 5 C H5 H 5.035 0.005 1 49 17 5 C H5'' H 3.862 0.005 1 50 17 5 C H6 H 7.374 0.005 1 51 17 5 C H41 H 8.037 0.005 1 52 17 5 C H42 H 6.767 0.005 1 53 17 5 C C1' C 90.72 0.05 1 54 17 5 C C5 C 94.32 0.05 1 55 17 5 C C6 C 137.91 0.05 1 56 18 6 U H1' H 5.322 0.005 1 57 18 6 U H2' H 4.191 0.005 1 58 18 6 U H3 H 13.569 0.005 1 59 18 6 U H3' H 4.347 0.005 1 60 18 6 U H4' H 4.336 0.005 1 61 18 6 U H5 H 5.153 0.005 1 62 18 6 U H5'' H 3.860 0.005 1 63 18 6 U H6 H 7.606 0.005 1 64 18 6 U C1' C 90.69 0.05 1 65 18 6 U C5 C 101.02 0.05 1 66 18 6 U C6 C 138.54 0.05 1 67 19 7 G H1 H 12.222 0.005 1 68 19 7 G H1' H 5.677 0.005 1 69 19 7 G H2' H 3.865 0.005 1 70 19 7 G H3' H 4.122 0.005 1 71 19 7 G H4' H 4.049 0.005 1 72 19 7 G H8 H 7.509 0.005 1 73 19 7 G C1' C 88.3 0.05 1 74 19 7 G C8 C 134.81 0.05 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (7B-MER)' _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 59 1 C H1' H 5.231 0.005 1 2 59 1 C H2' H 4.349 0.005 1 3 59 1 C H3' H 4.094 0.005 1 4 59 1 C H4' H 4.368 0.005 1 5 59 1 C H5 H 5.762 0.005 1 6 59 1 C H5' H 3.813 0.005 1 7 59 1 C H5'' H 3.712 0.005 1 8 59 1 C H6 H 7.869 0.005 1 9 59 1 C H41 H 8.038 0.005 1 10 59 1 C H42 H 6.896 0.005 1 11 59 1 C C1' C 90.74 0.05 1 12 59 1 C C5 C 95.09 0.05 1 13 59 1 C C6 C 141.71 0.05 1 14 60 2 A H1' H 5.793 0.005 1 15 60 2 A H2 H 7.041 0.005 1 16 60 2 A H2' H 4.582 0.005 1 17 60 2 A H3' H 4.290 0.005 1 18 60 2 A H4' H 4.341 0.005 1 19 60 2 A H5'' H 4.018 0.005 1 20 60 2 A H8 H 8.013 0.005 1 21 60 2 A H62 H 6.183 0.005 1 22 60 2 A C1' C 90.02 0.05 1 23 60 2 A C2 C 150.03 0.05 1 24 60 2 A C8 C 138.03 0.05 1 25 61 3 G H1 H 13.141 0.005 1 26 61 3 G H1' H 5.399 0.005 1 27 61 3 G H2' H 4.167 0.005 1 28 61 3 G H3' H 4.265 0.005 1 29 61 3 G H4' H 4.252 0.005 1 30 61 3 G H5'' H 3.908 0.005 1 31 61 3 G H8 H 7.075 0.005 1 32 61 3 G H21 H 8.069 0.005 1 33 61 3 G H22 H 5.934 0.005 1 34 61 3 G C1' C 90.07 0.05 1 35 61 3 G C8 C 133.64 0.05 1 36 62 4 U H1' H 5.315 0.005 1 37 62 4 U H2' H 4.469 0.005 1 38 62 4 U H3 H 13.366 0.005 1 39 62 4 U H3' H 4.329 0.005 1 40 62 4 U H4' H 4.229 0.005 1 41 62 4 U H5 H 4.858 0.005 1 42 62 4 U H5'' H 3.880 0.005 1 43 62 4 U H6 H 7.474 0.005 1 44 62 4 U C1' C 90.46 0.05 1 45 62 4 U C5 C 100.51 0.05 1 46 62 4 U C6 C 138.14 0.05 1 47 63 5 G H1 H 12.472 0.005 1 48 63 5 G H1' H 5.590 0.005 1 49 63 5 G H2' H 4.449 0.005 1 50 63 5 G H3' H 4.249 0.005 1 51 63 5 G H4' H 4.300 0.005 1 52 63 5 G H5' H 3.928 0.005 1 53 63 5 G H5'' H 3.871 0.005 1 54 63 5 G H8 H 7.419 0.005 1 55 63 5 G H21 H 7.587 0.005 1 56 63 5 G H22 H 5.792 0.005 1 57 63 5 G C1' C 87.97 0.05 1 58 63 5 G C8 C 133.14 0.05 1 59 64 6 U H1' H 5.640 0.005 1 60 64 6 U H2' H 3.900 0.005 1 61 64 6 U H3 H 11.992 0.005 1 62 64 6 U H3' H 4.009 0.005 1 63 64 6 U H4' H 3.809 0.005 1 64 64 6 U H5 H 5.227 0.005 1 65 64 6 U H6 H 7.626 0.005 1 66 64 6 U C1' C 91.02 0.05 1 67 64 6 U C5 C 101.47 0.05 1 68 64 6 U C6 C 137.88 0.05 1 69 65 7 C H1' H 5.512 0.005 1 70 65 7 C H2' H 4.338 0.005 1 71 65 7 C H3' H 4.323 0.005 1 72 65 7 C H4' H 3.865 0.005 1 73 65 7 C H5 H 5.477 0.005 1 74 65 7 C H6 H 7.627 0.005 1 75 65 7 C H41 H 8.038 0.005 1 76 65 7 C H42 H 6.741 0.005 1 77 65 7 C C1' C 90.23 0.05 1 78 65 7 C C5 C 94.74 0.05 1 79 65 7 C C6 C 140.08 0.05 1 stop_ save_