data_18336 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of the RNA claw of the DNA packaging motor of bacteriophage 29 ; _BMRB_accession_number 18336 _BMRB_flat_file_name bmr18336.str _Entry_type original _Submission_date 2012-03-19 _Accession_date 2012-03-19 _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 Harjes Elena J. . 2 Matsuo Hiroshi J. . 3 Kitamura Aya J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 209 "13C chemical shifts" 69 "15N chemical shifts" 9 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-02-11 update BMRB 'update entry citation' 2012-07-30 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure of the RNA claw of the DNA packaging motor of bacteriophage 29.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22879380 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Harjes Elena . . 2 Kitamura Aya . . 3 Zhao Wei . . 4 Morais Marc C. . 5 Jardine Paul J. . 6 Grimes Shelley . . 7 Matsuo Hiroshi . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 40 _Journal_issue 19 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9953 _Page_last 9963 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name RNA_(27-MER) _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (27-MER)' $RNA_(27-MER) 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_RNA_(27-MER) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA_(27-MER) _Molecular_mass 8586.186 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; GGACUUCCAUUGCUUCGGCA AAAGUCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 A 4 4 C 5 5 U 6 6 U 7 7 C 8 8 C 9 9 A 10 10 U 11 11 U 12 12 G 13 13 C 14 14 U 15 15 U 16 16 C 17 17 G 18 18 G 19 19 C 20 20 A 21 21 A 22 22 A 23 23 A 24 24 G 25 25 U 26 26 C 27 27 C 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 $RNA_(27-MER) . . . . Phi 29 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 $RNA_(27-MER) 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA_(27-MER) 300 uM '[U-100% 13C; U-100% 15N]' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger A. T. et.al.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 900 _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_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_DQF-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 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 . K pH 6.5 . pH pressure 1 . atm 'ionic strength' 50 . mM 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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 1H-1H NOESY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (27-MER)' _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 