data_6307 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Solution Structure of d(G3T4G4)2 ; _BMRB_accession_number 6307 _BMRB_flat_file_name bmr6307.str _Entry_type new _Submission_date 2004-08-30 _Accession_date 2004-08-30 _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 Sket P. . . 2 Crnugelj M. . . 3 Plavec J. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 178 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2004-12-06 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; d(G3T4G4) forms unusual dimeric G-quadruplex structure with the same general fold in the presence of K+, Na+ or NH4+ ions ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15498650 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sket P. . . 2 Crnugelj M. . . 3 Plavec J. . . stop_ _Journal_abbreviation 'Bioorg. Med. Chem.' _Journal_volume 12 _Journal_issue 22 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5735 _Page_last 5744 _Year 2004 _Details . loop_ _Keyword G-quadruplex NMR 'monovalent cations' stop_ save_ ################################## # Molecular system description # ################################## save_system_d(g3t4g4)2 _Saveframe_category molecular_system _Mol_system_name 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3' _Abbreviation_common d(g3t4g4)2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3', chain 1' $d(G3T4G4)2 '5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3', chain 2' $d(G3T4G4)2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_d(G3T4G4)2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common G-quadruplex _Abbreviation_common G-quadruplex _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence GGGTTTTGGGG loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DG 4 DT 5 DT 6 DT 7 DT 8 DG 9 DG 10 DG 11 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 _Details $d(G3T4G4)2 . . unclassified . none none 'This sequence was made synthetically on DNA synthesizer.' 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 $d(G3T4G4)2 '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 _Isotopic_labeling $d(G3T4G4)2 4 mM . KCl 15 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1B loop_ _Task collection stop_ _Details Varian save_ save_FELIX _Saveframe_category software _Name FELIX _Version 2000 loop_ _Task processing stop_ _Details Accelerys save_ save_AMBER _Saveframe_category software _Name AMBER _Version 7 loop_ _Task refinement stop_ _Details 'Kollman, at all' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _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_PE-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name PE-COSY _Sample_label . save_ save_2D_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _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_3 _Saveframe_category NMR_applied_experiment _Experiment_name PE-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _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 