data_15898 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; H1, C13, 31P chemical shifts of dGCGAAAGC ; _BMRB_accession_number 15898 _BMRB_flat_file_name bmr15898.str _Entry_type new _Submission_date 2008-07-29 _Accession_date 2008-07-29 _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 Santini Guillaume P.H. . 2 Cognet Jean A.H. . 3 Xu Duanxiang . . 4 Singarapu Kiran K. . 5 'Herve du Penhoat' Catherine . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 72 "13C chemical shifts" 42 "31P chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 2009-05-18 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Nucleic Acid Folding Determined by Mesoscale Modeling and NMR Spectroscopy: Solution Structure of d(GCGAAAGC)' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19374420 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Santini Guillaume P.H. . 2 Cognet Jean A.H. . 3 Xu Duanxiang . . 4 Singarapu Kiran K. . 5 'Herve du Penhoat' Catherine . . stop_ _Journal_abbreviation 'J. Phys. Chem. B' _Journal_name_full 'The Journal of Physical Chemistry B' _Journal_volume 113 _Journal_issue 19 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6881 _Page_last 6893 _Year 2009 _Details . loop_ _Keyword 'DNA hairpin' 'sheared base pair' 'NMR nucleic acid structure' 'Biopolymer Chain Elasticity approach' 'molecular dynamics' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA GAAA tetraloop' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'chain A' $dGCGAAAGC stop_ _System_molecular_weight 2443.6 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function unknown stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_dGCGAAAGC _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common dGCGAAAGC _Molecular_mass 2443.6 _Mol_thiol_state 'not present' loop_ _Biological_function unknown stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence GCGAAAGC loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DA 6 DA 7 DG 8 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 $dGCGAAAGC 'phage G4' 10843 Viruses . Microvirus 'Enterobacteria phage G4 sensu lato' 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 $dGCGAAAGC 'obtained from a vendor' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 10 mM sodium phosphate buffer pH 6.8, 50 mM Na Cl, 5 micromolar EDTA, 2.5 micromolar NaN3 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $dGCGAAAGC 4 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'sodium azide' 0.0025 mM 'natural abundance' EDTA 0.005 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details ; 10 mM sodium phosphate buffer pH 6.8, 50 mM Na Cl, 5 micromolar EDTA, 2.5 micromolar NaN3 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $dGCGAAAGC 4 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'sodium azide' 0.0025 mM 'natural abundance' EDTA 0.005 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' D2O 10 % 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_PROSA _Saveframe_category software _Name PROSA _Version . loop_ _Vendor _Address _Electronic_address Guntert . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task visualisation stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 750 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity _Field_strength 400 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-31P_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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 temperature 298.15 0.1 K pH 6.8 0.1 pH pressure 1 . atm 'ionic strength' 50 . mM stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 274.15 0.1 K pH 6.8 0.1 pH pressure 1 . atm 'ionic strength' 50 . mM stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_DSS _Saveframe_category chemical_shift_reference _Details 'Indirect referencing to DSS according to Wishart et al J Biomol NMR 1995' 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 0.000 external direct . 'separate tube (no insert) similar to the experimental sample tube' . 