data_4244 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Solution Structure of [d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2] ; _BMRB_accession_number 4244 _BMRB_flat_file_name bmr4244.str _Entry_type original _Submission_date 1998-10-14 _Accession_date 1998-10-14 _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 Aramini J. M. . 2 Mujeeb A. . . 3 Germann M. W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 94 "31P chemical shifts" 9 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-08-09 update BMRB 'update non-standard residue saveframe' 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 2000-03-02 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 4235 'DNA decamer' stop_ _Original_release_date 1998-10-14 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Aramini J. M., Mujeeb A., and Germann M. W., "NMR Solution Structures of [d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2] and its Unmodified Control," Nucleic Acids Res. 26, 5644-5654 (1998). ; _Citation_title ; NMR Solution Structures of [d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2] and its Unmodified Control ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 99058075 _PubMed_ID 9837995 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Aramini J. M. . 2 Mujeeb A. . . 3 Germann M. W. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 26 _Journal_issue 24 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5644 _Page_last 5654 _Year 1998 _Details . loop_ _Keyword DNA 'alpha anomeric' 'polarity reversals' stop_ save_ ################################## # Molecular system description # ################################## save_system_alphaT_decamer_duplex _Saveframe_category molecular_system _Mol_system_name 'alphaT decamer duplex' _Abbreviation_common 'alphaT decamer duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'alphaT strand-A' $alphaT_decamer_DNA 'alphaT strand-B' $alphaT_decamer_DNA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'alphaT strand-A' 1 'alphaT strand-B' stop_ _Database_query_date . _Details ; self-complementary DNA duplex: each strand contains 1 alpha anomeric T flanked by 3'-3' and 5'-5' phosphodiester linkages ; save_ ######################## # Monomeric polymers # ######################## save_alphaT_decamer_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'alphaT decamer DNA' _Abbreviation_common 'alphaT decamer DNA' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; GCGAATXCGC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DA 6 DT 7 ATD 8 DC 9 DG 10 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ATD _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common THYMIDINE-3'-PHOSPHATE _BMRB_code ATD _PDB_code ATD _Standard_residue_derivative . _Molecular_mass 322.208 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 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 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? C5 C5 C . 0 . ? C5M C5M C . 0 . ? C6 C6 C . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? HO'5 HO'5 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H1' H1' H . 0 . ? H3 H3 H . 0 . ? H71 H71 H . 0 . ? H72 H72 H . 0 . ? H73 H73 H . 0 . ? H6 H6 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 DOUB P OP1 ? ? SING P OP2 ? ? SING P OP3 ? ? SING P O3' ? ? SING OP2 HOP2 ? ? SING OP3 HOP3 ? ? SING O5' C5' ? ? SING O5' HO'5 ? ? 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 C2' C1' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING N3 C4 ? ? SING N3 H3 ? ? DOUB C4 O4 ? ? SING C4 C5 ? ? SING C5 C5M ? ? DOUB C5 C6 ? ? SING C5M H71 ? ? SING C5M H72 ? ? SING C5M H73 ? ? SING C6 H6 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $alphaT_decamer_DNA . . . . . . 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 $alphaT_decamer_DNA 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $alphaT_decamer_DNA 6.8 mM . NaCl 50 mM . 