data_4556 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 31P NMR analysis of the DNA conformation induced by protein binding:SRY-DNA complexes ; _BMRB_accession_number 4556 _BMRB_flat_file_name bmr4556.str _Entry_type original _Submission_date 1999-12-11 _Accession_date 1999-12-13 _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 Castagne Claire . . 2 Murphy Elizabeth C. . 3 Gronenborn Angela M. . 4 Delepierre Muriel . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 137 "31P chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2000-01-11 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; 31P NMR analysis of the DNA conformation induced by protein binding:SRY-DNA complexes ; _Citation_status submitted _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Castagne Claire . . 2 Murphy Elizabeth C. . 3 Gronenborn Angela M. . 4 Delepierre Muriel . . stop_ _Journal_abbreviation 'Eur. J. Biochem.' _Journal_name_full 'European Journal of Biochemistry' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . loop_ _Keyword '31P NMR on protein:DNA complexes' stop_ save_ ################################## # Molecular system description # ################################## save_SRY-8mer_duplex _Saveframe_category molecular_system _Mol_system_name 'SRY-8mer duplex' _Abbreviation_common '8mer duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '8mer strand 1' $SRY_8-mer_strand_1 '8mer strand 2' $SRY_8-mer_strand_2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_SRY_8-mer_strand_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'SRY 8mer strand 1' _Abbreviation_common 'SRY 8-mer strand 1' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence GCACAAAC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DG 2 2 DC 3 3 DA 4 4 DC 5 5 DA 6 6 DA 7 7 DA 8 8 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_SRY_8-mer_strand_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'SRY 8mer strand 2' _Abbreviation_common 'SRY 8-mer strand 2' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 8 _Mol_residue_sequence GTTTGTGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 9 DG 2 10 DT 3 11 DT 4 12 DT 5 13 DG 6 14 DT 7 15 DG 8 16 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 $SRY_8-mer_strand_1 . . Eukaryota . na na $SRY_8-mer_strand_2 . . Eukaryota . na na 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 $SRY_8-mer_strand_1 'chemical synthesis' . . . . . $SRY_8-mer_strand_2 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_SRY-8mer _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SRY_8-mer_strand_1 2.5 mM . $SRY_8-mer_strand_2 2.5 mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H COSY' _Sample_label $SRY-8mer save_ save_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _Sample_label $SRY-8mer save_ save_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label $SRY-8mer save_ save_1H-31P_HSQC-TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P HSQC-TOCSY' _Sample_label $SRY-8mer save_ save_1H-31P_HCOSYINV_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P HCOSYINV' _Sample_label $SRY-8mer save_ save_31P-31P_NOESY_Exchange_6 _Saveframe_category NMR_applied_experiment _Experiment_name '31P-31P NOESY Exchange' _Sample_label $SRY-8mer save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P HSQC-TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-31P HCOSYINV' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_6 _Saveframe_category NMR_applied_experiment _Experiment_name '31P-31P NOESY Exchange' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_cond1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 0.2 n/a temperature 298 .5 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 P 31 'methyl protons' ppm 0.0 . indirect . . . 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_SRY-8mer-c1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $SRY-8mer stop_ _Sample_conditions_label $cond1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '8mer strand 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 DG H8 H 7.92 .03 1 2 . 1 DG H1' H 5.93 .03 1 3 . 1 DG H2' H 2.60 .03 1 4 . 1 DG H2'' H 2.76 .03 1 5 . 1 DG H3' H 4.84 .03 1 6 . 1 DG H4' H 4.26 .03 1 7 . 1 DG H5' H 3.72 .03 2 8 . 1 DG H5'' H 3.72 .03 2 9 . 1 DG P P -4.18 .03 1 10 . 2 DC H41 H 6.50 .03 2 11 . 2 DC H42 H 8.43 .03 2 12 . 2 DC H5 H 5.44 .03 1 13 . 2 DC H6 H 7.47 .03 1 14 . 2 DC H1' H 5.63 .03 1 15 . 2 DC H2' H 2.09 .03 1 16 . 2 DC H2'' H 2.42 .03 1 17 . 2 DC H3' H 4.87 .03 1 18 . 2 DC H4' H 4.21 .03 1 19 . 2 DC H5' H 4.06 .03 2 20 . 2 DC H5'' H 4.13 .03 2 21 . 2 DC P P -4.00 .03 1 22 . 3 DA H2 H 7.72 .03 1 23 . 3 DA H8 H 8.28 .03 1 24 . 3 DA H1' H 6.19 .03 1 25 . 3 DA H2' H 2.70 .03 1 26 . 3 DA H2'' H 2.87 .03 1 27 . 3 DA H3' H 5.03 .03 1 28 . 3 DA H4' H 4.42 .03 1 29 . 3 DA P P -4.28 .03 1 30 . 4 DC H5 H 5.36 .03 1 31 . 4 DC H6 H 7.25 .03 1 32 . 4 DC H1' H 5.30 .03 1 33 . 4 DC H2' H 1.81 .03 1 34 . 4 DC H2'' H 2.17 .03 1 35 . 4 DC H3' H 5.04 .03 1 36 . 4 DC H4' H 4.10 .03 1 37 . 4 DC P P -4.01 .03 1 38 . 5 DA H2 H 7.12 .03 1 39 . 5 DA H61 H 6.47 .03 2 40 . 5 DA H62 H 8.23 .03 2 41 . 5 DA H8 H 8.16 .03 1 42 . 5 DA H1' H 5.73 .03 1 43 . 5 DA H2' H 2.68 .03 1 44 . 5 DA H2'' H 2.81 .03 1 45 . 5 DA H3' H 5.02 .03 1 46 . 5 DA H4' H 4.35 .03 1 47 . 5 DA H5' H 4.19 .03 2 48 . 5 DA H5'' H 4.19 .03 2 49 . 5 DA P P -4.22 .03 1 50 . 6 DA H2 H 7.20 .03 1 51 . 6 DA H8 H 8.10 .03 1 52 . 6 DA H1' H 5.85 .03 1 53 . 6 DA H2' H 2.61 .03 1 54 . 6 DA H2'' H 2.81 .03 1 55 . 6 DA H3' H 5.04 .03 1 56 . 6 DA H4' H 4.42 .03 1 57 . 6 DA P P -4.15 .03 1 58 . 