pH 5.5 0.2 n/a temperature 278 0.5 K 'ionic strength' 15 . mM pressure 1 . atm stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.5 0.2 n/a temperature 298 0.5 K 'ionic strength' 15 . mM pressure 1 . atm 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 TMSPA H 1 'methyl protons' ppm 0.00 internal direct spherical internal parallel 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3', 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 DG H1' H 6.003 0.02 1 2 . 1 DG H2' H 2.806 0.02 1 3 . 1 DG H2'' H 2.628 0.02 1 4 . 1 DG H3' H 4.998 0.02 1 5 . 1 DG H4' H 4.467 0.02 1 6 . 1 DG H8 H 7.376 0.02 1 7 . 1 DG H1 H 11.937 0.02 1 8 . 2 DG H1' H 5.954 0.02 1 9 . 2 DG H2' H 1.815 0.02 1 10 . 2 DG H2'' H 2.209 0.02 1 11 . 2 DG H3' H 4.947 0.02 1 12 . 2 DG H4' H 4.403 0.02 1 13 . 2 DG H8 H 7.601 0.02 1 14 . 2 DG H1 H 11.799 0.02 1 15 . 3 DG H1' H 5.656 0.02 1 16 . 3 DG H2' H 2.770 0.02 1 17 . 3 DG H2'' H 2.574 0.02 1 18 . 3 DG H3' H 5.001 0.02 1 19 . 3 DG H4' H 4.446 0.02 1 20 . 3 DG H8 H 8.075 0.02 1 21 . 4 DT H1' H 5.808 0.02 1 22 . 4 DT H2' H 2.031 0.02 1 23 . 4 DT H2'' H 2.181 0.02 1 24 . 4 DT H3' H 4.749 0.02 1 25 . 4 DT H4' H 3.992 0.02 1 26 . 4 DT H71 H 1.366 0.02 1 27 . 4 DT H72 H 1.366 0.02 1 28 . 4 DT H73 H 1.366 0.02 1 29 . 4 DT H6 H 7.354 0.02 1 30 . 5 DT H1' H 6.095 0.02 1 31 . 5 DT H2' H 2.112 0.02 1 32 . 5 DT H2'' H 2.418 0.02 1 33 . 5 DT H3' H 4.593 0.02 1 34 . 5 DT H4' H 4.178 0.02 1 35 . 5 DT H5' H 3.948 0.02 1 36 . 5 DT H5'' H 3.772 0.02 1 37 . 5 DT H71 H 1.804 0.02 1 38 . 5 DT H72 H 1.804 0.02 1 39 . 5 DT H73 H 1.804 0.02 1 40 . 5 DT H6 H 7.543 0.02 1 41 . 6 DT H1' H 5.844 0.02 1 42 . 6 DT H2' H 1.747 0.02 1 43 . 6 DT H2'' H 2.432 0.02 1 44 . 6 DT H3' H 4.646 0.02 1 45 . 6 DT H4' H 4.265 0.02 1 46 . 6 DT H5' H 4.091 0.02 1 47 . 6 DT H5'' H 4.014 0.02 1 48 . 6 DT H71 H 1.646 0.02 1 49 . 6 DT H72 H 1.646 0.02 1 50 . 6 DT H73 H 1.646 0.02 1 51 . 6 DT H6 H 7.206 0.02 1 52 . 7 DT H1' H 5.708 0.02 1 53 . 7 DT H2' H 1.927 0.02 1 54 . 7 DT H2'' H 2.365 0.02 1 55 . 7 DT H3' H 4.604 0.02 1 56 . 7 DT H4' H 4.056 0.02 1 57 . 7 DT H5' H 2.734 0.02 1 58 . 7 DT H71 H 1.875 0.02 1 59 . 7 DT H72 H 1.875 0.02 1 60 . 7 DT H73 H 1.875 0.02 1 61 . 7 DT H6 H 7.228 0.02 1 62 . 8 DG H1' H 6.054 0.02 1 63 . 8 DG H2' H 3.753 0.02 1 64 . 8 DG H2'' H 3.021 0.02 1 65 . 8 DG H3' H 4.930 0.02 1 66 . 8 DG H4' H 4.429 0.02 1 67 . 8 DG H8 H 7.429 0.02 1 68 . 8 DG H1 H 11.736 0.02 1 69 . 9 DG H1' H 6.004 0.02 1 70 . 9 DG H2' H 2.694 0.02 1 71 . 9 DG H2'' H 2.868 0.02 1 72 . 9 DG H3' H 5.105 0.02 1 73 . 9 DG H4' H 4.524 0.02 1 74 . 9 DG H8 H 8.174 0.02 1 75 . 9 DG H1 H 11.668 0.02 1 76 . 10 DG H1' H 6.078 0.02 1 77 . 10 DG H2' H 2.251 0.02 1 78 . 10 DG H2'' H 2.752 0.02 1 79 . 10 DG H3' H 5.017 0.02 1 80 . 10 DG H4' H 4.530 0.02 1 81 . 10 DG H8 H 7.453 0.02 1 82 . 10 DG H1 H 11.279 0.02 1 83 . 11 DG H1' H 6.001 0.02 1 84 . 