data_4170 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 2'-Deoxy-Isoguanosine Base Paired to Thymidine, NMR Minimized Average Structure ; _BMRB_accession_number 4170 _BMRB_flat_file_name bmr4170.str _Entry_type new _Submission_date 1998-08-03 _Accession_date 1998-08-13 _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 Robinson H. . . 2 Gao Y.-G. . . 3 Bauer C. . . 4 Roberts C. . . 5 Switzer C. . . 6 Wang A. H.-J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 131 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2000-03-31 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; 2'-Deoxyisoguanosine Adopts more than one Tautomer to Base Pair with Thymidine Observed by High Resolution Crystal Structure Analysis ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 98359763 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Robinson H. . . 2 Gao Y.-G. . . 3 Bauer C. . . 4 Roberts C. . . 5 Switzer C. . . 6 Wang A. H.-J. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 37 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 10897 _Page_last 10905 _Year 1998 _Details . loop_ _Keyword NMR 'nuclear magnetic resonance' 'deoxyribonucleic acid' isoguanosine-thymidine mismatch stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_one _Saveframe_category citation _Citation_full 'Robinson, H., and Wang, A.H.-J, Biochemistry 31, 3524-3533 (1992).' _Citation_title 'A simple spectral-driven procedure for the refinement of DNA structures by NMR spectroscopy.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 1554732 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Robinson H . . 2 Wang 'A H' H. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 31 _Journal_issue 13 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 3524 _Page_last 3533 _Year 1992 _Details ; We have developed a simple and quantitative procedure (SPEDREF) for the refinement of DNA structures using experimental two-dimensional nuclear Overhauser effect (2D NOE) data. The procedure calculates the simulated 2D NOE spectrum using the full matrix relaxation method on the basis of a molecular model. The volume of all NOE peaks is measured and compared between the experimental and the calculated spectra. The difference of the experimental and simulated volumes is minimized by a conjugated gradient procedure to adjust the interproton distances in the model. An agreement factor (analogous to the crystallographic R-factor) is used to monitor the progress of the refinement. The procedure is an The agreement is considered to be complete when several parameters, including the R-factor, the energy associated with the molecule, the local conformation (as judged by the sugar pseudorotation), and the global conformation (as judged by the helical x-displacement), are refined to their respective convergence. With the B-DNA structure of d(CGATCG) as an example, we show that DNA structure may be refined to produce calculated NOE spectra that are in excellent agreement with the experimental 2D NOE spectra. This is judged to be effective by the low R-factor of approximately 15%. Moreover, we demonstrate that not only are NOE data very powerful in providing details of the local structure but, with appropriate weighting of the NOE constraints, the global structure of the DNA double helix can also be determined, even when starting with a grossly different model. The reliability and limitations of a DNA structure as determined by NMR spectroscopy are discussed. ; save_ save_citation_two _Saveframe_category citation _Citation_full ; Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J., Oldfield, E., Markley, J. L., and Sykes, B. D. J. Biomol. NMR 6, 135-140 (1995). ; _Citation_title '1H, 13C and 15N chemical shift referencing in biomolecular NMR.