7 DA H2 H 7.75 .03 1 59 . 7 DA H8 H 8.02 .03 1 60 . 7 DA H1' H 6.10 .03 1 61 . 7 DA H2' H 2.48 .03 1 62 . 7 DA H2'' H 2.81 .03 1 63 . 7 DA H3' H 4.97 .03 1 64 . 7 DA H4' H 4.43 .03 1 65 . 7 DA H5' H 4.26 .03 2 66 . 7 DA H5'' H 4.26 .03 2 67 . 7 DA P P -4.07 .03 1 68 . 8 DC H5 H 5.05 .03 1 69 . 8 DC H6 H 7.18 .03 1 70 . 8 DC H1' H 5.95 .03 1 71 . 8 DC H2' H 2.05 .03 1 72 . 8 DC H2'' H 2.13 .03 1 73 . 8 DC H3' H 4.44 .03 1 74 . 8 DC H4' H 4.00 .03 1 stop_ save_ save_SRY-8mer-c2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $SRY-8mer stop_ _Sample_conditions_label $cond1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name '8mer strand 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 . 1 DG H1 H 12.46 .03 1 2 . 1 DG H8 H 7.91 .03 1 3 . 1 DG H1' H 5.99 .03 1 4 . 1 DG H2' H 2.71 .03 2 5 . 1 DG H2'' H 2.82 .03 2 6 . 1 DG H3' H 4.82 .03 1 7 . 1 DG H4' H 4.27 .03 1 8 . 1 DG H5' H 4.17 .03 2 9 . 1 DG H5'' H 4.17 .03 2 10 . 1 DG P P -4.23 .03 1 11 . 2 DT H3 H 14.06 .03 1 12 . 2 DT H6 H 7.48 .03 1 13 . 2 DT H71 H 1.33 .03 1 14 . 2 DT H72 H 1.33 .03 1 15 . 2 DT H73 H 1.33 .03 1 16 . 2 DT H1' H 6.20 .03 1 17 . 2 DT H2' H 2.24 .03 1 18 . 2 DT H2'' H 2.64 .03 1 19 . 2 DT H3' H 4.92 .03 1 20 . 2 DT H4' H 4.33 .03 1 21 . 2 DT P P -4.34 .03 1 22 . 3 DT H3 H 13.96 .03 1 23 . 3 DT H6 H 7.53 .03 1 24 . 3 DT H71 H 1.65 .03 1 25 . 3 DT H72 H 1.65 .03 1 26 . 3 DT H73 H 1.65 .03 1 27 . 3 DT H1' H 6.19 .03 1 28 . 3 DT H2' H 2.24 .03 1 29 . 3 DT H2'' H 2.64 .03 1 30 . 3 DT H3' H 4.93 .03 1 31 . 3 DT H4' H 4.23 .03 1 32 . 3 DT P P -4.34 .03 1 33 . 4 DT H3 H 13.64 .03 1 34 . 4 DT H6 H 7.40 .03 1 35 . 4 DT H71 H 1.73 .03 1 36 . 4 DT H72 H 1.73 .03 1 37 . 4 DT H73 H 1.73 .03 1 38 . 4 DT H1' H 5.85 .03 1 39 . 4 DT H2' H 2.21 .03 1 40 . 4 DT H2'' H 2.53 .03 1 41 . 4 DT H3' H 4.93 .03 1 42 . 4 DT H4' H 4.21 .03 1 43 . 4 DT P P -4.09 .03 1 44 . 5 DG H1 H 12.46 .03 1 45 . 5 DG H8 H 7.92 .03 1 46 . 5 DG H1' H 5.94 .03 1 47 . 5 DG H2' H 2.64 .03 1 48 . 5 DG H2'' H 2.77 .03 1 49 . 5 DG H3' H 4.99 .03 1 50 . 5 DG H4' H 4.42 .03 5 51 . 5 DG P P -4.33 .03 1 52 . 6 DT H3 H 13.66 .03 1 53 . 6 DT H6 H 7.19 .03 1 54 . 6 DT H71 H 1.43 .03 1 55 . 6 DT H72 H 1.43 .03 1 56 . 6 DT H73 H 1.43 .03 1 57 . 6 DT H1' H 5.80 .03 1 58 . 6 DT H2' H 2.02 .03 1 59 . 6 DT H2'' H 2.40 .03 1 60 . 6 DT H3' H 4.88 .03 1 61 . 6 DT H4' H 4.21 .03 1 62 . 6 DT P P -4.15 .03 1 63 . 7 DG H1 H 12.87 .03 1 64 . 7 DG H8 H 7.87 .03 1 65 . 7 DG H1' H 5.93 .03 1 66 . 7 DG H2' H 2.60 .03 1 67 . 7 DG H2'' H 2.70 .03 1 68 . 7 DG H3' H 4.98 .03 1 69 . 7 DG H4' H 4.35 .03 1 70 . 7 DG P P -3.91 .03 1 71 . 8 DC H5 H 5.31 .03 1 72 . 8 DC H6 H 7.40 .03 1 73 . 8 DC H1' H 6.15 .03 1 74 . 8 DC H2' H 2.22 .03 1 75 . 8 DC H2'' H 2.70 .03 5 76 . 8 DC H3' H 4.50 .03 1 77 . 8 DC H4' H 4.05 .03 1 stop_ save_