data_4250 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the 3' hairpin of the TYMV pseudoknot: Preformation in RNA folding ; _BMRB_accession_number 4250 _BMRB_flat_file_name bmr4250.str _Entry_type original _Submission_date 1998-10-15 _Accession_date 1998-10-15 _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 Kolk M. H. . 2 'van der Graaf' M. . . 3 Fransen C. T.M. . 4 Wijmenga S. S. . 5 Pleij C. W.A. . 6 Heus H. A. . 7 Hilbers C. W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 149 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-02-25 original author . stop_ _Original_release_date 2000-02-25 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title "Structure of the 3' hairpin of the TYMV pseudoknot: Preformation in RNA folding" _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 9857204 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kolk M. H. . 2 'van der Graaf' M. . . 3 Fransen C. T.M. . 4 Wijmenga S. S. . 5 Pleij C. W.A. . 6 Heus H. A. . 7 Hilbers C. W. . stop_ _Journal_abbreviation 'EMBO J.' _Journal_volume 17 _Journal_issue 24 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 7498 _Page_last 7504 _Year 1998 _Details . loop_ _Keyword pseudoknot 'Ribonucleic acid' RNA TYMV stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_one _Saveframe_category citation _Citation_full ; Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J., Oldfield, E., Markley, J. L., and Sykes, B. D. J. Biomol. NMR 6, 135-140 (1995). ; _Citation_title '1H, 13C and 15N chemical shift referencing in biomolecular NMR.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8589602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wishart 'D S' S. . 2 Bigam 'C G' G. . 3 Yao J . . 4 Abildgaard F . . 5 Dyson 'H J' J. . 6 Oldfield E . . 7 Markley 'J L' L. . 8 Sykes 'B D' D. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 2 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 135 _Page_last 140 _Year 1995 _Details ; A considerable degree of variability exists in the way that 1H, 13C and 15N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common 1H, 13C and 15N chemical shift standards, now used in biomolecular NMR, to those proposed here. ; save_ save_citation_two _Saveframe_category citation _Citation_full 'Delaglio, F. et al. J.Biomol.NMR 6, 277-293 (1994).' _Citation_title 'NMRPipe: a multidimensional spectral processing system based on UNIX pipes.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8520220 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Delaglio F . . 2 Grzesiek S . . 3 Vuister 'G W' W. . 4 Zhu G . . 5 Pfeifer J . . 6 Bax A . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 3 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 277 _Page_last 293 _Year 1995 _Details ; The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks. ; save_ save_citation_three _Saveframe_category citation _Citation_full 'Garrett, D.S. J.Magn.Reson. 95, 214-220 (1991).' _Citation_title . _Citation_status . _Citation_type . _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? _Journal_abbreviation . _Journal_name_full . