data_6009 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+ ; _BMRB_accession_number 6009 _BMRB_flat_file_name bmr6009.str _Entry_type original _Submission_date 2003-11-18 _Accession_date 2003-11-18 _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 Mao X. . . 2 Marky L. A. . 3 Gmeiner W. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 162 "31P chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2004-08-30 original author 'original release' 2010-07-16 update BMRB 'update DNA residue label to two-letter code' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15214802 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mao X. . . 2 Marky L. A. . 3 Gmeiner W. H. . stop_ _Journal_abbreviation 'J. Biomol. Struct. Dyn.' _Journal_volume 22 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 25 _Page_last 33 _Year 2004 _Details . loop_ _Keyword quadruplex Sr2+ 'thrombin-binding DNA' stop_ save_ ################################## # Molecular system description # ################################## save_system_TBA _Saveframe_category molecular_system _Mol_system_name 'Thrombin-binding DNA aptamer' _Abbreviation_common TBA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Thrombin-binding DNA aptamer' $TBA 'Strontium (II) ion' $SR stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'potential thrombin inhibitor' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_TBA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'thrombin binding 15mer DNA aptamer' _Abbreviation_common TBA _Molecular_mass 4600 _Mol_thiol_state 'not present' _Details 'The quadruplex conformation is stabilized by metal ions.' ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence GGTTGGTGTGGTTGG loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DT 4 DT 5 DG 6 DG 7 DT 8 DG 9 DT 10 DG 11 DG 12 DT 13 DT 14 DG 15 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_SR _Saveframe_category ligand _Mol_type non-polymer _Name_common "SR (STRONTIUM ION)" _BMRB_code . _PDB_code SR _Molecular_mass 87.620 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Jun 20 11:43:03 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons SR SR SR . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_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 $TBA . . . . . . 'Not available' 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 $TBA '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $TBA 1 mM . . . $SR . mM 1 1.3 . D2O 100 % . . . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $TBA 1 mM . . . $SR . mM 1 1.3 . H2O 90 % . . . D2O 10 % . . . stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Task refinement stop_ _Details 'Brunger, A.T.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_E-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label . save_ save_P31-H1_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'P31-H1 COSY' _Sample_label . save_ save_ROESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'P31-H1 COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _BMRB_pulse_sequence_accession_number . _Details . 