G H1 H 12.672 0.000 1 2 1 1 G H1' H 5.876 0.000 1 3 1 1 G H2' H 4.910 0.000 1 4 1 1 G H3' H 4.850 0.000 1 5 1 1 G H4' H 4.550 0.000 1 6 1 1 G H5' H 4.540 0.000 1 7 1 1 G H8 H 8.233 0.000 1 8 1 1 G C8 C 139.643 0.000 1 9 2 2 G H1 H 12.510 0.000 1 10 2 2 G H1' H 5.850 0.000 1 11 2 2 G H2' H 4.650 0.000 1 12 2 2 G H3' H 4.710 0.000 1 13 2 2 G H4' H 4.400 0.000 1 14 2 2 G H5' H 4.200 0.000 1 15 2 2 G H8 H 7.650 0.000 1 16 2 2 G H22 H 6.670 0.000 1 17 2 2 G C1' C 92.819 0.000 1 18 2 2 G C8 C 136.791 0.000 1 19 3 3 A H1' H 5.970 0.000 1 20 3 3 A H2 H 7.827 0.000 1 21 3 3 A H2' H 4.580 0.000 1 22 3 3 A H3' H 4.630 0.000 1 23 3 3 A H4' H 4.500 0.000 1 24 3 3 A H5' H 4.520 0.000 1 25 3 3 A H8 H 7.891 0.000 1 26 3 3 A C1' C 93.177 0.000 1 27 3 3 A C2 C 154.680 0.000 1 28 3 3 A C8 C 139.883 0.000 1 29 4 4 C H1' H 5.340 0.000 1 30 4 4 C H2' H 4.187 0.000 1 31 4 4 C H3' H 4.327 0.000 1 32 4 4 C H4' H 4.400 0.000 1 33 4 4 C H5 H 5.250 0.000 1 34 4 4 C H5' H 7.170 0.000 1 35 4 4 C H6 H 7.470 0.000 1 36 4 4 C H41 H 8.280 0.000 1 37 4 4 C H42 H 7.050 0.000 1 38 4 4 C C1' C 91.419 0.000 1 39 4 4 C C5 C 94.530 0.000 1 40 4 4 C C6 C 138.599 0.000 1 41 5 5 U H1' H 5.782 0.000 1 42 5 5 U H2' H 4.332 0.000 1 43 5 5 U H3 H 14.175 0.000 1 44 5 5 U H3' H 7.826 0.000 1 45 5 5 U H4' H 4.592 0.000 1 46 5 5 U H5 H 5.393 0.000 1 47 5 5 U H5' H 4.582 0.000 1 48 5 5 U H6 H 7.826 0.000 1 49 5 5 U C5 C 103.746 0.000 1 50 5 5 U C6 C 142.071 0.000 1 51 5 5 U N1 N 190.487 0.000 1 52 6 6 U H1' H 5.832 0.000 1 53 6 6 U H2' H 4.462 0.000 1 54 6 6 U H3 H 13.300 0.000 1 55 6 6 U H3' H 4.561 0.000 1 56 6 6 U H4' H 4.462 0.000 1 57 6 6 U H5 H 5.684 0.000 1 58 6 6 U H5' H 4.449 0.000 1 59 6 6 U H6 H 7.829 0.000 1 60 6 6 U C1' C 92.299 0.000 1 61 6 6 U C5 C 104.155 0.000 1 62 6 6 U C6 C 142.755 0.000 1 63 6 6 U N1 N 190.863 0.000 1 64 7 7 C H1' H 5.853 0.000 1 65 7 7 C H2' H 4.301 0.000 1 66 7 7 C H3' H 4.422 0.000 1 67 7 7 C H4' H 4.422 0.000 1 68 7 7 C H5 H 6.002 0.000 1 69 7 7 C H5' H 4.498 0.000 1 70 7 7 C H6 H 7.907 0.000 1 71 7 7 C C1' C 90.057 0.000 1 72 7 7 C C5 C 96.044 0.000 1 73 7 7 C C6 C 139.612 0.000 1 74 8 8 C H1' H 5.814 0.000 1 75 8 8 C H2' H 4.422 0.000 1 76 8 8 C H3' H 4.682 0.000 1 77 8 8 C H4' H 4.431 0.000 1 78 8 8 C H5 H 5.832 0.000 1 79 8 8 C H5' H 4.391 0.000 1 80 8 8 C H6 H 7.898 0.000 1 81 8 8 C C1' C 90.342 0.000 1 82 8 8 C C5 C 95.498 0.000 1 83 8 8 C C6 C 140.743 0.000 1 84 9 9 A H1' H 6.109 0.000 1 85 9 9 A H2 H 8.097 0.000 1 86 9 9 A H2' H 4.690 0.000 1 87 9 9 A H3' H 