data_15157 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of the UGUU tetraloop of Duck Epsilon apical stem loop of the Hepatitis B virus ; _BMRB_accession_number 15157 _BMRB_flat_file_name bmr15157.str _Entry_type original _Submission_date 2007-03-08 _Accession_date 2007-03-08 _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 Girard F. C. . 2 Ottink O. M. . 3 Ampt K. A.M. . 4 Tessari M. . . 5 Wijmenga S. S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 27 "15N chemical shifts" 2 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-06-06 original author . stop_ _Original_release_date 2007-06-06 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17430968 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Girard F. C. . 2 Ottink O. M. . 3 Ampt K. A.M. . 4 Tessari M. . . 5 Wijmenga S. S. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 35 _Journal_issue 8 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2800 _Page_last 2811 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Duck HBV epsilon apical tetraloop' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label RNA $GCUGUUGU 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_GCUGUUGU _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common GCUGUUGU _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence GCUGUUGU loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 11 G 2 12 C 3 13 U 4 14 G 5 15 U 6 16 U 7 17 G 8 18 U 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 $GCUGUUGU . . . . . . 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 $GCUGUUGU 'chemical synthesis' . . . . . 'The Sequence of this RNA can be found in Duck Hepatitis B virus' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GCUGUUGU 1.2 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '1.0 mM 13C/15N/2H-U labeled RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, 95% H2O, 5% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GCUGUUGU 1 mM '[U-13C; U-15N; U-2H]' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details '1.2 mM RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GCUGUUGU 1.2 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details '1.0 mM 13C/15N/2H-U labeled RNA, 10mM Na phosphate buffer, pH 6.7, 0.1 mM EDTA, D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GCUGUUGU 1.0 mM '[U-13C; U-15N; U-2H]' 'sodium phosphate' 10 mM 'natural abundance' EDTA 0.1 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.851* loop_ _Vendor _Address _Electronic_address Brunger . . stop_ loop_ _Task refinement stop_ _Details 'Chemical shift refinement home written module was added' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_HMQC-15N/1H_3 _Saveframe_category NMR_applied_experiment _Experiment_name HMQC-15N/1H _Sample_label $sample_2 save_ save_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_3 save_ save_HMQC-13C/1H_5 _Saveframe_category NMR_applied_experiment _Experiment_name HMQC-13C/1H _Sample_label $sample_4 save_ save_2D_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_3 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' 10 . mM pH 6.7 . pH pressure 1 . atm temperature 278 . 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' 10 . mM pH 6.7 . pH pressure 1 . atm temperature 288 . K stop_ save_ save_sample_conditions_3 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 10 . mM pH 6.7 . pH pressure 1 . atm temperature 298 . 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 . indirect . . . 0.101329118 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 NOESY' HMQC-15N/1H 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 _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 11 1 G H1 H 11.22 0.005 1 2 12 2 C H41 H 8.173 0.005 1 3 12 2 C H42 H 7.051 0.005 1 4 13 3 U H3 H 10.93 0.005 1 5 13 3 U N3 N 157.7 0.08 1 6 17 7 G H1 H 13.3 0.005 1 7 18 8 U H3 H 12.26 0.005 1 8 18 8 U N3 N 158.7 0.08 1 stop_ save_ save_assigned_chem_shift_list_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label DQF-COSY '2D NOESY' stop_ loop_ _Sample_label $sample_3 stop_ _Sample_conditions_label $sample_conditions_3 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 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 11 1 G H8 H 7.705 0.005 1 2 11 1 G H1' H 5.748 0.005 1 3 12 2 C H5 H 5.253 0.005 1 4 12 2 C H6 H 7.541 0.005 1 5 12 2 C H1' H 5.582 0.005 1 6 13 3 U H5 H 5.606 0.005 1 7 13 3 U H6 H 7.609 0.005 1 8 13 3 U H1' H 5.510 0.005 1 9 14 4 G H8 H 7.709 0.005 1 10 14 4 G H1' H 5.521 0.005 1 11 15 5 U H5 H 5.776 0.005 1 12 15 5 U H6 H 7.664 0.005 1 13 15 5 U H1' H 5.864 0.005 1 14 16 6 U H5 H 5.853 0.005 1 15 16 6 U H6 H 7.813 0.005 1 16 16 6 U H1' H 5.845 0.005 1 17 17 7 G H8 H 7.669 0.005 1 18 17 7 G H1' H 5.715 0.005 1 19 18 8 U H5 H 5.521 0.005 1 20 18 8 U H6 H 7.718 0.005 1 21 18 8 U H1' H 5.771 0.005 1 stop_ save_