data_15033 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Dimeric solution structure of the cyclic octamer d(CCGTCCGT) ; _BMRB_accession_number 15033 _BMRB_flat_file_name bmr15033.str _Entry_type original _Submission_date 2006-11-16 _Accession_date 2006-11-16 _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 Escaja N. . . 2 Gomez-Pinto I. . . 3 Pedroso E. . . 4 Gonzalez C. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 43 "13C chemical shifts" 20 "31P chemical shifts" 4 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2007-10-16 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Four stranded DNA structures can be stabilized by two different types of minor groove G:C:G:C tetrads' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17260988 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Escaja N. . . 2 Gomez-Pinto I. . . 3 Pedroso E. . . 4 Gonzalez C. . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 129 _Journal_issue 7 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2004 _Page_last 2014 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cyclic octamer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'subunit 1' $5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3' 'subunit 2' $5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3' stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic ? _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence CCGTCCGT loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DG 4 DT 5 DC 6 DC 7 DG 8 DT 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 $5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3' . . . . . . 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 $5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3' 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '5mM oligonucleotide concentration, 100mM NaCl buffer, 90% H2O, 10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $5'-D(P*CP*CP*GP*TP*CP*CP*GP*T)-3' 5 mM 'natural abundance' 'sodium chloride' 100 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version 1.5 loop_ _Vendor _Address _Electronic_address 'T.L. James' . . stop_ loop_ _Task 'iterative matrix relaxation' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 7.0 loop_ _Vendor _Address _Electronic_address 'Kollman et al' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 800 _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 save_ save_2D_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample 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 . pH pressure 1 . atm temperature 289 . 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 TSP H 1 'methyl protons' ppm 0 internal direct . . . 1.0 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 _Saveframe_category assigned_chemical_shifts _Details ; This oligonucleotide adopts an unusual structural, so some chemical shifts deviate significantly from standard values. ; loop_ _Experiment_label '2D 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'subunit 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 H5 H 6.11 0.01 1 2 1 1 DC H6 H 8.05 0.01 1 3 1 1 DC H1' H 6.48 0.01 1 4 1 1 DC H2' H 2.26 0.01 1 5 1 1 DC H3' H 4.62 0.01 1 6 1 1 DC H4' H 4.62 0.01 1 7 1 1 DC H5' H 4.01 0.01 2 8 1 1 DC H2'' H 2.64 0.01 1 9 1 1 DC H5'' H 4.23 0.01 2 10 1 1 DC C1' C 79.90 0.01 1 11 1 1 DC C2' C 32.62 0.01 1 12 1 1 DC C3' C 70.48 0.01 1 13 1 1 DC C4' C 78.00 0.01 1 14 1 1 DC C5' C 59.30 0.01 1 15 1 1 DC P P -4.13 0.01 1 16 2 2 DC H5 H 6.01 0.01 1 17 2 2 DC H6 H 7.82 0.01 1 18 2 2 DC H41 H 9.04 0.01 1 19 2 2 DC H42 H 7.01 0.01 1 20 2 2 DC H1' H 6.34 0.01 1 21 2 2 DC H2' H 2.34 0.01 1 22 2 2 DC H3' H 4.96 0.01 1 23 2 2 DC H4' H 4.44 0.01 1 24 2 2 DC H5' H 4.09 0.01 1 25 2 2 DC H2'' H 2.81 0.01 1 26 2 2 DC H5'' H 4.21 0.01 1 27 2 2 DC C1' C 77.90 0.01 1 28 2 2 DC C2' C 30.62 0.01 1 29 2 2 DC C3' C 71.94 0.01 1 30 2 2 DC C4' C 77.80 0.01 1 31 2 2 DC C5' C 60.10 0.01 1 32 2 2 DC P P -4.27 0.01 1 33 3 3 DG H1 H 13.76 0.01 1 34 3 3 DG H8 H 7.86 0.01 1 35 3 3 DG H21 H 9.36 0.01 1 36 3 3 DG H22 H 8.01 0.01 1 37 3 3 DG H1' H 6.11 0.01 1 38 3 3 DG H2' H 2.71 0.01 1 39 3 3 DG H3' H 5.13 0.01 1 40 3 3 DG H4' H 4.51 0.01 1 41 3 3 DG H5' H 4.25 0.01 1 42 3 3 DG H2'' H 2.55 0.01 1 43 3 3 DG H5'' H 4.25 0.01 1 44 3 3 DG C1' C 74.9 0.01 1 45 3 3 DG C2' C 33.12 0.01 1 46 3 3 DG C3' C 67.72 0.01 1 47 3 3 DG C4' C 77.60 0.01 1 48 3 3 DG C5' C 58.50 0.01 1 49 3 3 DG P P -3.98 0.01 1 50 4 4 DT H3 H 10.51 0.01 1 51 4 4 DT H6 H 7.58 0.01 1 52 4 4 DT H71 H 1.70 0.01 1 53 4 4 DT H72 H 1.70 0.01 1 54 4 4 DT H73 H 1.70 0.01 1 55 4 4 DT H1' H 6.01 0.01 1 56 4 4 DT H2' H 1.95 0.01 1 57 4 4 DT H3' H 4.73 0.01 1 58 4 4 DT H4' H 3.84 0.01 1 59 4 4 DT H5' H 3.84 0.01 2 60 4 4 DT H2'' H 2.47 0.01 1 61 4 4 DT H5'' H 3.80 0.01 2 62 4 4 DT C1' C 80.60 0.01 1 63 4 4 DT C2' C 34.38 0.01 1 64 4 4 DT C3' C 71.58 0.01 1 65 4 4 DT C4' C 78.8 0.01 1 66 4 4 DT C5' C 59.4 0.01 1 67 4 4 DT P P -3.83 0.01 1 stop_ save_