data_10014 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignments of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus ; _BMRB_accession_number 10014 _BMRB_flat_file_name bmr10014.str _Entry_type original _Submission_date 2005-12-02 _Accession_date 2005-12-02 _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 Okada Kiyoshi . . 2 Takahashi Mari . . 3 Sakamoto Taiichi . . 4 Nakamura Kouji . . 5 Kanai Akio . . 6 Kawai Gota . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 64 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2006-11-21 original author . stop_ _Original_release_date 2006-11-21 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 16838833 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Okada Kiyoshi . . 2 Takahashi Mari . . 3 Sakamoto Taiichi . . 4 Kawai Gota . . 5 Nakamura Kouji . . 6 Kanai Akio . . stop_ _Journal_abbreviation 'Nucleos. Nucleot. Nucl.' _Journal_name_full 'Nucleosides, Nucleotides & Nucleic Acids' _Journal_volume 25 _Journal_issue 4-6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 383 _Page_last 395 _Year 2006 _Details . loop_ _Keyword 'GNRR motif' SRP tetraloop stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'helix6 in SRP RNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'helix6 in SRP RNA' $SRP_RNA_fragment stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state 'RNA single strand' _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SRP_RNA_fragment _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common pfHE6-12 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GGCUGAAGGGCC loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 U 5 G 6 A 7 A 8 G 9 G 10 G 11 C 12 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 _Strain _Fraction $SRP_RNA_fragment 'Pyrococcus furiosus' 186497 Archaea Euryarchaeota Pyrococcus 'Pyrococcus furiosus' DSM3638 no 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 $SRP_RNA_fragment 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_he6_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SRP_RNA_fragment 2.0 mM . 'sodium chloride' 50 mM . 'phosphate buffer Na' 20 mM . stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name xwinnmr _Version 2.6 _Details . save_ save_software_2 _Saveframe_category software _Name FELIX _Version 97.0 _Details . save_ save_software_3 _Saveframe_category software _Name DISCOVER _Version 97.0 _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $he6_1 save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $he6_1 save_ save_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HSQC' _Sample_label $he6_1 save_ save_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $he6_1 save_ save_NOESY _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_TOCSY _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_1H-13C_HSQC _Saveframe_category NMR_applied_experiment _Experiment_name '1H-13C HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_DQF-COSY _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 0.1 pH temperature 283 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_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 0.0 internal direct . . . 1.0 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_pfhe6 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NOESY TOCSY '1H-13C HSQC' DQF-COSY stop_ loop_ _Sample_label $he6_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $reference_1 _Mol_system_component_name 'helix6 in SRP RNA' _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 12.41 0.02 1 2 1 1 G H8 H 7.79 0.02 1 3 1 1 G H1' H 5.67 0.02 1 4 1 1 G H2' H 4.86 0.02 1 5 1 1 G H3' H 4.57 0.02 1 6 1 1 G H4' H 4.27 0.02 1 7 2 2 G H1 H 13.34 0.02 1 8 2 2 G H8 H 7.41 0.02 1 9 2 2 G H1' H 5.97 0.02 1 10 2 2 G H2' H 4.64 0.02 1 11 2 2 G H3' H 4.74 0.02 1 12 3 3 C H5 H 5.29 0.02 1 13 3 3 C H6 H 7.53 0.02 1 14 3 3 C H1' H 5.66 0.02 1 15 3 3 C H2' H 4.66 0.02 1 16 3 3 C H3' H 4.55 0.02 1 17 4 4 U H3 H 11.69 0.02 1 18 4 4 U H5 H 5.81 0.02 1 19 4 4 U H6 H 7.72 0.02 1 20 4 4 U H1' H 5.76 0.02 1 21 4 4 U H2' H 4.40 0.02 1 22 4 4 U H3' H 4.51 0.02 1 23 5 5 G H1 H 9.99 0.02 1 24 5 5 G H21 H 6.17 0.02 2 25 5 5 G H22 H 6.17 0.02 2 26 5 5 G H8 H 7.63 0.02 1 27 5 5 G H1' H 5.89 0.02 1 28 5 5 G H2' H 4.69 0.02 1 29 5 5 G H3' H 4.86 0.02 1 30 6 6 A H2 H 7.75 0.02 1 31 6 6 A H8 H 8.23 0.02 1 32 6 6 A H1' H 5.79 0.02 1 33 6 6 A H2' H 4.69 0.02 1 34 6 6 A H3' H 4.79 0.02 1 35 6 6 A H5' H 4.06 0.02 2 36 6 6 A H5'' H 4.06 0.02 2 37 7 7 A H8 H 7.95 0.02 1 38 7 7 A H1' H 5.83 0.02 1 39 7 7 A H2' H 4.54 0.02 1 40 7 7 A H3' H 4.85 0.02 1 41 7 7 A H5' H 4.06 0.02 2 42 7 7 A H5'' H 4.06 0.02 2 43 8 8 G H8 H 7.49 0.02 1 44 8 8 G H1' H 6.14 0.02 1 45 8 8 G H2' H 4.63 0.02 1 46 8 8 G H3' H 4.97 0.02 1 47 9 9 G H1 H 10.63 0.02 1 48 9 9 G H8 H 7.94 0.02 1 49 9 9 G H2' H 4.40 0.02 1 50 9 9 G H3' H 4.47 0.02 1 51 10 10 G H1 H 13.40 0.02 1 52 10 10 G H8 H 7.35 0.02 1 53 10 10 G H1' H 5.90 0.02 1 54 10 10 G H2' H 4.61 0.02 1 55 11 11 C H5 H 5.39 0.02 1 56 11 11 C H6 H 7.61 0.02 1 57 11 11 C H1' H 5.67 0.02 1 58 11 11 C H2' H 4.45 0.02 1 59 11 11 C H3' H 4.57 0.02 1 60 12 12 C H5 H 5.71 0.02 1 61 12 12 C H6 H 7.62 0.02 1 62 12 12 C H1' H 5.83 0.02 1 63 12 12 C H2' H 4.22 0.02 1 64 12 12 C H3' H 4.17 0.02 1 stop_ save_