data_4235 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Solution Structure of [d(GCGAATTCGC)2] ; _BMRB_accession_number 4235 _BMRB_flat_file_name bmr4235.str _Entry_type original _Submission_date 1998-09-29 _Accession_date 1998-09-29 _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 James M. . 2 Mujeeb A. . . 3 Germann Marcus W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 "31P chemical shifts" 9 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 1999-02-08 original author 'original release' stop_ 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. 15, 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 ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Aramini James M. . 2 Mujeeb A. . . 3 Germann Marcus W. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic Acids Research' _Journal_volume 15 _Journal_issue . _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 'EcoRI recognition site' stop_ save_ ################################## # Molecular system description # ################################## save_system_DNA_decamer _Saveframe_category molecular_system _Mol_system_name 'DNA decamer' _Abbreviation_common DNA_decamer _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label strand_A $DNA_decamer strand_B $DNA_decamer stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state . loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 strand_A 1 strand_B stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_decamer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA decamer' _Molecular_mass . _Mol_thiol_state . _Details 'Contains EcoRI recognition site' ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence GCGAATTCGC loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DA 6 DT 7 DT 8 DC 9 DG 10 DC 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 $DNA_decamer . . . . . . 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 $DNA_decamer '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 $system_DNA_decamer 2.6 mM . NaCl 50 mM . NaPhosphate 10 mM . EDTA 0.1 mM . stop_ save_ ############################ # Computer software used # ############################ save_software_one _Saveframe_category software _Name XWINNMR _Version . loop_ _Task 'acquisition, processing, assignment' stop_ _Details . save_ save_software-two _Saveframe_category software _Name SPARKY _Version 3.33 loop_ _Task '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,_DQF-COSY,_31P-1H_correlation_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'NOESY, DQF-COSY, 31P-1H correlation' _Sample_label $sample_one save_ save_1H-detected_31P-1H_correlation_experiment_used_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-detected 31P-1H correlation experiment used' _Sample_label $sample_one save_ save_in_the_assignment_of_31P_signals_was_that_of_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'in the assignment of 31P signals was that of' _Sample_label $sample_one save_ save_Sklenar_et_al.,_FEBS_Lett._208,_94-98_(1986)._4 _Saveframe_category NMR_applied_experiment _Experiment_name 'Sklenar et al., FEBS Lett. 208, 94-98 (1986).' _Sample_label $sample_one save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name 'NOESY, DQF-COSY, 31P-1H correlation' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-detected 31P-1H correlation experiment used' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'in the assignment of 31P signals was that of' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'Sklenar et al., FEBS Lett. 208, 94-98 (1986).' