data_18593 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of a RNA Duplex Containing a 2'-O-Pivaloyloxymethyl Modification ; _BMRB_accession_number 18593 _BMRB_flat_file_name bmr18593.str _Entry_type original _Submission_date 2012-07-13 _Accession_date 2012-07-13 _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 Baraguey Carine . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 178 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-04-08 original author . stop_ _Original_release_date 2013-04-08 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23455628 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Baraguey Carine . . 2 Lescrinier Eveline . . 3 Lavergne Thomas . . 4 Debart Francoise . . 5 Herdewijn Piet . . 6 Vasseur Jean-Jacques . . stop_ _Journal_abbreviation 'Org. Biomol. Chem.' _Journal_volume 11 _Journal_issue 16 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2638 _Page_last 2647 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'RNA Duplex Containing a 2'-O-Pivaloyloxymethyl Modification' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3')' $modified_strand 'DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3')' $non-modified_complementary_strand stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_modified_strand _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common modified_strand _Molecular_mass 2499.596 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence CGCXACGCX loop_ _Residue_seq_code _Residue_label 1 C 2 G 3 C 4 UPV 5 A 6 C 7 G 8 C 9 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_non-modified_complementary_strand _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common non-modified_complementary_strand _Molecular_mass 2885.813 _Mol_thiol_state 'not present' _Details . _Residue_count 9 _Mol_residue_sequence GCGUAGCGX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 10 G 2 11 C 3 12 G 4 13 U 5 14 A 6 15 G 7 16 C 8 17 G 9 18 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_UPV _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common '2'-O-{[(2,2-dimethylpropanoyl)oxy]methyl}uridine 5'-(dihydrogen phosphate)' _BMRB_code UPV _PDB_code UPV _Standard_residue_derivative . _Molecular_mass 438.324 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1' C1' C . 0 . ? C2 C2 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C6 C6 C . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CD3 CD3 C . 0 . ? CG CG C . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5 H5 H . 0 . ? H5' H5' H . 0 . ? H5'A H5'A H . 0 . ? H6 H6 H . 0 . ? HA HA H . 0 . ? HAA HAA H . 0 . ? HD1 HD1 H . 0 . ? HD1A HD1A H . 0 . ? HD1B HD1B H . 0 . ? HD2 HD2 H . 0 . ? HD2A HD2A H . 0 . ? HD2B HD2B H . 0 . ? HD3 HD3 H . 0 . ? HD3A HD3A H . 0 . ? HD3B HD3B H . 0 . ? HN3 HN3 H . 0 . ? HO3' HO3' H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? N1 N1 N . 0 . ? N3 N3 N . 0 . ? O2 O2 O . 0 . ? O2' O2' O . 0 . ? O3' O3' O . 0 . ? O4 O4 O . 0 . ? O4' O4' O . 0 . ? O5' O5' O . 0 . ? OB1 OB1 O . 0 . ? OB2 OB2 O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P P P . 