data_4835 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of the palindromic DNA decamer D(GCGTTAACGC)2 ; _BMRB_accession_number 4835 _BMRB_flat_file_name bmr4835.str _Entry_type new _Submission_date 2000-09-19 _Accession_date 2000-09-19 _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 Smith J. A. . 2 Tsui V. T. . 3 Chazin W. J. . 4 Case D. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 coupling_constants 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 "coupling constants" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 2000-12-07 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'DNA structure by 1H NMR methods: Studies of d(GCGTTAACGC)2' _Citation_status published _Citation_type thesis _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Smith Jarrod A. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Thesis_institution 'The Scripps Research Institute' _Thesis_institution_city 'La Jolla, CA' _Thesis_institution_country USA _Page_first . _Page_last . _Year 1999 _Details . loop_ _Keyword 'DOUBLE HELIX' B-DNA 'RESTRICTION SITE' 'HPA 1' stop_ save_ ################################## # Molecular system description # ################################## save_system_GCG10 _Saveframe_category molecular_system _Mol_system_name 5'-D(*GP*CP*GP*TP*TP*AP*AP*CP*GP*C)-3' _Abbreviation_common GCG10 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'GCG10 strand one' $GCG10 'GCG10 strand two' $GCG10 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state 'duplex DNA' _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'GCG10 strand one' 1 'GCG10 strand two' stop_ loop_ _Biological_function 'restriction site' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_GCG10 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-d(*GP*CP*GP*TP*TP*AP*AP*CP*GP*C)-3' _Abbreviation_common GCG10 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence GCGTTAACGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 11 DG 2 12 DC 3 13 DG 4 14 DT 5 15 DT 6 16 DA 7 17 DA 8 18 DC 9 19 DG 10 20 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 $GCG10 . . . . . . 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 $GCG10 . . . . . . 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 $GCG10 2 mM . Na3PO4 20 mM . NaCl 50 mM . NaN3 0.1 % . D2O 99.9 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GCG10 2 mM . Na3PO4 20 mM . NaCl 50 mM . NaN3 0.1 % . D2O 5 % . H2O 95 % . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version 95 loop_ _Task processing stop_ _Details 'Molecular Simulations, Inc.' save_ save_NAB _Saveframe_category software _Name NAB _Version 2.1 loop_ _Task 'structure calculation' stop_ _Details 'Macke, et. al.' save_ save_AMBER _Saveframe_category software _Name AMBER _Version 5.0 loop_ _Task 'refinement, iterative matrix relaxation' stop_ _Details 'Pearlman, et. al.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_Double-Quantum_1 _Saveframe_category NMR_applied_experiment _Experiment_name Double-Quantum _Sample_label . save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_E-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label . save_ save_2D_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name Double-Quantum _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _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 0.3 n/a temperature 300 5 K 'ionic strength' 70 . mM 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 DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 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 'GCG10 strand one' _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 5.989 0.1 . 