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' 3 . mM pH 4.7 0.1 n/a pressure 1 . atm temperature 288 0.5 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details ; The chemical shifts of HDO referenced to TSP were first determined at different temperatures, and then HDO was used as reference for real samples. ; 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label HDO H 1 protons ppm 4.875 internal direct cylindrical internal parallel 1.0 $entry_citation $entry_citation H3PO4 P 31 phosphorus ppm . external indirect cylindrical external parallel 1.0 $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 $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'Thrombin-binding DNA aptamer' _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 DG H1 H 11.80 0.004 1 2 . 1 DG H21 H 9.89 0.004 1 3 . 1 DG H22 H 6.82 0.004 1 4 . 1 DG H8 H 7.57 0.004 1 5 . 1 DG H1' H 6.11 0.004 1 6 . 1 DG H2' H 2.96 0.004 1 7 . 1 DG H2'' H 3.07 0.004 1 8 . 1 DG H3' H 4.95 0.004 1 9 . 1 DG H4' H 4.20 0.004 1 10 . 1 DG H5' H 4.05 0.004 2 11 . 1 DG H5'' H 4.41 0.004 2 12 . 2 DG H1 H 12.29 0.004 1 13 . 2 DG H21 H 10.16 0.004 1 14 . 2 DG H22 H 7.07 0.004 1 15 . 2 DG H8 H 8.44 0.004 1 16 . 2 DG H1' H 6.03 0.004 1 17 . 2 DG H2' H 3.07 0.004 1 18 . 2 DG H2'' H 2.47 0.004 1 19 . 2 DG H3' H 5.16 0.004 1 20 . 2 DG H4' H 4.44 0.004 1 21 . 2 DG H5' H 4.28 0.004 2 22 . 2 DG H5'' H 4.30 0.004 2 23 . 2 DG P P -2.59 0.004 1 24 . 3 DT H6 H 7.88 0.004 1 25 . 3 DT H71 H 1.99 0.004 1 26 . 3 DT H72 H 1.99 0.004 1 27 . 3 DT H73 H 1.99 0.004 1 28 . 3 DT H1' H 6.12 0.004 1 29 . 3 DT H2' H 2.15 0.004 1 30 . 3 DT H2'' H 2.55 0.004 1 31 . 3 DT H3' H 4.84 0.004 1 32 . 3 DT H4' H 4.22 0.004 1 33 . 3 DT H5' H 3.99 0.004 2 34 . 3 DT H5'' H 4.18 0.004 2 35 . 3 DT P P -0.81 0.004 1 36 . 4 DT H6 H 7.09 0.004 1 37 . 4 DT H71 H 1.99 0.004 1 38 . 4 DT H72 H 1.99 0.004 1 39 . 4 DT H73 H 1.99 0.004 1 40 . 4 DT H1' H 6.12 0.004 1 41 . 4 DT H2' H 2.15 0.004 1 42 . 4 DT H2'' H 2.55 0.004 1 43 . 4 DT H3' H 4.87 0.004 1 44 . 4 DT H4' H 4.24 0.004 1 45 . 4 DT H5' H 3.87 0.004 2 46 . 4 DT H5'' H 4.15 0.004 2 47 . 4 DT P P -1.44 0.004 1 48 . 5 DG H1 H 11.65 0.004 1 49 . 5 DG H21 H 9.87 0.004 1 50 . 5 DG H22 H 7.21 0.004 1 51 . 5 DG H8 H 7.55 0.004 1 52 . 5 DG H1' H 6.07 0.004 1 53 . 5 DG H2' H 3.27 0.004 1 54 . 5 DG H2'' H 2.89 0.004 1 55 . 5 DG H3' H 4.84 0.004 1 56 . 5 DG H4' H 4.44 0.004 1 57 . 5 DG H5' H 4.26 0.004 2 58 . 5 DG H5'' H 4.35 0.004 2 59 . 5 DG P P -1.61 0.004 1 60 . 6 DG H1 H 12.01 0.004 1 61 . 6 DG H21 H 10.48 0.004 1 62 . 6 DG H22 H 7.05 0.004 1 63 . 6 DG H8 H 7.72 0.004 1 64 . 6 DG H1' H 5.98 0.004 1 65 . 6 DG H2' H 2.81 0.004 1 66 . 6 DG H2'' H 2.61 0.004 1 67 . 6 DG H3' H 5.13 0.004 1 68 . 6 DG H4' H 4.48 0.004 1 69 . 6 DG H5' H 4.26 0.004 2 70 . 6 DG H5'' H 4.34 0.004 2 71 . 6 DG P P -2.64 0.004 1 72 . 7 DT H6 H 7.95 0.004 1 73 . 7 DT H71 H 1.97 0.004 1 74 . 7 DT H72 H 1.97 0.004 1 75 . 7 DT H73 H 1.97 0.004 1 76 . 7 DT H1' H 6.49 0.004 1 77 . 7 DT H2' H 2.53 0.004 1 78 . 