data_17697 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of a dimeric all-parallel-stranded G-quadruplex stacked via the 5'-to-5' interface ; _BMRB_accession_number 17697 _BMRB_flat_file_name bmr17697.str _Entry_type original _Submission_date 2011-06-10 _Accession_date 2011-06-10 _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 Do 'Ngoc Quang' . . 2 Lim 'Kah Wai' . . 3 Teo 'Ming Hoon' . . 4 Heddi Brahim . . 5 Phan 'Anh Tuan' . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 127 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-02-17 update BMRB 'update entry citation' 2011-08-19 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 21840903 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Do 'Ngoc Quang' . . 2 Lim 'Kah Wai' . . 3 Teo 'Ming Hoon' . . 4 Heddi Brahim . . 5 Phan 'Anh Tuan' . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 39 _Journal_issue 21 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9448 _Page_last 9457 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name G-quadruplex _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label G-quadruplex_strand_1 $G-quadruplex G-quadruplex_strand_2 $G-quadruplex 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_G-quadruplex _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(*GP*IP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')_ _Molecular_mass 5107.312 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence GXGTGGGTGGGTGGGT loop_ _Residue_seq_code _Residue_label 1 DG 2 DI 3 DG 4 DT 5 DG 6 DG 7 DG 8 DT 9 DG 10 DG 11 DG 12 DT 13 DG 14 DG 15 DG 16 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DI _Saveframe_category polymer_residue _Mol_type 'DNA linking' _Name_common 2'-DEOXYINOSINE-5'-MONOPHOSPHATE _BMRB_code . _PDB_code DI _Standard_residue_derivative . _Molecular_mass 332.207 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 23 10:38:58 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OP3 OP3 O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING OP3 P ? ? SING OP3 HOP3 ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING N1 C2 ? ? SING N1 H1 ? ? DOUB C2 N3 ? ? SING C2 H2 ? ? SING N3 C4 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $G-quadruplex . . . . . . 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 $G-quadruplex '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 $G-quadruplex . mM 0.5 2.0 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' 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 $G-quadruplex . mM 0.5 2.0 'natural abundance' D2O 100 % . . 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $G-quadruplex . mM 0.5 2.0 '[U-2% 15N; U-2% 13C]' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ save_sample_4 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $G-quadruplex . mM 0.5 2.0 '[U-100% 2H]' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version 2007 loop_ _Vendor _Address _Electronic_address 'Felix NMR, Inc.' . . stop_ loop_ _Task 'peak picking' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.27 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 10 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_JR_HMBC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C JR HMBC' _Sample_label $sample_1 save_ save_2D_1H-1H_JR_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H JR NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_H-D_exchange_7 _Saveframe_category NMR_applied_experiment _Experiment_name 'H-D exchange' _Sample_label $sample_2 save_ save_15N-filtered_8 _Saveframe_category NMR_applied_experiment _Experiment_name 15N-filtered _Sample_label $sample_3 save_ save_D-labeled_9 _Saveframe_category NMR_applied_experiment _Experiment_name D-labeled _Sample_label $sample_4 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 7 . pH pressure 1 . atm 'ionic strength' 90 . mM 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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 '2D 1H-13C JR HMBC' '2D 1H-1H JR NOESY' '2D 1H-1H NOESY' '2D 1H-1H COSY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' 15N-filtered D-labeled stop_ loop_ _Sample_label $sample_1 $sample_2 $sample_3 $sample_4 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name G-quadruplex_strand_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 1 DG H1 H 11.131 0.010 1 2 1 1 DG H1' H 6.081 0.010 1 3 1 1 DG H2' H 2.266 0.010 1 4 1 1 DG H2'' H 2.811 0.010 1 5 1 1 DG H3' H 4.874 0.010 1 6 1 1 DG H4' H 4.367 0.010 1 7 1 1 DG H5' H 3.948 0.010 1 8 1 1 DG H5'' H 3.948 0.010 1 9 1 1 DG H8 H 7.886 0.010 1 10 2 2 DI H1 H 13.859 0.010 1 11 2 2 DI H1' H 6.437 0.010 1 12 2 2 DI H2 H 7.719 0.010 1 13 2 2 DI H2' H 2.791 0.010 1 14 2 2 DI H2'' H 3.180 0.010 1 15 2 2 DI H3' H 5.103 0.010 1 16 2 2 DI H4' H 4.658 0.010 1 17 2 2 DI H8 H 8.246 0.010 1 18 3 3 DG H1 H 11.210 0.010 1 19 3 3 DG H1' H 6.203 0.010 1 20 3 3 DG H2' H 2.517 0.010 1 21 3 3 DG H2'' H 2.400 0.010 1 22 3 3 DG H3' H 5.106 0.010 1 23 3 3 DG H4' H 4.467 0.010 1 24 3 3 DG H8 H 7.591 0.010 1 25 4 4 DT H1' H 6.556 0.010 1 26 4 4 DT H2' H 2.518 0.010 1 27 4 4 DT H2'' H 2.742 0.010 1 28 4 4 DT H3' H 5.080 0.010 1 29 4 4 DT H4' H 4.620 0.010 1 30 4 4 DT H6 H 7.878 0.010 1 31 4 4 DT H71 H 1.991 0.010 1 32 4 4 DT H72 H 1.991 0.010 1 33 4 4 DT H73 H 1.991 0.010 1 34 5 5 DG H1 H 11.182 0.010 1 35 5 5 DG H1' H 6.218 0.010 1 36 5 5 DG H2' H 2.528 0.010 1 37 5 5 DG H2'' H 2.851 0.010 1 38 5 5 DG H3' H 5.180 0.010 1 39 5 5 DG H4' H 4.518 0.010 1 40 5 5 DG H8 H 7.898 0.010 1 41 6 6 DG H1 H 11.336 0.010 1 42 6 6 DG H1' H 6.054 0.010 1 43 6 6 DG H2' H 2.614 0.010 1 44 6 6 DG H2'' H 2.798 0.010 1 45 6 6 DG H3' H 5.056 0.010 1 46 6 6 DG H4' H 4.536 0.010 1 47 6 6 DG H8 H 7.693 0.010 1 48 7 7 DG H1 H 11.123 0.010 1 49 7 7 DG H1' H 6.391 0.010 1 50 7 7 DG H2' H 2.664 0.010 1 51 7 7 DG H2'' H 2.528 0.010 1 52 7 7 DG H3' H 5.097 0.010 1 53 7 7 DG H4' H 4.634 0.010 1 54 7 7 DG H8 H 7.756 0.010 1 55 8 8 DT H1' H 6.541 0.010 1 56 8 8 DT H2' H 2.493 0.010 1 57 8 8 DT H2'' H 2.732 0.010 1 58 8 8 DT H3' H 5.106 0.010 1 59 8 8 DT H4' H 4.579 0.010 1 60 8 8 DT H6 H 7.844 0.010 1 61 8 8 DT H71 H 1.990 0.010 1 62 8 8 DT H72 H 1.990 0.010 1 63 8 8 DT H73 H 1.990 0.010 1 64 9 9 DG H1 H 11.281 0.010 1 65 9 9 DG H1' H 6.209 0.010 1 66 9 9 DG H2' H 2.164 0.010 1 67 9 9 DG H2'' H 2.790 0.010 1 68 9 9 DG H3' H 5.169 0.010 1 69 9 9 DG H4' H 4.552 0.010 1 70 9 9 DG H8 H 7.853 0.010 1 71 10 10 DG H1 H 11.182 0.010 1 72 10 10 DG H1' H 6.093 0.010 1 73 10 10 DG H2' H 2.573 0.010 1 74 10 10 DG H2'' H 2.904 0.010 1 75 10 10 DG H3' H 5.064 0.010 1 76 10 10 DG H4' H 4.565 0.010 1 77 10 10 DG H8 H 7.752 0.010 1 78 11 11 DG H1 H 10.973 0.010 1 79 11 11 DG H1' H 6.395 0.010 1 80 11 11 DG H2' H 2.700 0.010 1 81 11 11 DG H2'' H 2.512 0.010 1 82 11 11 DG H3' H 5.108 0.010 1 83 11 11 DG H4' H 4.605 0.010 1 84 11 11 DG H8 H 7.769 0.010 1 85 12 12 DT H1' H 6.531 0.010 1 86 12 12 DT H2' H 2.502 0.010 1 87 12 12 DT H2'' H 2.736 0.010 1 88 12 12 DT H3' H 5.097 0.010 1 89 12 12 DT H4' H 4.548 0.010 1 90 12 12 DT H6 H 7.836 0.010 1 91 12 12 DT H71 H 1.986 0.010 1 92 12 12 DT H72 H 1.986 0.010 1 93 12 12 DT H73 H 1.986 0.010 1 94 13 13 DG H1 H 10.988 0.010 1 95 13 13 DG H1' H 6.250 0.010 1 96 13 13 DG H2' H 2.192 0.010 1 97 13 13 DG H2'' H 2.741 0.010 1 98 13 13 DG H3' H 5.159 0.010 1 99 13 13 DG H4' H 4.555 0.010 1 100 13 13 DG H8 H 7.856 0.010 1 101 14 14 DG H1 H 11.529 0.010 1 102 14 14 DG H1' H 5.985 0.010 1 103 14 14 DG H2' H 2.662 0.010 1 104 14 14 DG H2'' H 2.778 0.010 1 105 14 14 DG H3' H 5.066 0.010 1 106 14 14 DG H4' H 4.526 0.010 1 107 14 14 DG H8 H 7.740 0.010 1 108 15 15 DG H1 H 11.131 0.010 1 109 15 15 DG H1' H 6.135 0.010 1 110 15 15 DG H2' H 2.584 0.010 1 111 15 15 DG H2'' H 2.733 0.010 1 112 15 15 DG H3' H 4.938 0.010 1 113 15 15 DG H4' H 4.472 0.010 1 114 15 15 DG H5' H 4.286 0.010 1 115 15 15 DG H5'' H 4.201 0.010 1 116 15 15 DG H8 H 7.640 0.010 1 117 16 16 DT H1' H 5.871 0.010 1 118 16 16 DT H2' H 2.040 0.010 1 119 16 16 DT H2'' H 2.040 0.010 1 120 16 16 DT H3' H 4.405 0.010 1 121 16 16 DT H4' H 3.928 0.010 1 122 16 16 DT H5' H 4.245 0.010 1 123 16 16 DT H5'' H 4.041 0.010 1 124 16 16 DT H6 H 7.078 0.010 1 125 16 16 DT H71 H 1.477 0.010 1 126 16 16 DT H72 H 1.477 0.010 1 127 16 16 DT H73 H 1.477 0.010 1 stop_ save_