data_17351 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Ribonucleotide Perturbation of DNA Structure: Solution Structure of [d(CGC)r(G)d(AATTCGCG)]2 ; _BMRB_accession_number 17351 _BMRB_flat_file_name bmr17351.str _Entry_type original _Submission_date 2010-12-07 _Accession_date 2010-12-07 _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 DeRose Eugene F. . 2 Perera Lalith . . 3 Michael Murray S. . 4 Thomas Kunkel A. . 5 Robert London E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 127 "31P chemical shifts" 11 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-10-22 original BMRB . stop_ _Original_release_date 2015-10-22 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22390730 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 DeRose Eugene F. . 2 Perera Lalith . . 3 Murray Michael S. . 4 Kunkel Thomas A. . 5 London Robert E. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 51 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2407 _Page_last 2416 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'rG4 substituted Drew Dickerson dodecamer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'rG4 substituted Drew Dickerson dodecamer, 1' $rG4_substituted_Drew_Dickerson_dodecamer 'rG4 substituted Drew Dickerson dodecamer, 2' $rG4_substituted_Drew_Dickerson_dodecamer stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'rG4 substituted Drew Dickerson dodecamer, 1' 2 'rG4 substituted Drew Dickerson dodecamer, 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_rG4_substituted_Drew_Dickerson_dodecamer _Saveframe_category monomeric_polymer _Mol_type polymer _Name_common rG4_substituted_Drew_Dickerson_dodecamer _Molecular_mass 111.103 _Mol_thiol_state 'not present' _Details d(CGC)r(G)d(AATTCGCG) ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; CGCGAATTCGCG ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 G 5 DA 6 DA 7 DT 8 DT 9 DC 10 DG 11 DC 12 DG 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 $rG4_substituted_Drew_Dickerson_dodecamer . . . . . . 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 $rG4_substituted_Drew_Dickerson_dodecamer '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 _Isotopic_labeling $rG4_substituted_Drew_Dickerson_dodecamer 2.0 mM 'natural abundance' 'sodium chloride' 50.0 mM 'natural abundance' 'sodium phosphate' 50.0 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $rG4_substituted_Drew_Dickerson_dodecamer 2.0 mM 'natural abundance' 'sodium chloride' 50.0 mM 'natural abundance' 'sodium phosphate' 50.0 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type 'filamentous virus' _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $rG4_substituted_Drew_Dickerson_dodecamer 2.0 mM 'natural abundance' 'sodium chloride' 50.0 mM 'natural abundance' 'sodium phosphate' 50.0 mM 'natural abundance' EDTA 0.5 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version 2.1B loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 2010.190.16.149 loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version 8.0.b64 loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_XPLOR-NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.25 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 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_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-31P_COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P COSY' _Sample_label $sample_1 save_ save_2D_1H-31P_J-COSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P J-COSY' _Sample_label $sample_1 save_ save_2D_1H-31P_HSQC_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HSQC' _Sample_label $sample_1 save_ save_2D_1H-31P_HSQC_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HSQC' _Sample_label $sample_2 save_ save_2D_CT-NOESY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D CT-NOESY' _Sample_label $sample_1 save_ save_2D_CT-NOESY_11 _Saveframe_category NMR_applied_experiment _Experiment_name '2D CT-NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 100 . mM pH 7.0 . pH pressure 1 . atm temperature 298 . K 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 external direct cylindrical 'separate tube (no insert) similar to the experimental sample tube' parallel 1.000000000 TMP P 31 phosphorus ppm 0.00 external direct cylindrical 'separate tube (no insert) similar to the experimental sample tube' parallel 0.404808636 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-31P COSY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'rG4 substituted Drew Dickerson dodecamer, 1' _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 DC H1' H 5.7528 0.005 1 2 1 1 DC H2' H 1.9560 0.005 2 3 1 1 DC H2'' H 2.3141 0.005 2 4 1 1 DC H3' H 4.6982 0.005 1 5 1 1 DC H4' H 4.0569 0.005 1 6 1 1 DC H5 H 5.9014 0.005 1 7 1 1 DC H5' H 3.7144 0.005 2 8 1 1 DC H6 H 7.6241 0.005 1 9 2 2 DG H1 H 13.0325 0.005 1 10 2 2 DG H1' H 5.8600 0.005 1 11 2 2 DG H2' H 2.6476 0.005 2 12 2 2 DG H2'' H 2.7000 0.005 2 13 2 2 DG H3' H 4.9567 0.005 1 14 2 2 DG H4' H 4.3314 0.005 1 15 2 2 DG H5' H 4.0768 0.005 2 16 2 2 DG H5'' H 3.9756 0.005 2 17 2 2 DG H8 H 7.9401 0.005 1 18 2 2 DG P P -4.1741 0.005 1 19 3 3 DC H1' H 5.7929 0.005 1 20 3 3 DC H2' H 1.8043 0.005 2 21 3 3 DC H2'' H 2.1508 0.005 2 22 3 3 DC H3' H 4.8457 0.005 1 23 3 3 DC H4' H 4.1576 0.005 1 24 3 3 DC H5 H 5.3396 0.005 1 25 3 3 DC H5' H 4.1064 0.005 2 26 3 3 DC H6 H 7.1879 0.005 1 27 3 3 DC H41 H 8.3476 0.005 2 28 3 3 DC H42 H 6.4116 0.005 2 29 3 3 DC P P -4.3245 0.005 1 30 4 4 G H1 H 12.7737 0.005 1 31 4 4 G H1' H 5.7897 0.005 1 32 4 4 G H2' H 4.7415 0.005 1 33 4 4 G H3' H 4.8636 0.005 1 34 4 4 G H4' H 4.3032 0.005 1 35 4 4 G H5' H 4.0784 0.005 2 36 4 4 G H5'' H 4.0025 0.005 2 37 4 4 G H8 H 7.8653 0.005 1 38 4 4 G HO2' H 4.9799 0.005 1 39 4 4 G P P -4.2852 0.005 1 40 5 5 DA H1' H 6.1147 0.005 1 41 5 5 DA H2 H 7.5808 0.005 1 42 5 5 DA H2' H 2.7033 0.005 2 43 5 5 DA H2'' H 2.9767 0.005 2 44 5 5 DA H3' H 5.0177 0.005 1 45 5 5 DA H4' H 4.4524 0.005 1 46 5 5 DA H5' H 4.1716 0.005 2 47 5 5 DA H5'' H 4.1672 0.005 2 48 5 5 DA H8 H 8.2146 0.005 1 49 5 5 DA P P -2.6935 0.005 1 50 6 6 