'Na phosphate' 10 mM . EDTA 0.1 mM . D2O 100 % . stop_ save_ save_sample_two _Saveframe_category sample _Sample_type solution _Details ; Imino proton chemical shifts were obtained in the identical buffer as above, except the solvent was 90:10 H2O/D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $alphaT_decamer_DNA 6.8 mM . NaCl 50 mM . 'Na phosphate' 10 mM . EDTA 0.1 mM . D2O 10 % . H2O 90 % . stop_ save_ ############################ # Computer software used # ############################ save_software_one _Saveframe_category software _Name XWINNMR _Version 1.1 loop_ _Task 'data acquisition and processing' stop_ _Details . save_ save_software_two _Saveframe_category software _Name SPARKY _Version 3.33 loop_ _Task 'assignment and cross-peak integration' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_one save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH* 6.5 0.1 n/a pressure 1 . atm temperature 303 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 _Reference_correction_type DSS H 1 'methyl protons' ppm 0.00 internal direct cylindrical internal parallel 1.0000 temperature H3PO4_85% P 31 'phosphorus atom' ppm 0.00 external direct cylindrical 'external in the sample' parallel 2.471 temperature 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_assignment_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label NOESY DQF-COSY stop_ loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name 'alphaT strand-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 DG H1 H 13.040 . 1 2 . 1 DG H8 H 7.927 . 1 3 . 1 DG H1' H 5.943 . 1 4 . 1 DG H2' H 2.567 . 1 5 . 1 DG H2'' H 2.744 . 1 6 . 1 DG H3' H 4.835 . 1 7 . 1 DG H4' H 4.226 . 1 8 . 1 DG H5' H 3.693 . 1 9 . 1 DG H5'' H 3.693 . 1 10 . 2 DC H5 H 5.344 . 1 11 . 2 DC H6 H 7.359 . 1 12 . 2 DC H1' H 5.605 . 1 13 . 2 DC H2' H 2.015 . 1 14 . 2 DC H2'' H 2.347 . 1 15 . 2 DC H3' H 4.832 . 1 16 . 2 DC H4' H 4.149 . 1 17 . 2 DC H5' H 4.098 . 1 18 . 2 DC H5'' H 4.098 . 1 19 . 2 DC P P -0.54 . 1 20 . 3 DG H1 H 12.751 . 1 21 . 3 DG H8 H 7.822 . 1 22 . 3 DG H1' H 5.598 . 1 23 . 3 DG H2' H 2.648 . 1 24 . 3 DG H2'' H 2.801 . 1 25 . 3 DG H3' H 5.003 . 1 26 . 3 DG H4' H 4.336 . 1 27 . 3 DG H5' H 4.013 . 1 28 . 3 DG H5'' H 4.013 . 1 29 . 3 DG P P -0.24 . 1 30 . 4 DA H2 H 7.207 . 1 31 . 4 DA H8 H 8.043 . 1 32 . 4 DA H1' H 5.960 . 1 33 . 4 DA H2' H 2.639 . 1 34 . 4 DA H2'' H 2.931 . 1 35 . 4 DA H3' H 5.048 . 1 36 . 4 DA H4' H 4.446 . 1 37 . 4 DA H5' H 4.202 . 1 38 . 4 DA H5'' H 4.202 . 1 39 . 4 DA P P -0.77 . 1 40 . 5 DA H2 H 7.668 . 1 41 . 5 DA H8 H 8.139 . 1 42 . 5 DA H1' H 6.150 . 1 43 . 5 DA H2' H 2.567 . 1 44 . 5 DA H2'' H 2.927 . 1 45 . 5 DA H3' H 5.015 . 1 46 . 5 DA H4' H 4.452 . 1 47 . 5 DA H5' H 4.245 . 1 48 . 5 DA H5'' H 4.245 . 1 49 . 5 DA P P -0.65 . 1 50 . 6 DT H3 H 13.950 . 1 51 . 6 DT H6 H 7.190 . 1 52 . 6 DT H71 H 1.312 . 1 53 . 6 DT H72 H 1.312 . 1 54 . 6 DT H73 H 1.312 . 1 55 . 6 DT H1' H 5.922 . 1 56 . 6 DT H2' H 2.173 . 1 57 . 6 DT H2'' H 2.295 . 1 58 . 6 DT H3' H 4.855 . 1 59 . 6 DT H4' H 4.238 . 1 60 . 6 DT H5' H 4.123 . 1 61 . 6 DT H5'' H 4.123 . 1 62 . 6 DT P P -0.84 . 1 63 . 7 ATD H3 H 13.535 . 1 64 . 7 ATD H6 H 7.531 . 1 65 . 7 ATD H71 H 1.567 . 1 66 . 7 ATD H72 H 1.567 . 1 67 . 7 ATD H73 H 1.567 . 1 68 . 7 ATD H1' H 6.083 . 1 69 . 7 ATD H2' H 2.876 . 1 70 . 7 ATD H2'' H 1.936 . 1 71 . 7 ATD H3' H 5.002 . 1 72 . 7 ATD H4' H 4.752 . 1 73 . 7 ATD H5' H 4.091 . 1 74 . 7 ATD H5'' H 3.876 . 1 75 . 7 ATD P P -2.14 . 1 76 . 8 DC H5 H 5.671 . 1 77 . 8 DC H6 H 7.566 . 1 78 . 8 DC H1' H 5.788 . 1 79 . 8 DC H2' H 2.005 . 1 80 . 8 DC H2'' H 2.441 . 1 81 . 8 DC H3' H 4.720 . 1 82 . 8 DC H4' H 4.199 . 1 83 . 8 DC P P 0.77 . 1 84 . 9 DG H1 H 12.993 . 1 85 . 9 DG H8 H 7.903 . 1 86 . 9 DG H1' H 5.934 . 1 87 . 9 DG H2' H 2.588 . 1 88 . 9 DG H2'' H 2.722 . 1 89 . 9 DG H3' H 4.969 . 1 90 . 9 DG H4' H 4.344 . 1 91 . 9 DG H5' H 4.043 . 1 92 . 9 DG H5'' H 4.043 . 1 93 . 9 DG P P -0.57 . 1 94 . 10 DC H5 H 5.375 . 1 95 . 10 DC H6 H 7.404 . 1 96 . 10 DC H1' H 6.161 . 1 97 . 10 DC H2' H 2.176 . 1 98 . 10 DC H2'' H 2.176 . 1 99 . 10 DC H3' H 4.481 . 1 100 . 10 DC H4' H 4.041 . 1 101 . 10 DC H5' H 4.228 . 1 102 . 10 DC H5'' H 4.228 . 1 103 . 10 DC P P -0.37 . 1 stop_ save_