4.749 0.000 1 88 9 9 A H4' H 4.561 0.000 1 89 9 9 A H5' H 4.480 0.000 1 90 9 9 A H8 H 8.341 0.000 1 91 9 9 A C1' C 92.167 0.000 1 92 9 9 A C2 C 155.277 0.000 1 93 9 9 A C8 C 141.629 0.000 1 94 10 10 U H1' H 5.539 0.000 1 95 10 10 U H2' H 4.339 0.000 1 96 10 10 U H3' H 4.539 0.000 1 97 10 10 U H4' H 4.481 0.000 1 98 10 10 U H5 H 5.499 0.000 1 99 10 10 U H5' H 4.469 0.000 1 100 10 10 U H6 H 7.696 0.000 1 101 10 10 U C1' C 93.191 0.000 1 102 10 10 U C5 C 103.746 0.000 1 103 10 10 U C6 C 141.787 0.000 1 104 10 10 U N1 N 190.838 0.000 1 105 11 11 U H1' H 5.710 0.000 1 106 11 11 U H2' H 4.560 0.000 1 107 11 11 U H3 H 13.202 0.000 1 108 11 11 U H3' H 4.631 0.000 1 109 11 11 U H4' H 4.498 0.000 1 110 11 11 U H5 H 5.622 0.000 1 111 11 11 U H5' H 4.481 0.000 1 112 11 11 U H6 H 7.897 0.000 1 113 11 11 U C1' C 92.862 0.000 1 114 11 11 U C5 C 103.659 0.000 1 115 11 11 U C6 C 142.348 0.000 1 116 11 11 U N1 N 190.712 0.000 1 117 11 11 U N3 N 162.5 0.000 1 118 12 12 G H1 H 12.430 0.000 1 119 12 12 G H1' H 5.839 0.000 1 120 12 12 G H2' H 4.510 0.000 1 121 12 12 G H3' H 4.560 0.000 1 122 12 12 G H4' H 4.510 0.000 1 123 12 12 G H5' H 4.602 0.000 1 124 12 12 G H8 H 7.833 0.000 1 125 12 12 G C1' C 92.410 0.000 1 126 12 12 G C8 C 136.430 0.000 1 127 13 13 C H1' H 5.422 0.000 1 128 13 13 C H2' H 4.410 0.000 1 129 13 13 C H3' H 4.210 0.000 1 130 13 13 C H4' H 4.410 0.000 1 131 13 13 C H5 H 5.160 0.000 1 132 13 13 C H5' H 4.502 0.000 1 133 13 13 C H6 H 7.447 0.000 1 134 13 13 C H41 H 8.450 0.000 1 135 13 13 C H42 H 6.790 0.000 1 136 13 13 C C1' C 91.103 0.000 1 137 13 13 C C5 C 94.590 0.000 1 138 13 13 C C6 C 138.413 0.000 1 139 14 14 U H1' H 5.609 0.000 1 140 14 14 U H2' H 3.752 0.000 1 141 14 14 U H3' H 4.512 0.000 1 142 14 14 U H4' H 4.340 0.000 1 143 14 14 U H5 H 5.689 0.000 1 144 14 14 U H5' H 4.459 0.000 1 145 14 14 U H6 H 7.708 0.000 1 146 14 14 U C1' C 93.308 0.000 1 147 14 14 U C5 C 104.731 0.000 1 148 14 14 U C6 C 140.728 0.000 1 149 14 14 U N1 N 191.977 0.000 1 150 15 15 U H1' H 6.082 0.000 1 151 15 15 U H2' H 4.640 0.000 1 152 15 15 U H3 H 12.243 0.000 1 153 15 15 U H3' H 4.011 0.000 1 154 15 15 U H4' H 4.459 0.000 1 155 15 15 U H5 H 5.840 0.000 1 156 15 15 U H5' H 4.221 0.000 1 157 15 15 U H6 H 7.998 0.000 1 158 15 15 U C1' C 89.122 0.000 1 159 15 15 U C5 C 105.191 0.000 1 160 15 15 U C6 C 144.483 0.000 1 161 15 15 U N1 N 188.771 0.000 1 162 16 16 C H1' H 5.942 0.000 1 163 16 16 C H2' H 4.081 0.000 1 164 16 16 C H3' H 4.471 0.000 1 165 16 16 C H4' H 3.789 0.000 1 166 16 16 C H5 H 6.111 0.000 1 167 16 16 C H5' H 3.592 0.000 1 168 