1.000000000 DSS C 13 'methyl protons' ppm 0.000 external indirect . . . 0.251449530 DSS P 31 'methyl protons' ppm 0.000 external 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D DQF-COSY' '2D 1H-13C HSQC' '2D 1H-31P COSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $DSS _Mol_system_component_name 'chain A' _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 DG H1 H 12.84 0.01 1 2 1 1 DG H1' H 6.006 0.005 1 3 1 1 DG H2' H 2.580 0.005 2 4 1 1 DG H2'' H 2.766 0.005 2 5 1 1 DG H3' H 4.859 0.005 1 6 1 1 DG H4' H 4.252 0.005 1 7 1 1 DG H5' H 3.758 0.005 2 8 1 1 DG H5'' H 3.758 0.005 2 9 1 1 DG H8 H 7.998 0.005 1 10 1 1 DG C1' C 85.14 0.05 1 11 1 1 DG C2' C 40.01 0.05 1 12 1 1 DG C3' C 79.39 0.05 1 13 1 1 DG C4' C 89.06 0.05 1 14 1 1 DG C5' C 64.21 0.05 1 15 2 2 DC H1' H 6.093 0.005 1 16 2 2 DC H2' H 1.585 0.005 2 17 2 2 DC H2'' H 2.242 0.005 2 18 2 2 DC H3' H 4.747 0.005 1 19 2 2 DC H4' H 4.249 0.005 1 20 2 2 DC H5 H 5.198 0.005 1 21 2 2 DC H5' H 4.118 0.005 2 22 2 2 DC H5'' H 4.118 0.005 2 23 2 2 DC H6 H 7.118 0.005 1 24 2 2 DC H41 H 8.400 0.005 2 25 2 2 DC H42 H 6.746 0.005 2 26 2 2 DC C1' C 86.11 0.05 1 27 2 2 DC C2' C 38.42 0.05 1 28 2 2 DC C3' C 79.39 0.05 1 29 2 2 DC C4' C 86.13 0.05 1 30 2 2 DC C5 C 97.96 0.05 1 31 2 2 DC C5' C 67.79 0.05 1 32 2 2 DC P P -4.51 0.005 1 33 3 3 DG H1 H 10.8 0.01 1 34 3 3 DG H1' H 5.570 0.005 1 35 3 3 DG H2' H 2.733 0.005 2 36 3 3 DG H2'' H 2.629 0.005 2 37 3 3 DG H3' H 5.030 0.005 1 38 3 3 DG H4' H 4.527 0.005 1 39 3 3 DG H5' H 4.174 0.005 2 40 3 3 DG H5'' H 4.174 0.005 2 41 3 3 DG H8 H 8.057 0.005 1 42 3 3 DG C1' C 84.36 0.05 1 43 3 3 DG C2' C 39.85 0.05 1 44 3 3 DG C3' C 78.35 0.05 1 45 3 3 DG C4' C 87.36 0.05 1 46 3 3 DG C5' C 67.39 0.05 1 47 3 3 DG P P -4.95 0.005 1 48 4 4 DA H1' H 5.920 0.005 1 49 4 4 DA H2' H 2.216 0.005 2 50 4 4 DA H2'' H 2.324 0.005 2 51 4 4 DA H3' H 4.688 0.005 1 52 4 4 DA H4' H 3.496 0.005 1 53 4 4 DA H5' H 3.780 0.005 2 54 4 4 DA H5'' H 3.885 0.005 2 55 4 4 DA H8 H 8.160 0.005 1 56 4 4 DA C1' C 85.70 0.05 1 57 4 4 DA C2' C 41.31 0.05 1 58 4 4 DA C3' C 78.46 0.05 1 59 4 4 DA C4' C 87.03 0.05 1 60 4 4 DA C5' C 67.49 0.05 1 61 4 4 DA P P -3.81 0.005 1 62 5 5 DA H1' H 6.196 0.005 1 63 5 5 DA H2' H 2.563 0.005 2 64 5 5 DA H2'' H 2.653 0.005 2 65 5 5 DA H3' H 4.842 0.005 1 66 5 5 DA H4' H 4.129 0.005 1 67 5 5 DA H5' H 3.665 0.005 2 68 5 5 DA H5'' H 3.886 0.005 2 69 5 5 DA H8 H 8.109 0.005 1 70 5 5 DA C1' C 86.01 0.05 1 71 5 5 DA C2' C 41.00 0.05 1 72 5 5 DA C3' C 79.08 0.05 1 73 5 5 DA C4' C 87.13 0.05 1 74 5 5 DA C5' C 68.21 0.05 1 75 5 5 DA P P -4.72 0.005 1 76 6 6 DA H1' H 6.168 0.005 1 77 6 6 DA H2' H 2.432 0.005 2 78 6 6 DA H2'' H 2.751 0.005 2 79 6 6 DA H3' H 4.922 0.005 1 80 6 6 DA H4' H 4.416 0.005 1 81 6 6 DA H5' H 4.123 0.005 2 82 6 6 DA H5'' H 4.091 0.005 2 83 6 6 DA C1' C 85.29 0.05 1 84 6 6 DA C2' C 39.35 0.05 1 85 6 6 DA C3' C 79.70 0.05 1 86 6 6 DA C4' C 87.56 0.05 1 87 6 6 DA C5' C 68.73 0.05 1 88 6 6 DA P P -4.51 0.005 1 89 7 7 DG H1 H 12.93 0.01 1 90 7 7 DG H1' H 5.609 0.005 1 91 7 7 DG H2' H 2.614 0.005 2 92 7 7 DG H2'' H 2.614 0.005 2 93 7 7 DG H3' H 4.976 0.005 1 94 7 7 DG H4' H 4.395 0.005 1 95 7 7 DG H5' H 4.265 0.005 2 96 7 7 DG H5'' H 4.196 0.005 2 97 7 7 DG H8 H 8.034 0.005 1 98 7 7 DG C1' C 84.36 0.05 1 99 7 7 DG C2' C 40.57 0.05 1 100 7 7 DG C3' C 78.56 0.05 1 101 7 7 DG C4' C 86.95 0.05 1 102 7 7 DG C5' C 67.69 0.05 1 103 7 7 DG P P -4.87 0.005 1 104 8 8 DC H1' H 6.275 0.005 1 105 8 8 DC H2' H 2.241 0.005 2 106 8 8 DC H2'' H 2.293 0.005 2 107 8 8 DC H3' H 4.532 0.005 1 108 8 8 DC H4' H 4.117 0.005 1 109 8 8 DC H5 H 5.305 0.005 1 110 8 8 DC H5' H 4.249 0.005 2 111 8 8 DC H5'' H 4.087 0.005 2 112 8 8 DC H6 H 7.436 0.005 1 113 8 8 DC H41 H 8.032 0.005 2 114 8 8 DC H42 H 6.331 0.005 2 115 8 8 DC C1' C 86.84 0.05 1 116 8 8 DC C2' C 41.62 0.05 1 117 8 8 DC C3' C 71.94 0.05 1 118 8 8 DC C4' C 86.95 0.05 1 119 8 8 DC C5 C 98.22 0.05 1 120 8 8 DC C5' C 67.28 0.05 1 121 8 8 DC P P -4.18 0.005 1 stop_ save_