data_5282 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Refinement of d(GCGAAGC) Hairpin Structure Using One- and Two-Bonds Residual Dipolar Couplings ; _BMRB_accession_number 5282 _BMRB_flat_file_name bmr5282.str _Entry_type original _Submission_date 2002-02-07 _Accession_date 2002-02-07 _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 Padrta P. . . 2 Stefl R. . . 3 Zidek L. . . 4 Sklenar V. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 68 "13C chemical shifts" 35 "15N chemical shifts" 9 "31P chemical shifts" 6 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2003-02-20 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Refinement of d(GCGAAGC) Hairpin Structure Using One- and Two-bond Residual Dipolar Couplings ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22333288 _PubMed_ID 12449414 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Padrta P. . . 2 Stefl R. . . 3 Kralik L. . . 4 Zidek L. . . 5 Sklenar V. . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_volume 24 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1 _Page_last 14 _Year 2002 _Details . loop_ _Keyword hairpin DNA 'GA mismatch' stop_ save_ ################################## # Molecular system description # ################################## save_system_GCGAAGC_hairpin _Saveframe_category molecular_system _Mol_system_name 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' _Abbreviation_common 'GCGAAGC hairpin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' $GCGAAGC_hairpin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_GCGAAGC_hairpin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'GCGAAGC hairpin' _Abbreviation_common 'GCGAAGC hairpin' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence GCGAAGC loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DA 6 DG 7 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 _Details $GCGAAGC_hairpin 'Herpes simplex virus' 10294 Viruses . Simplexvirus n/a ; This sequence occurs naturally in replication origins of phage phix174, in herpes simplex virus, in E. coli heat-shock gene and rRNA genes. ; 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 $GCGAAGC_hairpin vendor . . . . . 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 $GCGAAGC_hairpin 6 mM . 'Na phosphate buffer' 10 mM . D2O 100 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GCGAAGC_hairpin 6 mM . 'Na phosphate buffer' 10 mM . H2O 90 % . D2O 10 % . stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GCGAAGC_hairpin 0.5 mM '[U-13C; U-15N]' 'Na phosphate buffer' 10 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name XwinNmr _Version 2.6,3.0 loop_ _Task 'spectra processing' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Sparky _Version 3.xx loop_ _Task 'assignment and integration' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name AMBER _Version 6.0 loop_ _Task 'structure refinement' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE-DRX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_E-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label . save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_COUPLED_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'COUPLED HSQC' _Sample_label . save_ save_S3E_E-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name 'S3E E-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 E-COSY _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_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'COUPLED HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name 'S3E E-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.7 . pH temperature 303 . K 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 _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.0 . indirect . . . 0.101329118 DSS C 13 'methyl protons' ppm 0.0 . indirect . . . 