data_18690 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; MOMERIC PIL-E G-QUADRUPLEX DNA FROM NEISSERIA GONORRHOEAE ; _BMRB_accession_number 18690 _BMRB_flat_file_name bmr18690.str _Entry_type original _Submission_date 2012-08-30 _Accession_date 2012-08-30 _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 Kuryavyi V. V . 2 Patel D. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 188 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-18 update BMRB 'update entry citation' 2012-11-02 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title "RecA-binding pilE G4 sequence essential for pilin antigenic variation forms monomeric and 5' end-stacked dimeric parallel G-quadruplexes." _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23085077 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kuryavyi Vitaly . . 2 Cahoon Laty A. . 3 Seifert 'H. Steven' . . 4 Patel Dinshaw J. . stop_ _Journal_abbreviation Structure _Journal_name_full 'Structure (London, England : 1993)' _Journal_volume 20 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2090 _Page_last 2102 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'MOMERIC PIL-E G-QUADRUPLEX DNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'MOMERIC PIL-E G-QUADRUPLEX DNA' $5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP_*T)-3'_ 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_5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP_*T)-3'_ _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP_*T)-3'_ _Molecular_mass 6999.553 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; TAGGGTGGGTTGGGTGGGGA AT ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DA 3 DG 4 DG 5 DG 6 DT 7 DG 8 DG 9 DG 10 DT 11 DT 12 DG 13 DG 14 DG 15 DT 16 DG 17 DG 18 DG 19 DG 20 DA 21 DA 22 DT 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 $5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP_*T)-3'_ 'Neisseria Gonorrhoeae' 485 Bacteria . Neisseria Gonorrhoeae 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 $5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP_*T)-3'_ 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 100 mM KCl 5 mM KPi buffer pH 6.8 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP_*T)-3'_ 0.8-6.0 mM 'natural abundance' $5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP_*T)-3'_ 0.8 mM '[U-13C; U-15N]' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 5 mM 'natural abundance' D2O 90 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '100 mM KCl 5 mM KPi pH 6.8' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $5'-D(*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP_*T)-3'_ 0.8 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' 'potassium phosphate' 5 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % '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, SCHWIETERS, KUSZEWSKI, TJ' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_UNITY_Inova _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_BRUKER _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_1H-15N_JRHMQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N JRHMQC' _Sample_label $sample_1 save_ save_1H-15N_HMBC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N HMBC' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 6.8 . pH pressure 1 . atm 'ionic strength' 0.105 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_H2O _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 water H 1 protons ppm 4.75 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_H1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '1H-15N JRHMQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $H2O _Mol_system_component_name 'MOMERIC PIL-E G-QUADRUPLEX DNA' _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 DT H1' H 5.815 . . 2 1 1 DT H2' H 1.742 . . 3 1 1 DT H2'' H 2.128 . . 4 1 1 DT H3' H 4.459 . . 5 1 1 DT H4' H 3.903 . . 6 1 1 DT H5' H 3.460 . 2 7 1 1 DT H5'' H 3.606 . 2 8 1 1 DT H6 H 7.162 . . 9 1 1 DT H71 H 1.584 . . 10 1 1 DT H72 H 1.584 . . 11 1 1 DT H73 H 1.584 . . 12 2 2 DA H1' H 5.814 . . 13 2 2 DA H2 H 7.817 . . 14 2 2 DA H2' H 2.369 . . 15 2 2 DA H2'' H 2.596 . . 16 2 2 DA H3' H 4.815 . . 17 2 2 DA H4' H 4.036 . . 18 2 2 DA H5' H 3.607 . 2 19 2 2 DA H5'' H 3.853 . 2 20 2 2 DA H8 H 7.935 . . 21 3 3 DG H1 H 11.72 . . 22 3 3 DG H1' H 6.098 . . 23 3 3 DG H2' H 2.784 . . 24 3 3 DG H2'' H 3.041 . . 25 3 3 DG H3' H 4.996 . . 26 3 3 DG H4' H 4.254 . . 27 3 3 DG H5' H 4.021 . 2 28 3 3 DG H5'' H 4.111 . 2 29 3 3 DG H8 H 8.048 . . 30 4 4 DG H1 H 11.36 . . 31 4 4 DG H1' H 6.148 . . 32 4 4 DG H2' H 2.88 . . 33 4 4 DG H2'' H 2.588 . . 34 4 4 DG H3' H 4.994 . . 35 4 4 DG H4' H 4.532 . . 36 4 4 DG H8 H 7.645 . . 37 5 5 DG H1 H 10.97 . . 38 5 5 DG H1' H 6.404 . . 39 5 5 DG H2' H 2.605 . . 40 5 5 DG H2'' H 2.676 . . 41 5 5 DG H3' H 5.133 . . 42 5 5 DG H4' H 4.611 . . 43 5 5 DG H5' H 4.287 . 2 44 5 5 DG H5'' H 4.392 . 2 45 5 5 DG H8 H 7.574 . . 46 6 6 DT H1' H 6.442 . . 47 6 6 DT H2' H 2.602 . . 48 6 6 DT H2'' H 2.373 . . 49 6 6 DT H3' H 4.731 . . 50 6 6 DT H4' H 4.464 . . 51 6 6 DT H6 H 7.799 . . 52 6 6 DT H71 H 1.957 . . 53 6 6 DT H72 H 1.957 . . 54 6 6 DT H73 H 1.957 . . 55 7 7 DG H1 H 11.76 . . 56 7 7 DG H1' H 6.166 . . 57 7 7 DG H2' H 2.938 . . 58 7 7 DG H2'' H 2.461 . . 59 7 7 DG H3' H 5.13 . . 60 7 7 DG H4' H 4.475 . . 61 7 7 DG H5' H 4.342 . 2 62 7 7 DG H5'' H 4.342 . 2 63 7 7 DG H8 H 8.015 . . 64 8 8 DG H1 H 11.66 . . 65 8 8 DG H1' H 6.181 . . 66 8 8 DG H2' H 2.688 . . 67 8 8 DG H2'' H 2.815 . . 68 8 8 DG H3' H 5.071 . . 69 8 8 DG H4' H 4.536 . . 70 8 8 DG H8 H 7.907 . . 71 9 9 DG H1 H 11.39 . . 72 9 9 DG H1' H 6.277 . . 73 9 9 DG H2' H 2.811 . . 74 9 9 DG H2'' H 2.566 . . 75 9 9 DG H3' H 5.015 . . 76 9 9 DG H4' H 4.326 . . 77 9 9 DG H8 H 7.897 . . 78 10 10 DT H1' H 6.536 . . 79 10 10 DT H2' H 2.476 . . 80 10 10 DT H2'' H 2.679 . . 81 10 10 DT H3' H 5.131 . . 82 10 10 DT H4' H 4.613 . . 83 10 10 DT H6 H 7.856 . . 84 10 10 DT H71 H 1.985 . . 85 10 10 DT H72 H 1.985 . . 