data_5737 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the parallel-stranded DNA quadruplex d(TTAGGGA)4 containing the human telomeric repeat: evidence for A-tetrad formation from NMR and molecular dynamics simulation. ; _BMRB_accession_number 5737 _BMRB_flat_file_name bmr5737.str _Entry_type new _Submission_date 2003-03-14 _Accession_date 2003-03-14 _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 Gavathiotis E. . . 2 Searle M. S. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 63 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2003-09-15 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of the Parallel-stranded DNA Quadruplex d(TTAGGGT)4 Containing the Human Telomeric Repeat: Evidence for A-tetrad Formation from NMR and Molecular Dynamics Simulations ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22807851 _PubMed_ID 12926351 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gavathiotis E. . . 2 Searle M. S. . stop_ _Journal_abbreviation 'Org. Biomol. Chem.' _Journal_name_full 'Organic and Biomolecular Chemistry' _Journal_volume 1 _Journal_issue 10 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1650 _Page_last 1656 _Year 2003 _Details . loop_ _Keyword 'PARALLEL-STRANDED QUADRUPLEX DNA' 'TTAGGGT REPEAT' A-TETRAD stop_ save_ ################################## # Molecular system description # ################################## save_system_QUADRUPLEX _Saveframe_category molecular_system _Mol_system_name 5'-D(*TP*TP*AP*GP*GP*GP*T)-3' _Abbreviation_common 5'-D(*TP*TP*AP*GP*GP*GP*T)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'TTAGGGT chain A' $TTAGGGT 'TTAGGGT chain B' $TTAGGGT 'TTAGGGT chain C' $TTAGGGT 'TTAGGGT chain D' $TTAGGGT stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state tetramer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'TTAGGGT chain A' 1 'TTAGGGT chain B' 1 'TTAGGGT chain C' 1 'TTAGGGT chain D' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_TTAGGGT _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*TP*TP*AP*GP*GP*GP*T)-3' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence TTAGGGT loop_ _Residue_seq_code _Residue_label 1 DT 2 DT 3 DA 4 DG 5 DG 6 DG 7 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 $TTAGGGT . . . . . . 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 $TTAGGGT . . . . . . 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 $TTAGGGT 6.4 mM . KCl 100 mM . K2HPO4 10 mM . EDTA 0.1 mM . NaN3 0.1 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 2.6 loop_ _Task collection processing stop_ _Details . save_ save_ANSIG _Saveframe_category software _Name ANSIG _Version v3.3 loop_ _Task 'data analysis' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 6 loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _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_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _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 DQF-COSY _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 7.0 . n/a temperature 298 . K 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 . H 1 . ppm . . . . . . 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 'TTAGGGT chain A' _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 DT H1' H 6 . 1 2 . 1 DT H2' H 2.1 . 1 3 . 1 DT H2'' H 2.34 . 1 4 . 1 DT H3' H 4.64 . 1 5 . 1 DT H4' H 4 . 1 6 . 1 DT H5' H 3.65 . 1 7 . 1 DT H6 H 7.41 . 1 8 . 1 DT H71 H 1.67 . 1 9 . 1 DT H72 H 1.67 . 1 10 . 1 DT H73 H 1.67 . 1 11 . 2 DT H1' H 6.25 . 1 12 . 2 DT H2' H 2.06 . 1 13 . 2 DT H2'' H 2.34 . 1 14 . 2 DT H3' H 4.74 . 1 15 . 2 DT H4' H 4.06 . 1 16 . 2 DT H5' H 3.93 . 1 17 . 2 DT H6 H 7.33 . 1 18 . 2 DT H71 H 1.78 . 1 19 . 2 DT H72 H 1.78 . 1 20 . 2 DT H73 H 1.78 . 1 21 . 3 DA H1' H 6.28 . 1 22 . 3 DA H2' H 2.86 . 1 23 . 3 DA H2'' H 2.92 . 1 24 . 3 DA H3' H 5.1 . 1 25 . 3 DA H4' H 4.44 . 1 26 . 3 DA H5' H 4.16 . 1 27 . 3 DA H5'' H 4.10 . 1 28 . 3 DA H8 H 8.43 . 1 29 . 3 DA H2 H 8.09 . 1 30 . 4 DG H1' H 6.01 . 1 31 . 4 DG H2' H 2.67 . 1 32 . 4 DG H2'' H 2.91 . 1 33 . 4 DG H3' H 5.05 . 1 34 . 4 DG H4' H 4.49 . 1 35 . 4 DG H5' H 4.27 . 1 36 . 4 DG H8 H 7.95 . 1 37 . 4 DG H1 H 11.2 . 1 38 . 5 DG H1' H 6.03 . 1 39 . 5 DG H2' H 2.66 . 1 40 . 5 DG H2'' H 2.74 . 1 41 . 5 DG H3' H 5.04 . 1 42 . 5 DG H4' H 4.51 . 1 43 . 5 DG H5' H 4.3 . 1 44 . 5 DG H8 H 7.79 . 1 45 . 5 DG H1 H 11.4 . 1 46 . 6 DG H1' H 6.27 . 1 47 . 6 DG H2' H 2.57 . 1 48 . 6 DG H2'' H 2.7 . 1 49 . 6 DG H3' H 4.91 . 1 50 . 6 DG H4' H 4.52 . 1 51 . 6 DG H5' H 4.27 . 1 52 . 6 DG H8 H 7.7 . 1 53 . 6 DG H1 H 11.8 . 1 54 . 7 DT H1' H 6.07 . 1 55 . 7 DT H2' H 2.17 . 1 56 . 7 DT H2'' H 2.19 . 1 57 . 7 DT H3' H 4.49 . 1 58 . 7 DT H4' H 4.23 . 1 59 . 7 DT H5' H 4.07 . 1 60 . 7 DT H6 H 7.36 . 1 61 . 7 DT H71 H 1.63 . 1 62 . 7 DT H72 H 1.63 . 1 63 . 7 DT H73 H 1.63 . 1 stop_ save_