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8589602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wishart 'D S' S. . 2 Bigam 'C G' G. . 3 Yao J . . 4 Abildgaard F . . 5 Dyson 'H J' J. . 6 Oldfield E . . 7 Markley 'J L' L. . 8 Sykes 'B D' D. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 2 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 135 _Page_last 140 _Year 1995 _Details ; A considerable degree of variability exists in the way that 1H, 13C and 15N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common 1H, 13C and 15N chemical shift standards, now used in biomolecular NMR, to those proposed here. ; save_ ################################## # Molecular system description # ################################## save_system_DNA-duplex-6GP _Saveframe_category molecular_system _Mol_system_name DNA-duplex-6GP _Abbreviation_common DNA _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label DNA-duplex-6GP-one $DNA-duplex-6GP DNA-duplex-6GP-two $DNA-duplex-6GP 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 DNA-duplex-6GP-one 1 DNA-duplex-6GP-two stop_ _Database_query_date . _Details ; DNA(5'-D(*CP*GP*CP*XP*AP*AP*TP*TP*TP*GP*CP*G)-3') self-complementary duplex where X is Isoguanosine ; save_ ######################## # Monomeric polymers # ######################## save_DNA-duplex-6GP _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA-duplex _Abbreviation_common DNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CGCXAATTTGCG loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 IGU 5 DA 6 DA 7 DT 8 DT 9 DT 10 DG 11 DC 12 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 1bhr . . . . . . stop_ save_ ###################### # Polymer residues # ###################### save_IGU _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 2'-DEOXY-ISOGUANOSINE _Abbreviation_common 6GP _BMRB_code . _PDB_code IGU _Standard_residue_derivative G loop_ _Mol_label _Residue_seq_code $DNA-duplex-6GP 4 stop_ _Molecular_mass . _Mol_paramagnetic no _Details . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA-duplex-6GP . . . . . . 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-duplex-6GP '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 $DNA-duplex-6GP 0.77 mM . stop_ save_ ############################ # Computer software used # ############################ save_software_one _Saveframe_category software _Name FELIX _Version 1.1 loop_ _Task 'primary data processing' stop_ _Details . save_ save_software_two _Saveframe_category software _Name spedref _Version . loop_ _Task 'integration based on fitting 2-D lineshapes' stop_ _Details . _Citation_label $citation_one save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer VARIAN _Model VXR _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label $sample_one save_ save_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_one save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 . n/a temperature 275 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 _Indirect_shift_ratio_citation_label DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.0 $citation_two 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 . 