data_34056 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of DNA AGCGA-quadruplex adopted by 15-mer oligonucleotide found in regulatory region of the PLEKHG3 human gene with G11 to I11 mutation, d(GCGAGGGAGCIAGGG),VK34_I11 ; _BMRB_accession_number 34056 _BMRB_flat_file_name bmr34056.str _Entry_type original _Submission_date 2016-10-19 _Accession_date 2016-10-19 _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 Kocman V. . . 2 Plavec J. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 79 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-05-25 original BMRB . stop_ _Original_release_date 2017-05-22 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28513602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kocman V. . . 2 Plavec J. . . stop_ _Journal_abbreviation 'Nat. Commun.' _Journal_volume 8 _Journal_issue . _Journal_ISSN 2041-1723 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 15355 _Page_last 15355 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common entity_1 _Molecular_mass 4750.071 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence ; GCGAGGGAGCXAGGG ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DG 6 DG 7 DG 8 DA 9 DG 10 DC 11 DI 12 DA 13 DG 14 DG 15 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DI _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common 2'-DEOXYINOSINE-5'-MONOPHOSPHATE _BMRB_code DI _PDB_code DI _Standard_residue_derivative . _Molecular_mass 332.207 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OP3 OP3 O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING OP3 P ? ? SING OP3 HOP3 ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING N1 C2 ? ? SING N1 H1 ? ? DOUB C2 N3 ? ? SING C2 H2 ? ? SING N3 C4 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 Human 9606 Eukaryota Metazoa Homo sapiens 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details "1 mM DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3'), 100 mM LiCl, 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' LiCl 100 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details "1 mM residue specific 15N labeled DNA (5'-D(*GP*CP*GP*AP*GP*GP*GP*AP*GP*CP*IP*AP*GP*GP*G)-3'), 100 mM LiCl, 90% H2O/10% D2O" loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'residue specific 15N labeled' LiCl 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model 'Uniform NMR System' _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent-Varian _Model 'Uniform NMR System' _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_1 save_ save_1D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H-15N HSQC' _Sample_label $sample_2 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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 6 . pH pressure 1 . atm temperature 273 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 TMS H 1 'methyl protons' ppm 0 external 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '1D 1H-15N HSQC' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 'entity_1, 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 DG H1 H 12.753 0.003 1 2 1 1 DG H1' H 5.93 0.002 1 3 1 1 DG H2' H 2.485 0.006 1 4 1 1 DG H2'' H 2.7 0.006 1 5 1 1 DG H3' H 4.793 0.006 1 6 1 1 DG H8 H 7.911 0.002 1 7 2 2 DC H1' H 6.031 0.001 1 8 2 2 DC H2' H 1.657 0.003 1 9 2 2 DC H2'' H 2.254 0.005 1 10 2 2 DC H3' H 4.829 0.003 1 11 2 2 DC H5 H 4.973 0 1 12 2 2 DC H6 H 7.022 0.001 1 13 2 2 DC H41 H 8.42 0.003 1 14 2 2 DC H42 H 6.817 0.003 1 15 3 3 DG H1 H 10.385 0.005 1 16 3 3 DG H1' H 6.035 0.002 1 17 3 3 DG H2' H 2.795 0.008 1 18 3 3 DG H2'' H 2.869 0.003 1 19 3 3 DG H3' H 4.531 0.004 1 20 3 3 DG H8 H 8.24 0.001 1 21 3 3 DG H21 H 9.299 0.007 1 22 4 4 DA H1' H 5.366 0.004 1 23 4 4 DA H2 H 7.65 0.002 1 24 4 4 DA H2' H 2.206 0.002 1 25 4 4 DA H2'' H 0.558 0.003 1 26 4 4 DA H3' H 4.77 0.002 1 27 4 4 DA H8 H 7.491 0.003 1 28 5 5 DG H1 H 10.517 0.004 1 29 5 5 DG H1' H 5.663 0.002 1 30 5 5 DG H2' H 2.452 0.002 1 31 5 5 DG H2'' H 2.939 0.001 1 32 5 5 DG H3' H 4.735 0.002 1 33 5 5 DG H8 H 6.919 0.001 1 34 6 6 DG H1 H 10.986 0.003 1 35 6 6 DG H1' H 5.687 0.007 1 36 6 6 DG H2' H 1.967 0.003 1 37 6 6 DG H2'' H 2.113 0.004 1 38 6 6 DG H3' H 4.864 0.003 1 39 6 6 DG H8 H 7.386 0.003 1 40 7 7 DG H1 H 10.441 0.005 1 41 7 7 DG H1' H 5.938 0.003 1 42 7 7 DG H2' H 2.685 0.009 1 43 7 7 DG H2'' H 2.897 0.014 1 44 7 7 DG H3' H 4.506 0.006 1 45 7 7 DG H8 H 8.144 0.003 1 46 7 7 DG H21 H 8.823 0.004 1 47 8 8 DA H1' H 5.568 0.003 1 48 8 8 DA H2 H 7.888 0.003 1 49 8 8 DA H2' H 1.01 0.002 1 50 8 8 DA H2'' H 2.328 0.004 1 51 8 8 DA H3' H 4.761 0.002 1 52 8 8 DA H8 H 7.274 0.005 1 53 9 9 DG H1 H 12.947 0.003 1 54 9 9 DG H1' H 5.33 0.004 1 55 9 9 DG H2' H 2.473 0.005 1 56 9 9 DG H2'' H 2.615 0.002 1 57 9 9 DG H3' H 4.897 0.001 1 58 9 9 DG H8 H 7.93 0.003 1 59 10 10 DC H1' H 5.826 0.002 1 60 10 10 DC H2' H 1.829 0.004 1 61 10 10 DC H2'' H 2.25 0.006 1 62 10 10 DC H3' H 4.758 0.002 1 63 10 10 DC H5 H 5.248 0.003 1 64 10 10 DC H6 H 7.208 0.003 1 65 10 10 DC H41 H 8.052 0.003 1 66 10 10 DC H42 H 6.589 0.002 1 67 11 11 DI H1' H 5.659 0.002 1 68 11 11 DI H2' H 2.111 0.002 1 69 11 11 DI H2'' H 2.369 0.001 1 70 11 11 DI H8 H 7.966 0.004 1 71 12 12 DA H1' H 5.713 0 1 72 12 12 DA H2' H 2.369 0 1 73 12 12 DA H2'' H 2.442 0 1 74 12 12 DA H8 H 7.992 0.001 1 75 13 13 DG H1' H 6.035 0.001 1 76 13 13 DG H2' H 2.403 0.003 1 77 13 13 DG H2'' H 2.626 0 1 78 13 13 DG H3' H 4.705 0.001 1 79 13 13 DG H8 H 7.912 0.001 1 stop_ save_