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_system_TYMV-RNA _Saveframe_category molecular_system _Mol_system_name "3' hairpin of TYMV pseudoknot" _Abbreviation_common TYMV-RNA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label TYMV-RNA $TYMV-RNA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'Involved in the nucleotide excision repair' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_TYMV-RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common "3' hairpin of TYMV pseudoknot" _Abbreviation_common TYMV _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 23 _Mol_residue_sequence ; GGUUCCGAGGGUCAUCGGAA CCA ; loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 U 4 U 5 C 6 C 7 G 8 A 9 G 10 G 11 G 12 U 13 C 14 A 15 U 16 C 17 G 18 G 19 A 20 A 21 C 22 C 23 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 $TYMV-RNA TYMV 12154 viruses . Tymovirus 'Turnip yellow mosaic virus' 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 $TYMV-RNA 'enzymatic semisynthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $TYMV-RNA 3.5 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AM _Field_strength 400 _Details . save_ save_NMR_spectrometer_two _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_one save_ save_DQF_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'DQF COSY' _Sample_label $sample_one save_ save_{31P-1H}_HETCOR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '{31P-1H} HETCOR' _Sample_label $sample_one save_ save_{13C-1H}_HMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '{13C-1H} HMQC' _Sample_label $sample_one save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'DQF COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '{31P-1H} HETCOR' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '{13C-1H} HMQC' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 6.8 0.1 n/a temperature 295 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 TSP H 1 'methyl protons' ppm 0.00 external direct spherical external_to_the_sample parallel_to_Bo 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_chemical_shifts_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name TYMV-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 G H8 H 8.20 0.02 1 2 . 1 G H1' H 5.95 0.02 1 3 . 1 G H2' H 4.93 0.02 1 4 . 1 G H3' H 4.71 0.02 1 5 . 1 G H4' H 4.58 0.02 1 6 . 1 G H1 H 12.18 0.02 1 7 . 2 G H8 H 7.42 0.02 1 8 . 2 G H1' H 5.83 0.02 1 9 . 2 G H2' H 4.54 0.02 1 10 . 2 G H3' H 4.18 0.02 1 11 . 2 G H4' H 4.55 0.02 1 12 . 2 G H1 H 13.24 0.02 1 13 . 3 U H6 H 7.79 0.02 1 14 . 3 U H5 H 5.13 0.02 1 15 . 3 U H1' H 5.60 0.02 1 16 . 3 U H2' H 4.53 0.02 1 17 . 3 U H3' H 4.48 0.02 1 18 . 3 U H4' H 4.11 0.02 1 19 . 3 U H3 H 14.41 0.02 1 20 . 4 U H6 H 8.00 0.02 1 21 . 4 U H5 H 5.62 0.02 1 22 . 4 U H1' H 5.67 0.02 1 23 . 4 U H2' H 4.53 0.02 1 24 . 4 U H3' H 4.49 0.02 1 25 . 4 U H4' H 4.45 0.02 1 26 . 4 U H3 H 13.89 0.02 1 27 . 5 C H6 H 7.84 0.02 1 28 . 5 C H5 H 5.67 0.02 1 29 . 5 C H1' H 5.51 0.02 1 30 . 5 C H2' H 4.31 0.02 1 31 . 5 C H3' H 4.45 0.02 1 32 . 5 C H4' H 4.10 0.02 1 33 . 5 C H41 H 8.41 0.02 1 34 . 5 C H42 H 7.00 0.02 1 35 . 6 C H6 H 7.70 0.02 1 36 . 6 C H5 H 5.46 0.02 1 37 . 6 C H1' H 5.41 0.02 1 38 . 