86 10 10 DT H73 H 1.985 . . 87 11 11 DT H1' H 6.594 . . 88 11 11 DT H2' H 2.651 . . 89 11 11 DT H2'' H 2.652 . . 90 11 11 DT H3' H 5.052 . . 91 11 11 DT H4' H 4.477 . . 92 11 11 DT H5' H 4.073 . 2 93 11 11 DT H5'' H 4.217 . 2 94 11 11 DT H6 H 7.854 . . 95 11 11 DT H71 H 2.051 . . 96 11 11 DT H72 H 2.051 . . 97 11 11 DT H73 H 2.051 . . 98 12 12 DG H1 H 12.04 . . 99 12 12 DG H1' H 6.203 . . 100 12 12 DG H2' H 2.581 . . 101 12 12 DG H2'' H 2.994 . . 102 12 12 DG H3' H 5.047 . . 103 12 12 DG H4' H 4.481 . . 104 12 12 DG H5' H 4.077 . 2 105 12 12 DG H5'' H 4.212 . 2 106 12 12 DG H8 H 8.089 . . 107 13 13 DG H1 H 11.26 . . 108 13 13 DG H1' H 6.234 . . 109 13 13 DG H2' H 2.709 . . 110 13 13 DG H2'' H 3.001 . . 111 13 13 DG H3' H 5.069 . . 112 13 13 DG H4' H 4.556 . . 113 13 13 DG H8 H 7.7 . . 114 14 14 DG H1 H 11.36 . . 115 14 14 DG H1' H 6.485 . . 116 14 14 DG H2' H 2.733 . . 117 14 14 DG H2'' H 2.614 . . 118 14 14 DG H3' H 5.153 . . 119 14 14 DG H4' H 4.476 . . 120 14 14 DG H8 H 7.825 . . 121 15 15 DT H1' H 6.526 . . 122 15 15 DT H2' H 2.679 . . 123 15 15 DT H2'' H 2.477 . . 124 15 15 DT H3' H 5.126 . . 125 15 15 DT H4' H 4.613 . . 126 15 15 DT H6 H 7.883 . . 127 15 15 DT H71 H 1.991 . . 128 15 15 DT H72 H 1.991 . . 129 15 15 DT H73 H 1.991 . . 130 16 16 DG H1 H 11.26 . . 131 16 16 DG H1' H 6.056 . . 132 16 16 DG H2' H 2.415 . . 133 16 16 DG H2'' H 2.827 . . 134 16 16 DG H3' H 5.117 . . 135 16 16 DG H4' H 4.345 . . 136 16 16 DG H5' H 4.476 . 2 137 16 16 DG H5'' H 4.264 . 2 138 16 16 DG H8 H 7.982 . . 139 17 17 DG H1 H 11.36 . . 140 17 17 DG H1' H 5.97 . . 141 17 17 DG H2' H 2.599 . . 142 17 17 DG H2'' H 2.712 . . 143 17 17 DG H3' H 5.062 . . 144 17 17 DG H4' H 4.49 . . 145 17 17 DG H8 H 7.912 . . 146 18 18 DG H1 H 10.91 . . 147 18 18 DG H1' H 5.892 . . 148 18 18 DG H2' H 2.029 . . 149 18 18 DG H2'' H 2.469 . . 150 18 18 DG H3' H 4.902 . . 151 18 18 DG H4' H 4.433 . . 152 18 18 DG H5' H 4.117 . 2 153 18 18 DG H5'' H 4.243 . 2 154 18 18 DG H8 H 7.316 . . 155 19 19 DG H1' H 5.232 . . 156 19 19 DG H2' H 2.358 . . 157 19 19 DG H2'' H 2.367 . . 158 19 19 DG H3' H 4.854 . . 159 19 19 DG H4' H 4.301 . . 160 19 19 DG H5' H 4.094 . . 161 19 19 DG H8 H 7.714 . . 162 20 20 DA H1' H 5.632 . . 163 20 20 DA H2 H 7.52 . . 164 20 20 DA H2' H 2.253 . . 165 20 20 DA H2'' H 2.371 . . 166 20 20 DA H3' H 4.704 . . 167 20 20 DA H4' H 3.961 . . 168 20 20 DA H8 H 7.914 . . 169 21 21 DA H1' H 5.843 . . 170 21 21 DA H2 H 7.62 . . 171 21 21 DA H2' H 2.464 . . 172 21 21 DA H2'' H 2.533 . . 173 21 21 DA H3' H 4.761 . . 174 21 21 DA H4' H 4.222 . . 175 21 21 DA H5' H 3.489 . 2 176 21 21 DA H5'' H 3.716 . 2 177 21 21 DA H8 H 7.892 . . 178 22 22 DT H1' H 5.86 . . 179 22 22 DT H2' H 2.073 . . 180 22 22 DT H2'' H 2.169 . . 181 22 22 DT H3' H 4.375 . . 182 22 22 DT H4' H 4.227 . . 183 22 22 DT H5' H 3.895 . 2 184 22 22 DT H5'' H 3.976 . 2 185 22 22 DT H6 H 7.261 . . 186 22 22 DT H71 H 1.54 . . 187 22 22 DT H72 H 1.54 . . 188 22 22 DT H73 H 1.54 . . stop_ save_