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 P OP3 ? ? SING N1 C6 ? ? SING N1 C1' ? ? SING C2 N1 ? ? DOUB O2 C2 ? ? SING N3 C2 ? ? SING N3 C4 ? ? SING C4 C5 ? ? DOUB O4 C4 ? ? SING C5 H5 ? ? DOUB C5 C6 ? ? SING C6 H6 ? ? SING CA HAA ? ? SING CA O2' ? ? SING CB OB1 ? ? DOUB CB OB2 ? ? SING CG CB ? ? SING C1' O4' ? ? SING C1' C2' ? ? SING C2' O2' ? ? SING C2' C3' ? ? SING C3' O3' ? ? SING O3' HO3' ? ? SING C4' C3' ? ? SING C4' C5' ? ? SING C4' H4' ? ? SING O4' C4' ? ? SING C5' H5'A ? ? SING O5' P ? ? SING O5' C5' ? ? SING OB1 CA ? ? SING CD1 CG ? ? SING CD1 HD1B ? ? SING CD1 HD1A ? ? SING CD2 CG ? ? SING CD2 HD2B ? ? SING CD2 HD2 ? ? SING CD3 CG ? ? SING CD3 HD3 ? ? SING CD3 HD3B ? ? SING OP3 HOP3 ? ? SING OP2 P ? ? SING OP2 HOP2 ? ? SING HN3 N3 ? ? SING H5' C5' ? ? SING H1' C1' ? ? SING HD1 CD1 ? ? SING H2' C2' ? ? SING HD2A CD2 ? ? SING H3' C3' ? ? SING HD3A CD3 ? ? SING HA CA ? ? DOUB P OP1 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $modified_strand . . . . . . 'synthetic compound' $non-modified_complementary_strand . . . . . . 'synthetic compound' 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 $modified_strand 'chemical synthesis' . . . . . $non-modified_complementary_strand 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 5'-r(CGCU*ACGC)dT-3' 5'-r(GCGUAGCG)dT-3' 1:1 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $modified_strand 0.9 mM 'natural abundance' $non-modified_complementary_strand 0.9 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details ; 5'-r(CGCU*ACGC)dT-3' 5'-r(GCGUAGCG)dT-3' 1:1 ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $modified_strand 0.9 mM 'natural abundance' $non-modified_complementary_strand 0.9 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version 2.25 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _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-31P_HETCOR_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P HETCOR' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_2 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 293 . K pH 6.7 . pH pressure 1 . atm 'ionic strength' 0 . M stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 283 . K pH 6.7 . pH pressure 1 . atm 'ionic strength' 0 . M 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 water H 1 protons ppm 4.70 na direct . . . 1 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA/RNA (5'-R(CP*GP*CP*(UPV)*AP*CP*GP*C)-D(P*T)-3')' _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 C H1' H 5.554 0 1 2 1 1 C H2' H 4.534 0 1 3 1 1 C H3' H 4.494 0 1 4 1 1 C H4' H 4.277 0 1 5 1 1 C H5 H 5.942 0 1 6 1 1 C H5' H 3.859 0 1 7 1 1 C H5'' H 3.989 0 1 8 1 1 C H6 H 8.009 0 1 9 1 1 C H41 H 8.217 0 1 10 1 1 C H42 H 6.912 0 1 11 2 2 G H1 H 12.916 0 1 12 2 2 G H1' H 5.696 0 1 13 2 2 G H2' H 4.527 0 1 14 2 2 G H3' H 4.578 0 1 15 2 2 G H4' H 4.415 0 1 16 2 2 G H5' H 4.087 0 1 17 2 2 G H5'' H 4.429 0 1 18 2 2 G H8 H 7.714 0 1 19 2 2 G H21 H 5.935 0 1 20 2 2 G H22 H 8.268 0 1 21 3 3 C H1' H 5.428 0 1 22 3 3 C H2' H 4.273 0 1 23 3 3 C H3' H 4.351 0 1 24 3 3 C H4' H 4.472 0 1 25 3 3 C H5 H 5.192 0 1 26 3 3 C H5' H 4.015 0 1 27 3 3 C H5'' H 4.474 0 1 28 3 3 C H6 H 7.625 0 1 29 3 3 C H41 H 8.481 0 1 30 3 3 C H42 H 6.823 0 1 31 4 4 UPV H1' H 5.632 0 1 32 4 4 UPV H2' H 4.523 0 1 33 4 4 UPV H3' H 4.589 0 1 34 4 4 UPV H4' H 4.26 0 1 35 4 4 UPV H5 H 5.353 0 1 36 4 4 UPV H5' H 3.997 0 1 37 4 4 UPV H5'A H 4.465 0 1 38 4 4 UPV H6 H 7.791 0 1 39 4 4 UPV HA H 5.424 0 1 40 4 4 UPV HAA H 5.655 0 1 41 4 4 UPV HD1B H 1.206 0 1 42 4 4 UPV HN3 H 13.124 0 1 43 5 5 A H1' H 5.88 0 1 44 5 5 A H2 H 6.839 0 1 45 5 5 A H2' H 4.32 0 1 46 5 5 A H3' H 4.473 0 1 47 5 5 A H4' H 4.524 0 1 48 5 5 A H5' H 4.123 0 1 49 5 5 A H5'' H 4.355 0 1 50 5 5 A H8 H 8.009 0 1 51 5 5 A H61 H 