DA H1' H 6.1332 0.005 1 51 6 6 DA H2 H 7.6232 0.005 1 52 6 6 DA H2' H 2.5572 0.005 2 53 6 6 DA H2'' H 2.9079 0.005 2 54 6 6 DA H3' H 4.9892 0.005 1 55 6 6 DA H4' H 4.4446 0.005 1 56 6 6 DA H5' H 4.2384 0.005 2 57 6 6 DA H5'' H 4.2295 0.005 2 58 6 6 DA H8 H 8.0959 0.005 1 59 6 6 DA P P -4.5003 0.005 1 60 7 7 DT H1' H 5.8883 0.005 1 61 7 7 DT H2' H 1.9698 0.005 2 62 7 7 DT H2'' H 2.5482 0.005 2 63 7 7 DT H3 H 13.6091 0.005 1 64 7 7 DT H3' H 4.8004 0.005 1 65 7 7 DT H4' H 4.1916 0.005 1 66 7 7 DT H5' H 4.3175 0.005 2 67 7 7 DT H5'' H 4.3227 0.005 2 68 7 7 DT H6 H 7.1071 0.005 1 69 7 7 DT H71 H 1.2692 0.005 1 70 7 7 DT H72 H 1.2692 0.005 1 71 7 7 DT H73 H 1.2692 0.005 1 72 7 7 DT P P -4.5520 0.005 1 73 8 8 DT H1' H 6.1031 0.005 1 74 8 8 DT H2' H 2.1265 0.005 2 75 8 8 DT H2'' H 2.5306 0.005 2 76 8 8 DT H3 H 13.7132 0.005 1 77 8 8 DT H3' H 4.8771 0.005 1 78 8 8 DT H4' H 4.1930 0.005 1 79 8 8 DT H5' H 4.1089 0.005 2 80 8 8 DT H6 H 7.3667 0.005 1 81 8 8 DT H71 H 1.5198 0.005 1 82 8 8 DT H72 H 1.5198 0.005 1 83 8 8 DT H73 H 1.5198 0.005 1 84 8 8 DT P P -4.5348 0.005 1 85 9 9 DC H1' H 5.5563 0.005 1 86 9 9 DC H2' H 2.1046 0.005 2 87 9 9 DC H2'' H 2.3625 0.005 2 88 9 9 DC H3' H 4.7337 0.005 1 89 9 9 DC H4' H 4.1136 0.005 1 90 9 9 DC H5 H 5.6650 0.005 1 91 9 9 DC H5' H 4.0977 0.005 2 92 9 9 DC H6 H 7.5006 0.005 1 93 9 9 DC H41 H 8.3679 0.005 2 94 9 9 DC H42 H 6.8582 0.005 2 95 9 9 DC P P -4.4044 0.005 1 96 10 10 DG H1 H 5.8817 0.005 1 97 10 10 DG H1' H 5.8849 0.005 1 98 10 10 DG H2' H 2.6326 0.005 2 99 10 10 DG H2'' H 2.7059 0.005 2 100 10 10 DG H3' H 4.9851 0.005 1 101 10 10 DG H4' H 4.3741 0.005 1 102 10 10 DG H5' H 4.1143 0.005 2 103 10 10 DG H5'' H 4.0323 0.005 2 104 10 10 DG H8 H 7.8849 0.005 1 105 10 10 DG P P -3.8562 0.005 1 106 11 11 DC H1' H 5.7422 0.005 1 107 11 11 DC H2' H 1.8894 0.005 2 108 11 11 DC H2'' H 2.3278 0.005 2 109 11 11 DC H3' H 4.8121 0.005 1 110 11 11 DC H4' H 4.1320 0.005 1 111 11 11 DC H5 H 5.4337 0.005 1 112 11 11 DC H6 H 7.3217 0.005 1 113 11 11 DC H41 H 8.4510 0.005 2 114 11 11 DC H42 H 6.5735 0.005 2 115 11 11 DC P P -4.2421 0.005 1 116 12 12 DG H1' H 6.1499 0.005 1 117 12 12 DG H2' H 2.4832 0.005 2 118 12 12 DG H2'' H 2.4460 0.005 2 119 12 12 DG H3' H 4.6686 0.005 1 120 12 12 DG H4' H 4.1667 0.005 1 121 12 12 DG H5' H 4.0635 0.005 2 122 12 12 DG H5'' H 4.0612 0.005 2 123 12 12 DG H8 H 7.9319 0.005 1 124 12 12 DG P P -4.0181 0.005 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-31P COSY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'rG4 substituted Drew Dickerson dodecamer, 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 14 2 DG H1 H 13.0384 0.005 1 2 15 3 DC H5 H 5.3322 0.005 1 3 15 3 DC H41 H 6.4140 0.005 2 4 16 4 G H1 H 12.7779 0.005 1 5 17 5 DA H2 H 7.2806 0.005 1 6 18 6 DA H2 H 7.6250 0.005 1 7 20 8 DT H3 H 13.7165 0.005 1 8 20 8 DT H71 H 1.5064 0.005 1 9 20 8 DT H72 H 1.5064 0.005 1 10 20 8 DT H73 H 1.5064 0.005 1 11 21 9 DC H1' H 5.5504 0.005 1 12 21 9 DC H41 H 6.8577 0.005 2 13 22 10 DG H1 H 12.8370 0.005 1 14 23 11 DC H5 H 5.4324 0.005 1 stop_ save_