6 C H2' H 4.50 0.02 1 39 . 6 C H3' H 4.40 0.02 1 40 . 6 C H4' H 4.37 0.02 1 41 . 6 C H41 H 8.29 0.02 1 42 . 6 C H42 H 6.74 0.02 1 43 . 7 G H8 H 7.51 0.02 1 44 . 7 G H1' H 5.65 0.02 1 45 . 7 G H2' H 4.60 0.02 1 46 . 7 G H3' H 4.47 0.02 1 47 . 7 G H4' H 4.46 0.02 1 48 . 7 G H1 H 11.89 0.02 1 49 . 8 A H8 H 7.60 0.02 1 50 . 8 A H2 H 7.64 0.02 1 51 . 8 A H1' H 5.90 0.02 1 52 . 8 A H2' H 4.63 0.02 1 53 . 8 A H3' H 4.55 0.02 1 54 . 8 A H4' H 4.48 0.02 1 55 . 9 G H8 H 7.09 0.02 1 56 . 9 G H1' H 5.23 0.02 1 57 . 9 G H2' H 4.41 0.02 1 58 . 9 G H3' H 4.38 0.02 1 59 . 9 G H4' H 4.36 0.02 1 60 . 9 G H1 H 11.15 0.02 1 61 . 9 G H21 H 6.64 0.02 1 62 . 9 G H22 H 6.64 0.02 1 63 . 10 G H8 H 7.38 0.02 1 64 . 10 G H1' H 5.22 0.02 1 65 . 10 G H2' H 4.38 0.02 1 66 . 10 G H3' H 4.50 0.02 1 67 . 10 G H4' H 4.12 0.02 1 68 . 10 G H1 H 10.59 0.02 1 69 . 11 G H8 H 7.76 0.02 1 70 . 11 G H1' H 5.65 0.02 1 71 . 11 G H2' H 4.83 0.02 1 72 . 11 G H3' H 4.66 0.02 1 73 . 11 G H4' H 4.38 0.02 1 74 . 12 U H6 H 7.78 0.02 1 75 . 12 U H5 H 5.80 0.02 1 76 . 12 U H1' H 5.92 0.02 1 77 . 12 U H2' H 4.38 0.02 1 78 . 12 U H3' H 4.61 0.02 1 79 . 13 C H6 H 7.76 0.02 1 80 . 13 C H5 H 5.99 0.02 1 81 . 13 C H1' H 5.92 0.02 1 82 . 13 C H2' H 4.41 0.02 1 83 . 13 C H3' H 4.61 0.02 1 84 . 14 A H8 H 8.40 0.02 1 85 . 14 A H2 H 8.33 0.02 1 86 . 14 A H1' H 6.17 0.02 1 87 . 14 A H2' H 4.85 0.02 1 88 . 14 A H3' H 4.80 0.02 1 89 . 14 A H4' H 4.67 0.02 1 90 . 15 U H6 H 7.96 0.02 1 91 . 15 U H5 H 5.81 0.02 1 92 . 15 U H1' H 5.35 0.02 1 93 . 15 U H2' H 4.51 0.02 1 94 . 15 U H3' H 4.05 0.02 1 95 . 15 U H4' H 4.44 0.02 1 96 . 15 U H3 H 14.15 0.02 1 97 . 16 C H6 H 7.86 0.02 1 98 . 16 C H5 H 5.70 0.02 1 99 . 16 C H1' H 5.61 0.02 1 100 . 16 C H2' H 4.56 0.02 1 101 . 16 C H3' H 4.44 0.02 1 102 . 16 C H4' H 4.46 0.02 1 103 . 16 C H41 H 8.25 0.02 1 104 . 16 C H42 H 8.25 0.02 1 105 . 17 G H8 H 7.51 0.02 1 106 . 17 G H1' H 5.67 0.02 1 107 . 17 G H2' H 4.61 0.02 1 108 . 17 G H3' H 4.53 0.02 1 109 . 17 G H1 H 12.16 0.02 1 110 . 18 G H8 H 7.17 0.02 1 111 . 18 G H1' H 5.67 0.02 1 112 . 18 G H2' H 4.56 0.02 1 113 . 18 G H3' H 4.51 0.02 1 114 . 18 G H4' H 4.47 0.02 1 115 . 18 G H1 H 12.39 0.02 1 116 . 19 A H8 H 7.68 0.02 1 117 . 19 A H2 H 7.10 0.02 1 118 . 19 A H1' H 5.88 0.02 1 119 . 19 A H2' H 4.56 0.02 1 120 . 19 A H3' H 4.66 0.02 1 121 . 19 A H4' H 4.50 0.02 1 122 . 20 A H8 H 7.82 0.02 1 123 . 20 A H2 H 7.80 0.02 1 124 . 20 A H1' H 5.92 0.02 1 125 . 20 A H2' H 4.46 0.02 1 126 . 20 A H3' H 4.59 0.02 1 127 . 20 A H4' H 4.41 0.02 1 128 . 21 C H6 H 7.47 0.02 1 129 . 21 C H5 H 5.16 0.02 1 130 . 21 C H1' H 5.39 0.02 1 131 . 21 C H2' H 4.22 0.02 1 132 . 21 C H3' H 4.34 0.02 1 133 . 21 C H4' H 4.36 0.02 1 134 . 21 C H41 H 8.40 0.02 1 135 . 21 C H42 H 8.40 0.02 1 136 . 22 C H6 H 7.60 0.02 1 137 . 22 C H5 H 5.40 0.02 1 138 . 22 C H1' H 5.49 0.02 1 139 . 22 C H2' H 4.41 0.02 1 140 . 22 C H3' H 4.38 0.02 1 141 . 22 C H4' H 4.47 0.02 1 142 . 22 C H41 H 8.21 0.02 1 143 . 22 C H42 H 8.21 0.02 1 144 . 23 A H8 H 8.03 0.02 1 145 . 23 A H2 H 7.36 0.02 1 146 . 23 A H1' H 5.98 0.02 1 147 . 23 A H2' H 4.05 0.02 1 148 . 23 A H3' H 4.30 0.02 1 149 . 23 A H4' H 4.25 0.02 1 stop_ save_