0.251449530 DSS P 31 'methyl protons' ppm 0.0 . indirect . . . 0.404808688 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 $sample_2 $sample_3 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 5'-D(*GP*CP*GP*AP*AP*GP*C)-3' _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 H2' H 2.483 0.003 1 2 . 1 DG H2'' H 2.703 0.005 1 3 . 1 DG H3' H 4.798 0.001 1 4 . 1 DG H4' H 4.206 0.000 1 5 . 1 DG H5' H 3.708 0.001 2 6 . 1 DG H5'' H 3.708 0.001 2 7 . 1 DG H8 H 7.926 0.002 1 8 . 1 DG H1 H 12.821 0.000 1 9 . 1 DG C1' C 84.842 0.000 1 10 . 1 DG C2' C 40.042 0.000 1 11 . 1 DG C3' C 79.392 0.000 1 12 . 1 DG C4' C 88.919 0.000 1 13 . 1 DG C5' C 64.105 0.000 1 14 . 1 DG N7 N 237 0.000 1 15 . 2 DC H1' H 6.033 0.004 1 16 . 2 DC H2' H 1.615 0.004 1 17 . 2 DC H2'' H 2.293 0.001 1 18 . 2 DC H3' H 4.792 0.001 1 19 . 2 DC H4' H 4.218 0.003 1 20 . 2 DC H5 H 5.023 0.001 1 21 . 2 DC H5' H 4.06 0.000 2 22 . 2 DC H5'' H 4.06 0.000 2 23 . 2 DC H6 H 7.008 0.002 1 24 . 2 DC H41 H 8.107 0.000 1 25 . 2 DC H42 H 6.609 0.005 1 26 . 2 DC C1' C 85.995 0.000 1 27 . 2 DC C2' C 37.729 0.000 1 28 . 2 DC C3' C 78.969 0.000 1 29 . 2 DC C4' C 86.079 0.000 1 30 . 2 DC C5' C 67.805 0.000 1 31 . 2 DC P P -4.327 0.000 1 32 . 3 DG H1' H 5.37 0.003 1 33 . 3 DG H2' H 2.66 0.006 1 34 . 3 DG H2'' H 2.524 0.006 1 35 . 3 DG H3' H 4.9 0.001 1 36 . 3 DG H4' H 4.45 0.001 1 37 . 3 DG H5' H 4.091 0.001 2 38 . 3 DG H5'' H 4.091 0.001 2 39 . 3 DG H8 H 8.06 0.001 1 40 . 3 DG H1 H 10.425 0.001 1 41 . 3 DG C1' C 83.66 0.000 1 42 . 3 DG C2' C 39.218 0.000 1 43 . 3 DG C3' C 79.16 0.000 1 44 . 3 DG C4' C 86.986 0.000 1 45 . 3 DG C5' C 67.461 0.000 1 46 . 3 DG P P -4.898 0.000 1 47 . 3 DG N7 N 236.9 0.000 1 48 . 4 DA H1' H 5.975 0.011 1 49 . 4 DA H2 H 8.134 0.000 1 50 . 4 DA H2' H 2.255 0.005 1 51 . 4 DA H2'' H 2.32 0.000 1 52 . 4 DA H3' H 4.583 0.002 1 53 . 4 DA H4' H 2.14 0.007 1 54 . 4 DA H5' H 3.395 0.004 2 55 . 4 DA H5'' H 3.086 0.005 2 56 . 4 DA H8 H 8.11 0.001 1 57 . 4 DA C1' C 85.089 0.000 1 58 . 4 DA C2' C 42.934 0.000 1 59 . 4 DA C3' C 79.572 0.000 1 60 . 4 DA C4' C 86.663 0.000 1 61 . 4 DA C5' C 67.507 0.000 1 62 . 4 DA P P -4.595 0.000 1 63 . 4 DA N1 N 225.2 0.000 1 64 . 4 DA N3 N 216.3 0.000 1 65 . 4 DA N7 N 233.5 0.000 1 66 . 5 DA H1' H 6.294 0.003 1 67 . 5 DA H2 H 8.133 0.000 1 68 . 5 DA H2' H 2.897 0.000 1 69 . 5 DA H2'' H 2.897 0.000 1 70 . 5 DA H3' H 4.837 0.000 1 71 . 5 DA H4' H 4.352 0.006 1 72 . 5 DA H5' H 3.986 0.004 2 73 . 5 DA H5'' H 3.812 0.001 2 74 . 5 DA H8 H 8.019 0.001 1 75 . 5 DA H61 H 7.745 0.006 1 76 . 5 DA C1' C 86.271 0.000 1 77 . 5 DA C2' C 36.228 0.000 1 78 . 5 DA C3' C 79.804 0.000 1 79 . 5 DA C4' C 88.707 0.000 1 80 . 5 DA C5' C 69.708 0.000 1 81 . 5 DA P P -4.737 0.000 1 82 . 5 DA N1 N 227 0.000 1 83 . 5 DA N3 N 216.4 0.000 1 84 . 6 DG H1' H 5.557 0.003 1 85 . 6 DG H2' H 2.578 0.005 1 86 . 6 DG H2'' H 2.578 0.005 1 87 . 6 DG H3' H 4.905 0.001 1 88 . 6 DG H4' H 4.381 0.000 1 89 . 6 DG H5' H 4.161 0.000 2 90 . 6 DG H5'' H 4.29 0.002 2 91 . 6 DG H8 H 7.995 0.001 1 92 . 6 DG H1 H 12.83 0.002 1 93 . 6 DG H22 H 7.813 0.000 1 94 . 6 DG C1' C 84.051 0.000 1 95 . 6 DG C2' C 40.448 0.000 1 96 . 6 DG C3' C 78.049 0.000 1 97 . 6 DG C4' C 86.798 0.000 1 98 . 6 DG C5' C 67.676 0.000 1 99 . 6 DG P P -5.058 0.000 1 100 . 6 DG N1 N 147.7 0.000 1 101 . 6 DG N7 N 236.9 0.000 1 102 . 7 DC H1' H 6.246 0.003 1 103 . 7 DC H2' H 2.147 0.004 1 104 . 7 DC H2'' H 2.258 0.009 1 105 . 7 DC H3' H 4.454 0.002 1 106 . 7 DC H4' H 4.111 0.001 1 107 . 7 DC H5 H 5.285 0.002 1 108 . 7 DC H5' H 4.24 0.000 2 109 . 7 DC H5'' H 4.042 0.008 2 110 . 7 DC H6 H 7.437 0.003 1 111 . 7 DC H41 H 7.913 0.000 1 112 . 7 DC H42 H 6.179 0.000 1 113 . 7 DC C1' C 86.967 0.000 1 114 . 7 DC C2' C 41.765 0.000 1 115 . 7 DC C3' C 71.899 0.000 1 116 . 7 DC C4' C 86.986 0.000 1 117 . 7 DC C5' C 67.487 0.000 1 118 . 7 DC P P -3.82 0.000 1 stop_ save_