6.307 0 1 52 5 5 A H62 H 7.79 0 1 53 6 6 C H1' H 5.252 0 1 54 6 6 C H2' H 4.199 0 1 55 6 6 C H3' H 4.326 0 1 56 6 6 C H4' H 4.247 0 1 57 6 6 C H5 H 5.054 0 1 58 6 6 C H5' H 3.935 0 1 59 6 6 C H5'' H 4.385 0 1 60 6 6 C H6 H 7.396 0 1 61 6 6 C H41 H 8.14 0 1 62 6 6 C H42 H 6.73 0 1 63 7 7 G H1 H 12.887 0 1 64 7 7 G H1' H 5.572 0 1 65 7 7 G H2' H 4.377 0 1 66 7 7 G H3' H 4.383 0 1 67 7 7 G H4' H 4.3 0 1 68 7 7 G H5' H 3.941 0 1 69 7 7 G H5'' H 3.936 0 1 70 7 7 G H8 H 7.388 0 1 71 7 7 G H21 H 5.935 0 1 72 7 7 G H22 H 8.298 0 1 73 8 8 C H1' H 5.411 0 1 74 8 8 C H2' H 4.24 0 1 75 8 8 C H3' H 4.136 0 1 76 8 8 C H4' H 4.25 0 1 77 8 8 C H5 H 5.018 0 1 78 8 8 C H5' H 3.89 0 1 79 8 8 C H5'' H 4.356 0 1 80 8 8 C H6 H 7.318 0 1 81 8 8 C H41 H 6.9 0 1 82 8 8 C H42 H 8.305 0 1 83 9 9 DT H1' H 5.877 0 1 84 9 9 DT H2' H 1.901 0 1 85 9 9 DT H2'' H 2.123 0 1 86 9 9 DT H3' H 4.267 0 1 87 9 9 DT H4' H 3.837 0 1 88 9 9 DT H5' H 3.886 0 1 89 9 9 DT H5'' H 4.146 0 1 90 9 9 DT H6 H 7.483 0 1 91 9 9 DT H71 H 1.486 0 1 92 9 9 DT H72 H 1.486 0 1 93 9 9 DT H73 H 1.486 0 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA/RNA (5'-R(GP*CP*GP*UP*AP*CP*GP*C)-D(P*T)-3')' _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 10 1 G H1 H 13.16 0 1 2 10 1 G H1' H 5.728 0 1 3 10 1 G H2' H 4.718 0 1 4 10 1 G H3' H 4.458 0 1 5 10 1 G H4' H 4.31 0 1 6 10 1 G H5' H 3.991 0 1 7 10 1 G H5'' H 3.832 0 1 8 10 1 G H8 H 7.989 0 1 9 11 2 C H1' H 5.548 0 1 10 11 2 C H2' H 4.613 0 1 11 11 2 C H3' H 4.481 0 1 12 11 2 C H4' H 4.382 0 1 13 11 2 C H5 H 5.202 0 1 14 11 2 C H5' H 4.472 0 1 15 11 2 C H5'' H 4.079 0 1 16 11 2 C H6 H 7.708 0 1 17 11 2 C H41 H 8.472 0 1 18 11 2 C H42 H 6.624 0 1 19 12 3 G H1 H 12.825 0 1 20 12 3 G H1' H 5.657 0 1 21 12 3 G H2' H 4.408 0 1 22 12 3 G H3' H 4.405 0 1 23 12 3 G H4' H 4.474 0 1 24 12 3 G H5' H 4.389 0 1 25 12 3 G H5'' H 4.038 0 1 26 12 3 G H8 H 7.464 0 1 27 12 3 G H21 H 5.76 0 1 28 12 3 G H22 H 7.955 0 1 29 13 4 U H1' H 5.393 0 1 30 13 4 U H2' H 4.374 0 1 31 13 4 U H3 H 13.479 0 1 32 13 4 U H3' H 4.504 0 1 33 13 4 U H4' H 4.336 0 1 34 13 4 U H5 H 5.066 0 1 35 13 4 U H5' H 4.338 0 1 36 13 4 U H5'' H 4.01 0 1 37 13 4 U H6 H 7.666 0 1 38 14 5 A H1' H 5.884 0 1 39 14 5 A H2 H 6.764 0 1 40 14 5 A H2' H 4.48 0 1 41 14 5 A H3' H 4.646 0 1 42 14 5 A H4' H 4.404 0 1 43 14 5 A H5' H 4.414 0 1 44 14 5 A H5'' H 4.062 0 1 45 14 5 A H8 H 7.966 0 1 46 14 5 A H61 H 7.636 0 1 47 14 5 A H62 H 6.242 0 1 48 15 6 G H1 H 13.335 0 1 49 15 6 G H1' H 5.407 0 1 50 15 6 G H2' H 4.268 0 1 51 15 6 G H3' H 4.337 0 1 52 15 6 G H4' H 4.315 0 1 53 15 6 G H5' H 4.371 0 1 54 15 6 G H5'' H 3.969 0 1 55 15 6 G H8 H 7.21 0 1 56 15 6 G H21 H 5.505 0 1 57 15 6 G H22 H 8.304 0 1 58 16 7 C H1' H 5.308 0 1 59 16 7 C H2' H 4.322 0 1 60 16 7 C H3' H 4.274 0 1 61 16 7 C H4' H 4.252 0 1 62 16 7 C H5 H 5.062 0 1 63 16 7 C H5' H 3.903 0 1 64 16 7 C H5'' H 3.918 0 1 65 16 7 C H6 H 7.312 0 1 66 16 7 C H41 H 8.238 0 1 67 16 7 C H42 H 6.628 0 1 68 17 8 G H1' H 5.675 0 1 69 17 8 G H2' H 4.208 0 1 70 17 8 G H3' H 4.32 0 1 71 17 8 G H4' H 4.283 0 1 72 17 8 G H5' H 3.905 0 1 73 17 8 G H5'' H 3.914 0 1 74 17 8 G H8 H 7.362 0 1 75 18 9 DT H1' H 5.966 0 1 76 18 9 DT H2' H 1.952 0 1 77 18 9 DT H2'' H 2.122 0 1 78 18 9 DT H3' H 4.286 0 1 79 18 9 DT H4' H 3.903 0 1 80 18 9 DT H5' H 4.165 0 1 81 18 9 DT H5'' H 3.89 0 1 82 18 9 DT H6 H 7.357 0 1 83 18 9 DT H71 H 1.296 0 1 84 18 9 DT H72 H 1.296 0 1 85 18 9 DT H73 H 1.296 0 1 stop_ save_