2 . 1 DG H2'' H 2.797 0.1 . 3 . 1 DG H2' H 2.608 0.1 . 4 . 1 DG H3' H 4.855 0.1 . 5 . 1 DG H4' H 4.258 0.1 . 6 . 1 DG H5'' H 3.715 0.1 . 7 . 1 DG H5' H 3.715 0.1 . 8 . 1 DG H8 H 7.952 0.1 . 9 . 2 DC H1' H 5.760 0.1 . 10 . 2 DC H2'' H 2.482 0.1 . 11 . 2 DC H2' H 2.161 0.1 . 12 . 2 DC H3' H 4.889 0.1 . 13 . 2 DC H4' H 4.226 0.1 . 14 . 2 DC H5 H 5.395 0.1 . 15 . 2 DC H6 H 7.416 0.1 . 16 . 3 DG H1' H 6.046 0.1 . 17 . 3 DG H2'' H 2.828 0.1 . 18 . 3 DG H2' H 2.673 0.1 . 19 . 3 DG H3' H 5.004 0.1 . 20 . 3 DG H4' H 4.416 0.1 . 21 . 3 DG H5'' H 4.091 0.1 . 22 . 3 DG H5' H 4.151 0.1 . 23 . 3 DG H8 H 7.935 0.1 . 24 . 4 DT H1' H 5.995 0.1 . 25 . 4 DT H2'' H 2.531 0.1 . 26 . 4 DT H2' H 2.043 0.1 . 27 . 4 DT H3' H 4.849 0.1 . 28 . 4 DT H4' H 4.231 0.1 . 29 . 4 DT H5'' H 4.168 0.1 . 30 . 4 DT H5' H 4.291 0.1 . 31 . 4 DT H6 H 7.247 0.1 . 32 . 4 DT H71 H 1.466 0.1 . 33 . 4 DT H72 H 1.466 0.1 . 34 . 4 DT H73 H 1.466 0.1 . 35 . 5 DT H1' H 5.668 0.1 . 36 . 5 DT H2'' H 2.381 0.1 . 37 . 5 DT H2' H 2.010 0.1 . 38 . 5 DT H3' H 4.872 0.1 . 39 . 5 DT H4' H 4.101 0.1 . 40 . 5 DT H6 H 7.339 0.1 . 41 . 5 DT H71 H 1.688 0.1 . 42 . 5 DT H72 H 1.688 0.1 . 43 . 5 DT H73 H 1.688 0.1 . 44 . 6 DA H1' H 5.880 0.1 . 45 . 6 DA H2 H 6.915 0.1 . 46 . 6 DA H2'' H 2.885 0.1 . 47 . 6 DA H2' H 2.743 0.1 . 48 . 6 DA H3' H 5.044 0.1 . 49 . 6 DA H4' H 4.409 0.1 . 50 . 6 DA H5'' H 4.094 0.1 . 51 . 6 DA H5' H 4.144 0.1 . 52 . 6 DA H8 H 8.264 0.1 . 53 . 7 DA H1' H 6.052 0.1 . 54 . 7 DA H2 H 7.593 0.1 . 55 . 7 DA H2'' H 2.787 0.1 . 56 . 7 DA H2' H 2.572 0.1 . 57 . 7 DA H3' H 4.998 0.1 . 58 . 7 DA H4' H 4.438 0.1 . 59 . 7 DA H8 H 8.103 0.1 . 60 . 8 DC H1' H 5.554 0.1 . 61 . 8 DC H2'' H 2.258 0.1 . 62 . 8 DC H2' H 1.831 0.1 . 63 . 8 DC H3' H 4.757 0.1 . 64 . 8 DC H4' H 4.111 0.1 . 65 . 8 DC H5 H 5.178 0.1 . 66 . 8 DC H5'' H 4.098 0.1 . 67 . 8 DC H5' H 4.227 0.1 . 68 . 8 DC H6 H 7.156 0.1 . 69 . 9 DG H1' H 5.932 0.1 . 70 . 9 DG H2'' H 2.706 0.1 . 71 . 9 DG H2' H 2.580 0.1 . 72 . 9 DG H3' H 4.952 0.1 . 73 . 9 DG H4' H 4.338 0.1 . 74 . 9 DG H5'' H 4.091 0.1 . 75 . 9 DG H5' H 4.013 0.1 . 76 . 9 DG H8 H 7.837 0.1 . 77 . 10 DC H1' H 6.178 0.1 . 78 . 10 DC H2' H 2.183 0.1 . 79 . 10 DC H3' H 4.494 0.1 . 80 . 10 DC H4' H 4.045 0.1 . 81 . 10 DC H5 H 5.431 0.1 . 82 . 10 DC H6 H 7.433 0.1 . stop_ save_ ######################## # Coupling constants # ######################## save_J-values_set_1 _Saveframe_category coupling_constants _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Spectrometer_frequency_1H 500 _Mol_system_component_name 'GCG10 strand one' _Text_data_format . _Text_data . loop_ _Coupling_constant_ID _Coupling_constant_code _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_name _Coupling_constant_value _Coupling_constant_min_value _Coupling_constant_max_value _Coupling_constant_value_error 1 JH1'H2' 1 DG H1' 1 DG H2' 9.1 . . . 2 JH1'H2' 2 DC H1' 2 DC H2' 9.3 . . . 3 JH1'H2' 3 DG H1' 3 DG H2' 9.5 . . . 4 JH1'H2' 4 DT H1' 4 DT H2' 8.7 . . . 5 JH1'H2' 5 DT H1' 5 DT H2' 9.0 . . . 6 JH1'H2' 6 DA H1' 6 DA H2' 9.5 . . . 7 JH1'H2' 7 DA H1' 7 DA H2' 9.2 . . . 8 JH1'H2' 8 DC H1' 8 DC H2' 8.1 . . . 9 JH1'H2' 9 DG H1' 9 DG H2' 8.8 . . . 10 JH1'H2'' 1 DG H1' 1 DG H2'' 5.8 . . . 11 JH1'H2'' 2 DC H1' 2 DC H2'' 5.5 . . . 12 JH1'H2'' 3 DG H1' 3 DG H2'' 5.6 . . . 13 JH1'H2'' 4 DT H1' 4 DT H2'' 6.4 . . . 14 JH1'H2'' 5 DT H1' 5 DT H2'' 6.4 . . . 15 JH1'H2'' 6 DA H1' 6 DA H2'' 5.5 . . . 16 JH1'H2'' 7 DA H1' 7 DA H2'' 5.8 . . . 17 JH1'H2'' 8 DC H1' 8 DC H2'' 6.3 . . . 18 JH1'H2'' 9 DG H1' 9 DG H2'' 6.2 . . . stop_ save_