7 DT H2'' H 2.61 0.004 1 79 . 7 DT H3' H 4.88 0.004 1 80 . 7 DT H4' H 4.43 0.004 1 81 . 7 DT H5' H 4.20 0.004 2 82 . 7 DT H5'' H 4.31 0.004 2 83 . 7 DT P P -1.44 0.004 1 84 . 8 DG H8 H 7.54 0.004 1 85 . 8 DG H1' H 5.73 0.004 1 86 . 8 DG H2' H 1.96 0.004 1 87 . 8 DG H2'' H 2.28 0.004 1 88 . 8 DG H3' H 4.83 0.004 1 89 . 8 DG H4' H 3.83 0.004 1 90 . 8 DG H5' H 3.96 0.004 2 91 . 8 DG H5'' H 4.13 0.004 2 92 . 8 DG P P -2.08 0.004 1 93 . 9 DT H6 H 7.22 0.004 1 94 . 9 DT H71 H 1.90 0.004 1 95 . 9 DT H72 H 1.90 0.004 1 96 . 9 DT H73 H 1.90 0.004 1 97 . 9 DT H1' H 5.72 0.004 1 98 . 9 DT H2' H 2.03 0.004 1 99 . 9 DT H2'' H 2.49 0.004 1 100 . 9 DT H3' H 4.65 0.004 1 101 . 9 DT H4' H 3.87 0.004 1 102 . 9 DT H5' H 2.97 0.004 2 103 . 9 DT H5'' H 3.61 0.004 2 104 . 9 DT P P -2.19 0.004 1 105 . 10 DG H1 H 11.68 0.004 1 106 . 10 DG H21 H 9.78 0.004 1 107 . 10 DG H22 H 7.15 0.004 1 108 . 10 DG H8 H 7.65 0.004 1 109 . 10 DG H1' H 6.12 0.004 1 110 . 10 DG H2' H 3.71 0.004 1 111 . 10 DG H2'' H 2.94 0.004 1 112 . 10 DG H3' H 4.91 0.004 1 113 . 10 DG H4' H 4.46 0.004 1 114 . 10 DG H5' H 4.16 0.004 2 115 . 10 DG H5'' H 4.30 0.004 2 116 . 10 DG P P -3.14 0.004 1 117 . 11 DG H1 H 12.22 0.004 1 118 . 11 DG H21 H 10.19 0.004 1 119 . 11 DG H22 H 7.08 0.004 1 120 . 11 DG H8 H 8.44 0.004 1 121 . 11 DG H1' H 6.02 0.004 1 122 . 11 DG H2' H 3.03 0.004 1 123 . 11 DG H2'' H 2.40 0.004 1 124 . 11 DG H3' H 5.16 0.004 1 125 . 11 DG H4' H 4.42 0.004 1 126 . 11 DG H5' H 4.31 0.004 2 127 . 11 DG H5'' H 4.33 0.004 2 128 . 11 DG P P -2.78 0.004 1 129 . 12 DT H6 H 7.88 0.004 1 130 . 12 DT H71 H 1.99 0.004 1 131 . 12 DT H72 H 1.99 0.004 1 132 . 12 DT H73 H 1.99 0.004 1 133 . 12 DT H1' H 6.11 0.004 1 134 . 12 DT H2' H 2.14 0.004 1 135 . 12 DT H2'' H 2.54 0.004 1 136 . 12 DT H3' H 4.85 0.004 1 137 . 12 DT H4' H 4.23 0.004 1 138 . 12 DT H5' H 4.20 0.004 2 139 . 12 DT H5'' H 4.32 0.004 2 140 . 12 DT P P -0.74 0.004 1 141 . 13 DT H6 H 7.19 0.004 1 142 . 13 DT H71 H 0.65 0.004 1 143 . 13 DT H72 H 0.65 0.004 1 144 . 13 DT H73 H 0.65 0.004 1 145 . 13 DT H1' H 6.03 0.004 1 146 . 13 DT H2' H 2.10 0.004 1 147 . 13 DT H2'' H 2.66 0.004 1 148 . 13 DT H3' H 4.89 0.004 1 149 . 13 DT H4' H 4.19 0.004 1 150 . 13 DT H5' H 3.88 0.004 2 151 . 13 DT H5'' H 4.21 0.004 2 152 . 13 DT P P -1.42 0.004 1 153 . 14 DG H1 H 11.52 0.004 1 154 . 14 DG H21 H 10.13 0.004 1 155 . 14 DG H22 H 7.33 0.004 1 156 . 14 DG H8 H 7.56 0.004 1 157 . 14 DG H1' H 6.09 0.004 1 158 . 14 DG H2' H 3.37 0.004 1 159 . 14 DG H2'' H 2.95 0.004 1 160 . 14 DG H3' H 4.90 0.004 1 161 . 14 DG H4' H 4.34 0.004 1 162 . 14 DG H5' H 3.88 0.004 2 163 . 14 DG H5'' H 4.47 0.004 2 164 . 14 DG P P -1.66 0.004 1 165 . 15 DG H1 H 12.23 0.004 1 166 . 15 DG H21 H 9.89 0.004 1 167 . 15 DG H22 H 7.10 0.004 1 168 . 15 DG H8 H 8.22 0.004 1 169 . 15 DG H1' H 6.20 0.004 1 170 . 15 DG H2' H 2.67 0.004 1 171 . 15 DG H2'' H 2.47 0.004 1 172 . 15 DG H3' H 4.80 0.004 1 173 . 15 DG H4' H 4.25 0.004 1 174 . 15 DG H5' H 4.19 0.004 2 175 . 15 DG H5'' H 4.34 0.004 2 176 . 15 DG P P -2.37 0.004 1 stop_ save_