data_18699 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DIMERIC PIL-E G-QUADRUPLEX DNA FROM NEISSERIA GONORRHOEAE, N STRUCTURES ; _BMRB_accession_number 18699 _BMRB_flat_file_name bmr18699.str _Entry_type original _Submission_date 2012-08-31 _Accession_date 2012-08-31 _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. . . 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" 134 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 'DIMERIC PIL-E G-QUADRUPLEX DNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'di_PIL-E, chain 1' $di_PIL-E 'di_PIL-E, chain 2' $di_PIL-E 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_di_PIL-E _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*GP*GP _Molecular_mass 5122.327 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence GGGTGGGTTGGGTGGG loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DT 5 DG 6 DG 7 DG 8 DT 9 DT 10 DG 11 DG 12 DG 13 DT 14 DG 15 DG 16 DG 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 $di_PIL-E '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 $di_PIL-E 'chemical synthesis' . . . . n/a stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '100 mM NaCl, 5mM NaPi buffer, pH 6.8 at 25deg C' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $di_PIL-E . mM 0.3 3.5 'natural abundance' 'sodium chloride' 100 mM . . 'natural abundance' 'sodium phosphate' 5 mM . . 'natural abundance' D2O 10 % . . 'natural abundance' H2O 90 % . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '100 mM NaCl, 5mM NaPi, pH 6.8' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $di_PIL-E . mM 0.3 3.5 'natural abundance' D2O 100 % . . '[U-100% 2H]' 'sodium chloride' 100 mM . . 'natural abundance' 'sodium phosphate' 5 mM . . '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_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label $sample_1 save_ save_1H-15N_JRHMQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N JRHMQC' _Sample_label $sample_1 save_ save_1H-15N_HMBC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-15N HMBC' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_aromatic_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_2 save_ save_1H-31P_COSY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P COSY' _Sample_label $sample_2 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_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 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '1H-1H NOESY' '1H-15N HMBC' '2D 1H-1H NOESY' '2D 1H-1H TOCSY' 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 'di_PIL-E, chain 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 1 DG H1 H 11.58 . . 2 1 1 DG H1' H 6.032 . . 3 1 1 DG H2' H 2.477 . . 4 1 1 DG H2'' H 2.93 . . 5 1 1 DG H3' H 4.902 . . 6 1 1 DG H4' H 4.541 . . 7 1 1 DG H5' H 3.985 . 2 8 1 1 DG H5'' H 4.296 . 2 9 1 1 DG H8 H 7.818 . . 10 2 2 DG H1 H 11.39 . . 11 2 2 DG H1' H 6.014 . . 12 2 2 DG H2' H 2.761 . . 13 2 2 DG H2'' H 2.638 . . 14 2 2 DG H3' H 5.036 . . 15 2 2 DG H4' H 4.542 . . 16 2 2 DG H8 H 7.626 . . 17 3 3 DG H1 H 10.75 . . 18 3 3 DG H1' H 6.372 . . 19 3 3 DG H2' H 2.481 . . 