data_4614 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The G7(syn)-G4(anti) structure of r(GCAGGCGUGC)2 ; _BMRB_accession_number 4614 _BMRB_flat_file_name bmr4614.str _Entry_type original _Submission_date 2000-06-12 _Accession_date 2000-09-07 _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 Burkard Mark E. . 2 Turner Douglas H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 54 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2000-11-30 original author . stop_ _Original_release_date 2000-11-30 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 10995243 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Burkard Mark E. . 2 Turner Douglas H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 39 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11748 _Page_last 11762 _Year 2000 _Details . loop_ _Keyword 'base flipping' 'conformational exchange' 'GG mismatch' guanine-guanine 'syn glycosidic torsion' stop_ save_ ################################## # Molecular system description # ################################## save_r(GCAGGCGUGC)2 _Saveframe_category molecular_system _Mol_system_name 5'-r(*GP*CP*AP*GP*GP*CP*GP*UP*GP*C)-3' _Abbreviation_common r(5'GCAGGCGUGC3')2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'GCAGGCGUGC strand 1' $RNA 'GCAGGCGUGC strand 2' $RNA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'GCAGGCGUGC strand 1' 1 'GCAGGCGUGC strand 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 5'-r(*GP*CP*AP*GP*GP*CP*GP*UP*GP*C)-3' _Abbreviation_common 5'GCAGGCGUGC3' _Molecular_mass . _Mol_thiol_state 'not present' _Details 'Forms a self-complementary duplex with two single guanine-guanine base pairs' ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence GCAGGCGUGC loop_ _Residue_seq_code _Residue_label 1 G 2 C 3 A 4 G 5 G 6 C 7 G 8 U 9 G 10 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 _Details $RNA . . . . . . 'No natural source exists for this sequence' 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 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_D2O_sample _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA 3.0 mM . NaCl 80 mM . phosphate 10 mM . D2O 100 % . stop_ save_ save_H2O_sample _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA 1.0 mM . NaCl 80 mM . Na_phosphate 10 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 5.2 loop_ _Task 'data collection' stop_ _Details Varian save_ save_FELIX _Saveframe_category software _Name FELIX _Version 95.0 loop_ _Task 'data analysis' stop_ _Details Biosym save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 95.0 loop_ _Task 'structure solution' stop_ _Details Biosym save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 90 . mEq pH 7 0.2 pH temperature 310.15 0.3 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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_citation_label _Correction_value_citation_label HDO H 1 protons ppm 4.662 internal direct cylindrical internal parallel_to_Bo $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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $D2O_sample $H2O_sample stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'GCAGGCGUGC strand 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 . 1 G H8 H 7.990 0.02 1 2 . 1 G H1' H 5.680 0.02 1 3 . 1 G H2' H 4.730 0.02 1 4 . 1 G H3' H 4.540 0.02 1 5 . 1 G H4' H 4.310 0.02 1 6 . 2 C H5 H 5.310 0.02 1 7 . 2 C H6 H 7.860 0.02 1 8 . 2 C H1' H 5.600 0.02 1 9 . 2 C H2' H 4.490 0.02 1 10 . 2 C H3' H 4.610 0.02 1 11 . 2 C H4' H 4.190 0.02 1 12 . 3 A H2 H 7.100 0.02 1 13 . 3 A H8 H 8.000 0.02 1 14 . 3 A H1' H 5.950 0.02 1 15 . 3 A H2' H 4.890 0.02 1 16 . 3 A H3' H 4.760 0.02 1 17 . 3 A H4' H 4.480 0.02 1 18 . 4 G H8 H 7.450 0.02 1 19 . 4 G H1' H 5.800 0.02 1 20 . 4 G H2' H 4.470 0.02 1 21 . 4 G H3' H 4.500 0.02 1 22 . 4 G H4' H 4.390 0.02 1 23 . 5 G H8 H 7.120 0.02 1 24 . 5 G H1' H 5.787 0.02 1 25 . 5 G H2' H 4.570 0.02 1 26 . 5 G H3' H 4.420 0.02 1 27 . 5 G H4' H 4.470 0.02 1 28 . 6 C H5 H 5.130 0.02 1 29 . 6 C H6 H 7.630 0.02 1 30 . 6 C H1' H 5.540 0.02 1 31 . 6 C H2' H 4.830 0.02 1 32 . 6 C H3' H 4.510 0.02 1 33 . 6 C H4' H 4.390 0.02 1 34 . 7 G H8 H 7.510 0.02 1 35 . 7 G H1' H 5.870 0.02 1 36 . 7 G H2' H 4.490 0.02 1 37 . 7 G H3' H 4.320 0.02 9 38 . 8 U H5 H 5.080 0.02 1 39 . 8 U H6 H 7.660 0.02 1 40 . 8 U H1' H 5.620 0.02 1 41 . 8 U H2' H 4.620 0.02 1 42 . 8 U H3' H 4.560 0.02 1 43 . 8 U H4' H 4.470 0.02 1 44 . 9 G H8 H 7.750 0.02 1 45 . 9 G H1' H 5.820 0.02 1 46 . 9 G H2' H 4.400 0.02 1 47 . 9 G H3' H 4.630 0.02 1 48 . 9 G H4' H 4.480 0.02 1 49 . 10 C H5 H 5.280 0.02 1 50 . 10 C H6 H 7.510 0.02 1 51 . 10 C H1' H 5.680 0.02 1 52 . 10 C H2' H 3.970 0.02 1 53 . 10 C H3' H 4.110 0.02 1 54 . 10 C H4' H 4.170 0.02 1 stop_ save_