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 DNA-duplex-6GP-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 DC H41 H 8.22 . . 2 . 1 DC H42 H 7.20 . . 3 . 1 DC H5 H 5.92 . . 4 . 1 DC H6 H 7.68 . . 5 . 1 DC H1' H 5.75 . . 6 . 1 DC H2' H 2.05 . . 7 . 1 DC H2'' H 2.44 . . 8 . 1 DC H3' H 4.72 . . 9 . 1 DC H4' H 4.06 . . 10 . 1 DC H5' H 3.72 . . 11 . 1 DC H5'' H 3.72 . . 12 . 2 DG H1 H 13.17 . . 13 . 2 DG H8 H 7.97 . . 14 . 2 DG H1' H 5.91 . . 15 . 2 DG H2' H 2.63 . . 16 . 2 DG H2'' H 2.73 . . 17 . 2 DG H3' H 4.96 . . 18 . 2 DG H4' H 4.35 . . 19 . 2 DG H5' H 3.97 . . 20 . 2 DG H5'' H 4.10 . . 21 . 3 DC H41 H 8.48 . . 22 . 3 DC H42 H 6.71 . . 23 . 3 DC H5 H 5.42 . . 24 . 3 DC H6 H 7.26 . . 25 . 3 DC H1' H 5.64 . . 26 . 3 DC H2' H 1.60 . . 27 . 3 DC H2'' H 2.15 . . 28 . 3 DC H3' H 4.78 . . 29 . 3 DC H4' H 4.10 . . 30 . 3 DC H5' H 4.07 . . 31 . 3 DC H5'' H 4.17 . . 32 . 4 IGU H1 H 11.29 . . 33 . 4 IGU H61 H 7.35 . . 34 . 4 IGU H62 H 7.35 . . 35 . 4 IGU H8 H 8.06 . . 36 . 4 IGU H1' H 5.00 . . 37 . 4 IGU H2' H 2.74 . . 38 . 4 IGU H2'' H 2.61 . . 39 . 4 IGU H3' H 4.96 . . 40 . 4 IGU H4' H 4.25 . . 41 . 4 IGU H5' H 3.96 . . 42 . 4 IGU H5'' H 4.10 . . 43 . 5 DA H2 H 7.10 . . 44 . 5 DA H61 H 7.29 . . 45 . 5 DA H62 H 5.83 . . 46 . 5 DA H8 H 8.28 . . 47 . 5 DA H1' H 6.06 . . 48 . 5 DA H2' H 2.82 . . 49 . 5 DA H2'' H 2.95 . . 50 . 5 DA H3' H 5.12 . . 51 . 5 DA H4' H 4.50 . . 52 . 5 DA H5' H 4.08 . . 53 . 5 DA H5'' H 4.18 . . 54 . 6 DA H2 H 7.50 . . 55 . 6 DA H61 H 7.06 . . 56 . 6 DA H62 H 6.02 . . 57 . 6 DA H8 H 8.22 . . 58 . 6 DA H1' H 6.18 . . 59 . 6 DA H2' H 2.60 . . 60 . 6 DA H2'' H 3.00 . . 61 . 6 DA H3' H 5.04 . . 62 . 6 DA H4' H 4.50 . . 63 . 6 DA H5' H 4.25 . . 64 . 6 DA H5'' H 4.31 . . 65 . 7 DT H3 H 13.79 . . 66 . 7 DT H6 H 7.16 . . 67 . 7 DT H71 H 1.25 . . 68 . 7 DT H72 H 1.25 . . 69 . 7 DT H73 H 1.25 . . 70 . 7 DT H1' H 5.93 . . 71 . 7 DT H2' H 2.06 . . 72 . 7 DT H2'' H 2.63 . . 73 . 7 DT H3' H 4.88 . . 74 . 7 DT H4' H 4.25 . . 75 . 7 DT H5' H 4.36 . . 76 . 7 DT H5'' H 4.38 . . 77 . 8 DT H3 H 13.77 . . 78 . 8 DT H6 H 7.45 . . 79 . 8 DT H71 H 1.54 . . 80 . 8 DT H72 H 1.54 . . 81 . 8 DT H73 H 1.54 . . 82 . 8 DT H1' H 6.07 . . 83 . 8 DT H2' H 2.18 . . 84 . 8 DT H2'' H 2.65 . . 85 . 8 DT H3' H 4.92 . . 86 . 8 DT H4' H 4.23 . . 87 . 8 DT H5' H 4.11 . . 88 . 8 DT H5'' H 4.25 . . 89 . 9 DT H3 H 12.68 . . 90 . 9 DT H6 H 7.43 . . 91 . 9 DT H71 H 1.62 . . 92 . 9 DT H72 H 1.62 . . 93 . 9 DT H73 H 1.62 . . 94 . 9 DT H1' H 6.07 . . 95 . 9 DT H2' H 2.19 . . 96 . 9 DT H2'' H 2.63 . . 97 . 9 DT H3' H 4.93 . . 98 . 9 DT H4' H 4.26 . . 99 . 9 DT H5' H 4.12 . . 100 . 9 DT H5'' H 4.19 . . 101 . 10 DG H1 H 12.79 . . 102 . 10 DG H8 H 7.90 . . 103 . 10 DG H1' H 5.70 . . 104 . 10 DG H2' H 2.59 . . 105 . 10 DG H2'' H 2.62 . . 106 . 10 DG H3' H 4.97 . . 107 . 10 DG H4' H 4.35 . . 108 . 10 DG H5' H 4.15 . . 109 . 10 DG H5'' H 4.24 . . 110 . 11 DC H41 H 8.48 . . 111 . 11 DC H42 H 6.69 . . 112 . 11 DC H5 H 5.46 . . 113 . 11 DC H6 H 7.42 . . 114 . 11 DC H1' H 5.83 . . 115 . 11 DC H2' H 1.95 . . 116 . 11 DC H2'' H 2.39 . . 117 . 11 DC H3' H 4.85 . . 118 . 11 DC H4' H 4.19 . . 119 . 11 DC H5' H 4.11 . . 120 . 11 DC H5'' H 4.24 . . 121 . 12 DG H1 H 13.29 . . 122 . 12 DG H21 H 7.08 . . 123 . 12 DG H22 H 6.92 . . 124 . 12 DG H8 H 7.98 . . 125 . 12 DG H1' H 6.16 . . 126 . 12 DG H2' H 2.64 . . 127 . 12 DG H2'' H 2.35 . . 128 . 12 DG H3' H 4.68 . . 129 . 12 DG H4' H 4.18 . . 130 . 12 DG H5' H 4.11 . . 131 . 12 DG H5'' H 4.07 . . stop_ save_