11 DG H2' H 2.628 0.02 1 85 . 11 DG H2'' H 2.410 0.02 1 86 . 11 DG H3' H 4.756 0.02 1 87 . 11 DG H4' H 4.230 0.02 1 88 . 11 DG H8 H 7.910 0.02 1 stop_ save_ save_chemical_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3', chain 2' _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 5.970 0.02 1 2 . 1 DG H2' H 2.649 0.02 1 3 . 1 DG H2'' H 3.106 0.02 1 4 . 1 DG H3' H 4.971 0.02 1 5 . 1 DG H4' H 4.392 0.02 1 6 . 1 DG H8 H 7.283 0.02 1 7 . 1 DG H1 H 11.953 0.02 1 8 . 2 DG H1' H 5.996 0.02 1 9 . 2 DG H2' H 2.578 0.02 1 10 . 2 DG H2'' H 2.853 0.02 1 11 . 2 DG H3' H 5.111 0.02 1 12 . 2 DG H4' H 4.501 0.02 1 13 . 2 DG H8 H 8.052 0.02 1 14 . 2 DG H1 H 11.889 0.02 1 15 . 3 DG H1' H 6.239 0.02 1 16 . 3 DG H2' H 2.468 0.02 1 17 . 3 DG H2'' H 2.584 0.02 1 18 . 3 DG H3' H 5.043 0.02 1 19 . 3 DG H4' H 4.552 0.02 1 20 . 3 DG H5' H 4.388 0.02 1 21 . 3 DG H8 H 7.685 0.02 1 22 . 3 DG H1 H 11.638 0.02 1 23 . 4 DT H1' H 6.250 0.02 1 24 . 4 DT H2' H 2.315 0.02 1 25 . 4 DT H2'' H 2.486 0.02 1 26 . 4 DT H3' H 4.869 0.02 1 27 . 4 DT H4' H 4.316 0.02 1 28 . 4 DT H71 H 1.706 0.02 1 29 . 4 DT H72 H 1.706 0.02 1 30 . 4 DT H73 H 1.706 0.02 1 31 . 4 DT H6 H 7.639 0.02 1 32 . 5 DT H1' H 6.040 0.02 1 33 . 5 DT H2' H 2.188 0.02 1 34 . 5 DT H2'' H 2.317 0.02 1 35 . 5 DT H3' H 4.645 0.02 1 36 . 5 DT H4' H 4.134 0.02 1 37 . 5 DT H71 H 1.907 0.02 1 38 . 5 DT H72 H 1.907 0.02 1 39 . 5 DT H73 H 1.907 0.02 1 40 . 5 DT H6 H 7.641 0.02 1 41 . 6 DT H1' H 5.649 0.02 1 42 . 6 DT H2' H 1.793 0.02 1 43 . 6 DT H2'' H 2.177 0.02 1 44 . 6 DT H3' H 4.556 0.02 1 45 . 6 DT H4' H 3.777 0.02 1 46 . 6 DT H5' H 3.685 0.02 1 47 . 6 DT H5'' H 3.557 0.02 1 48 . 6 DT H71 H 1.576 0.02 1 49 . 6 DT H72 H 1.576 0.02 1 50 . 6 DT H73 H 1.576 0.02 1 51 . 6 DT H6 H 7.233 0.02 1 52 . 7 DT H1' H 5.436 0.02 1 53 . 7 DT H2' H 2.018 0.02 1 54 . 7 DT H2'' H 2.269 0.02 1 55 . 7 DT H3' H 4.681 0.02 1 56 . 7 DT H4' H 3.984 0.02 1 57 . 7 DT H5' H 3.741 0.02 1 58 . 7 DT H5'' H 3.679 0.02 1 59 . 7 DT H71 H 1.442 0.02 1 60 . 7 DT H72 H 1.442 0.02 1 61 . 7 DT H73 H 1.442 0.02 1 62 . 7 DT H6 H 7.119 0.02 1 63 . 8 DG H1' H 6.168 0.02 1 64 . 8 DG H2' H 2.633 0.02 1 65 . 8 DG H2'' H 2.879 0.02 1 66 . 8 DG H3' H 4.997 0.02 1 67 . 8 DG H4' H 4.453 0.02 1 68 . 8 DG H8 H 7.323 0.02 1 69 . 8 DG H1 H 11.182 0.02 1 70 . 9 DG H1' H 6.163 0.02 1 71 . 9 DG H2' H 3.050 0.02 1 72 . 9 DG H2'' H 2.768 0.02 1 73 . 9 DG H3' H 5.022 0.02 1 74 . 9 DG H4' H 4.182 0.02 1 75 . 9 DG H8 H 7.423 0.02 1 76 . 9 DG H1 H 11.551 0.02 1 77 . 10 DG H1' H 6.183 0.02 1 78 . 10 DG H2' H 3.019 0.02 1 79 . 10 DG H2'' H 2.644 0.02 1 80 . 10 DG H3' H 4.901 0.02 1 81 . 10 DG H4' H 4.429 0.02 1 82 . 10 DG H8 H 7.745 0.02 1 83 . 10 DG H1 H 11.702 0.02 1 84 . 11 DG H1' H 6.496 0.02 1 85 . 11 DG H2' H 2.674 0.02 1 86 . 11 DG H2'' H 2.570 0.02 1 87 . 11 DG H3' H 4.766 0.02 1 88 . 11 DG H4' H 4.472 0.02 1 89 . 11 DG H8 H 8.026 0.02 1 90 . 11 DG H1 H 11.458 0.02 1 stop_ save_