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details ; The imino proton assignments were made on the same sample, except in 90:10 H2O/D2O and 293 K ; loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 0.1 n/a temperature 303 0.1 K pressure 1 . atm 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 DSS H 1 'methyl protons' ppm 0.00 external direct cylindrical external_to_the_sample parallel_to_Bo 1.00 '85% H3PO4' P 31 PO4 ppm 0.00 external direct cylindrical external_to_the_sample parallel_to_Bo 2.471 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_chemical_shifts_one _Saveframe_category assigned_chemical_shifts _Details ; 1H and 31P Chemical Shift Data for: [d(GCGAATTCGC)2] in 50 mM NaCl, 10 mM phosphate, pH 6.5, D2O, 303 K imino 1H data were obtained at 293K; aminos were not assigned for the beta anomeric residues, only 1 proton on C5' could be assigned to a residue, but were not stereospecifically assigned due to overlap. See Aramini et al., 1996 Biochemistry 35, 9355-9365 (1996). ; 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 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 13.031 0.005 1 2 . 1 DG H8 H 7.926 0.005 1 3 . 1 DG H1' H 5.949 0.005 1 4 . 1 DG H2' H 2.554 0.005 1 5 . 1 DG H2'' H 2.744 0.005 1 6 . 1 DG H3' H 4.822 0.005 1 7 . 1 DG H4' H 4.210 0.005 1 8 . 1 DG H5' H 3.682 0.005 2 9 . 2 DC H5 H 5.350 0.005 1 10 . 2 DC H6 H 7.331 0.005 1 11 . 2 DC H1' H 5.616 0.005 1 12 . 2 DC H2' H 1.937 0.005 1 13 . 2 DC H2'' H 2.305 0.005 1 14 . 2 DC H3' H 4.820 0.005 1 15 . 2 DC H4' H 4.127 0.005 1 16 . 2 DC H5' H 4.085 0.005 2 17 . 2 DC P P -0.57 0.02 1 18 . 3 DG H1 H 12.727 0.005 1 19 . 3 DG H8 H 7.847 0.005 1 20 . 3 DG H1' H 5.457 0.005 1 21 . 3 DG H2' H 2.654 0.005 1 22 . 3 DG H2'' H 2.749 0.005 1 23 . 3 DG H3' H 4.987 0.005 1 24 . 3 DG H4' H 4.307 0.005 1 25 . 3 DG P P -0.28 0.02 1 26 . 4 DA H2 H 7.253 0.005 1 27 . 4 DA H8 H 8.102 0.005 1 28 . 4 DA H1' H 5.997 0.005 1 29 . 4 DA H2' H 2.690 0.005 1 30 . 4 DA H2'' H 2.920 0.005 1 31 . 4 DA H3' H 5.052 0.005 1 32 . 4 DA H4' H 4.444 0.005 1 33 . 4 DA H5' H 4.162 0.005 2 34 . 4 DA P P -0.50 0.02 1 35 . 5 DA H2 H 7.617 0.005 1 36 . 5 DA H8 H 8.090 0.005 1 37 . 5 DA H1' H 6.139 0.005 1 38 . 5 DA H2' H 2.548 0.005 1 39 . 5 DA H2'' H 2.902 0.005 1 40 . 5 DA H3' H 4.985 0.005 1 41 . 5 DA H4' H 4.453 0.005 1 42 . 5 DA H5' H 4.254 0.005 2 43 . 5 DA P P -0.63 0.02 1 44 . 6 DT H3 H 13.671 0.005 1 45 . 6 DT H6 H 7.089 0.005 1 46 . 6 DT H71 H 1.262 0.005 1 47 . 6 DT H72 H 1.262 0.005 1 48 . 6 DT H73 H 1.262 0.005 1 49 . 6 DT H1' H 5.883 0.005 1 50 . 6 DT H2' H 1.960 0.005 1 51 . 6 DT H2'' H 2.540 0.005 1 52 . 6 DT H3' H 4.793 0.005 1 53 . 6 DT H4' H 4.190 0.005 1 54 . 6 DT P P -0.77 0.02 1 55 . 7 DT H3 H 13.795 0.005 1 56 . 7 DT H6 H 7.364 0.005 1 57 . 7 DT H71 H 1.523 0.005 1 58 . 7 DT H72 H 1.523 0.005 1 59 . 7 DT H73 H 1.523 0.005 1 60 . 7 DT H1' H 6.083 0.005 1 61 . 7 DT H2' H 2.152 0.005 1 62 . 7 DT H2'' H 2.533 0.005 1 63 . 7 DT H3' H 4.881 0.005 1 64 . 7 DT H4' H 4.193 0.005 1 65 . 7 DT P P -0.76 0.02 1 66 . 8 DC H5 H 5.631 0.005 1 67 . 8 DC H6 H 7.442 0.005 1 68 . 8 DC H1' H 5.678 0.005 1 69 . 8 DC H2' H 2.025 0.005 1 70 . 8 DC H2'' H 2.387 0.005 1 71 . 8 DC H3' H 4.849 0.005 1 72 . 8 DC H4' H 4.130 0.005 1 73 . 8 DC H5' H 4.165 0.005 2 74 . 8 DC P P -0.61 0.02 1 75 . 9 DG H1 H 13.031 0.005 1 76 . 9 DG H8 H 7.899 0.005 1 77 . 9 DG H1' H 5.931 0.005 1 78 . 9 DG H2' H 2.611 0.005 1 79 . 9 DG H2'' H 2.718 0.005 1 80 . 9 DG H3' H 4.974 0.005 1 81 . 9 DG H4' H 4.349 0.005 1 82 . 9 DG P P -0.28 0.02 1 83 . 10 DC H5 H 5.459 0.005 1 84 . 10 DC H6 H 7.439 0.005 1 85 . 10 DC H1' H 6.169 0.005 1 86 . 10 DC H2' H 2.16 0.005 2 87 . 10 DC H2'' H 2.16 0.005 2 88 . 10 DC H3' H 4.475 0.005 1 89 . 10 DC H4' H 4.032 0.005 1 90 . 10 DC H5' H 4.224 0.005 2 91 . 10 DC P P -0.35 0.02 1 stop_ save_