20 3 3 DG H2'' H 2.497 . . 21 3 3 DG H3' H 5.082 . . 22 3 3 DG H4' H 4.644 . . 23 3 3 DG H5' H 4.247 . 2 24 3 3 DG H5'' H 4.346 . 2 25 3 3 DG H8 H 7.788 . . 26 4 4 DT H1' H 6.53 . . 27 4 4 DT H2' H 2.477 . . 28 4 4 DT H2'' H 2.734 . . 29 4 4 DT H3' H 5.09 . . 30 4 4 DT H4' H 4.584 . . 31 4 4 DT H6 H 7.84 . . 32 4 4 DT H71 H 1.977 . . 33 4 4 DT H72 H 1.977 . . 34 4 4 DT H73 H 1.977 . . 35 5 5 DG H1 H 11.26 . . 36 5 5 DG H1' H 6.172 . . 37 5 5 DG H2' H 2.756 . . 38 5 5 DG H2'' H 2.142 . . 39 5 5 DG H3' H 5.151 . . 40 5 5 DG H4' H 4.524 . . 41 5 5 DG H5' H 4.24 . 2 42 5 5 DG H5'' H 4.331 . 2 43 5 5 DG H8 H 7.835 . . 44 6 6 DG H1 H 11.26 . . 45 6 6 DG H1' H 6.053 . . 46 6 6 DG H2' H 2.584 . . 47 6 6 DG H2'' H 2.732 . . 48 6 6 DG H3' H 5.033 . . 49 6 6 DG H4' H 4.52 . . 50 6 6 DG H8 H 7.725 . . 51 7 7 DG H1 H 11.05 . . 52 7 7 DG H1' H 6.128 . . 53 7 7 DG H2' H 2.418 . . 54 7 7 DG H2'' H 2.66 . . 55 7 7 DG H3' H 4.921 . . 56 7 7 DG H4' H 4.249 . . 57 7 7 DG H8 H 7.764 . . 58 8 8 DT H1' H 6.435 . . 59 8 8 DT H2' H 2.35 . . 60 8 8 DT H2'' H 2.585 . . 61 8 8 DT H3' H 4.656 . . 62 8 8 DT H4' H 4.427 . . 63 8 8 DT H5' H 4.015 . 2 64 8 8 DT H5'' H 4.155 . 2 65 8 8 DT H6 H 7.76 . . 66 8 8 DT H71 H 1.91 . . 67 8 8 DT H72 H 1.91 . . 68 8 8 DT H73 H 1.91 . . 69 9 9 DT H1' H 6.548 . . 70 9 9 DT H2' H 2.636 . . 71 9 9 DT H2'' H 2.718 . . 72 9 9 DT H3' H 5.007 . . 73 9 9 DT H4' H 4.472 . . 74 9 9 DT H5'' H 4.228 . 2 75 9 9 DT H6 H 7.82 . . 76 9 9 DT H71 H 2.043 . . 77 9 9 DT H72 H 2.043 . . 78 9 9 DT H73 H 2.043 . . 79 10 10 DG H1 H 11.58 . . 80 10 10 DG H1' H 6.115 . . 81 10 10 DG H2' H 2.715 . . 82 10 10 DG H2'' H 2.215 . . 83 10 10 DG H3' H 5.000 . . 84 10 10 DG H4' H 4.471 . . 85 10 10 DG H5' H 4.341 . 2 86 10 10 DG H5'' H 4.343 . 2 87 10 10 DG H8 H 7.759 . . 88 11 11 DG H1 H 11.96 . . 89 11 11 DG H1' H 6.099 . . 90 11 11 DG H2' H 2.947 . . 91 11 11 DG H2'' H 2.95 . . 92 11 11 DG H3' H 5.042 . . 93 11 11 DG H4' H 4.57 . . 94 11 11 DG H8 H 7.63 . . 95 12 12 DG H1 H 10.88 . . 96 12 12 DG H1' H 6.328 . . 97 12 12 DG H2' H 2.456 . . 98 12 12 DG H2'' H 2.695 . . 99 12 12 DG H3' H 5.106 . . 100 12 12 DG H4' H 4.564 . . 101 12 12 DG H8 H 7.801 . . 102 13 13 DT H1' H 6.507 . . 103 13 13 DT H2' H 2.488 . . 104 13 13 DT H2'' H 2.736 . . 105 13 13 DT H3' H 5.089 . . 106 13 13 DT H4' H 4.538 . . 107 13 13 DT H6 H 7.815 . . 108 13 13 DT H71 H 1.977 . . 109 13 13 DT H72 H 1.977 . . 110 13 13 DT H73 H 1.977 . . 111 14 14 DG H1 H 11.13 . . 112 14 14 DG H1' H 6.206 . . 113 14 14 DG H2' H 2.226 . . 114 14 14 DG H2'' H 2.78 . . 115 14 14 DG H3' H 5.134 . . 116 14 14 DG H4' H 4.55 . . 117 14 14 DG H5' H 4.33 . 2 118 14 14 DG H5'' H 4.31 . 2 119 14 14 DG H8 H 7.865 . . 120 15 15 DG H1' H 6.307 . . 121 15 15 DG H2' H 3.049 . . 122 15 15 DG H2'' H 2.833 . . 123 15 15 DG H3' H 5.122 . . 124 15 15 DG H4' H 4.608 . . 125 15 15 DG H5' H 4.24 . 2 126 15 15 DG H5'' H 4.415 . 2 127 15 15 DG H8 H 8.172 . . 128 16 16 DG H1 H 10.95 . . 129 16 16 DG H1' H 6.128 . . 130 16 16 DG H2' H 2.245 . . 131 16 16 DG H2'' H 2.408 . . 132 16 16 DG H3' H 4.667 . . 133 16 16 DG H4' H 4.255 . . 134 16 16 DG H8 H 7.563 . . stop_ save_