16 16 C H6 H 7.692 0.000 1 169 16 16 C H41 H 7.100 0.000 1 170 16 16 C H42 H 6.290 0.000 1 171 16 16 C C1' C 86.483 0.000 1 172 16 16 C C5 C 95.995 0.000 1 173 16 16 C C6 C 140.810 0.000 1 174 17 17 G H1 H 9.830 0.000 1 175 17 17 G H1' H 5.928 0.000 1 176 17 17 G H2' H 4.800 0.000 1 177 17 17 G H3' H 5.601 0.000 1 178 17 17 G H4' H 4.389 0.000 1 179 17 17 G H5' H 4.393 0.000 1 180 17 17 G H8 H 7.846 0.000 1 181 17 17 G C1' C 94.309 0.000 1 182 17 17 G C8 C 143.016 0.000 1 183 18 18 G H1 H 13.300 0.000 1 184 18 18 G H1' H 4.389 0.000 1 185 18 18 G H2' H 4.369 0.000 1 186 18 18 G H3' H 4.208 0.000 1 187 18 18 G H4' H 4.549 0.000 1 188 18 18 G H5' H 4.459 0.000 1 189 18 18 G H8 H 8.255 0.000 1 190 18 18 G H21 H 8.700 0.000 1 191 18 18 G H22 H 6.400 0.000 1 192 18 18 G C1' C 92.936 0.000 1 193 18 18 G C8 C 138.598 0.000 1 194 19 19 C H1' H 5.441 0.000 1 195 19 19 C H2' H 4.512 0.000 1 196 19 19 C H3' H 4.471 0.000 1 197 19 19 C H4' H 4.352 0.000 1 198 19 19 C H5 H 5.170 0.000 1 199 19 19 C H5' H 4.471 0.000 1 200 19 19 C H6 H 7.650 0.000 1 201 19 19 C H41 H 8.480 0.000 1 202 19 19 C H42 H 6.730 0.000 1 203 19 19 C C1' C 91.193 0.000 1 204 19 19 C C5 C 94.441 0.000 1 205 19 19 C C6 C 138.869 0.000 1 206 20 20 A H1' H 5.886 0.000 1 207 20 20 A H2 H 6.936 0.000 1 208 20 20 A H2' H 4.611 0.000 1 209 20 20 A H3' H 4.591 0.000 1 210 20 20 A H4' H 4.471 0.000 1 211 20 20 A H5' H 4.512 0.000 1 212 20 20 A H8 H 7.837 0.000 1 213 20 20 A C1' C 93.221 0.000 1 214 20 20 A C2 C 152.799 0.000 1 215 20 20 A C8 C 139.859 0.000 1 216 21 21 A H1' H 5.651 0.000 1 217 21 21 A H2 H 7.740 0.000 1 218 21 21 A H2' H 4.591 0.000 1 219 21 21 A H3' H 4.471 0.000 1 220 21 21 A H4' H 4.410 0.000 1 221 21 21 A H5' H 4.514 0.000 1 222 21 21 A H8 H 7.486 0.000 1 223 21 21 A C1' C 92.749 0.000 1 224 21 21 A C2 C 154.313 0.000 1 225 21 21 A C8 C 139.206 0.000 1 226 22 22 A H1' H 5.932 0.000 1 227 22 22 A H2 H 7.517 0.000 1 228 22 22 A H2' H 4.020 0.000 1 229 22 22 A H3' H 4.260 0.000 1 230 22 22 A H4' H 4.220 0.000 1 231 22 22 A H8 H 7.989 0.000 1 232 22 22 A C2 C 154.145 0.000 1 233 23 23 A H1' H 5.617 0.000 1 234 23 23 A H2 H 7.578 0.000 1 235 23 23 A H2' H 4.552 0.000 1 236 23 23 A H3' H 4.572 0.000 1 237 23 23 A H4' H 4.060 0.000 1 238 23 23 A H5' H 4.421 0.000 1 239 23 23 A H8 H 7.832 0.000 1 240 23 23 A C1' C 93.225 0.000 1 241 23 23 A C2 C 153.824 0.000 1 242 23 23 A C8 C 139.705 0.000 1 243 24 24 G H1 H 13.520 0.000 1 244 24 24 G H1' H 5.529 0.000 1 245 24 24 G H2' H 4.320 0.000 1 246 24 24 G H3' H 4.390 0.000 1 247 24 24 G H4' H 4.339 0.000 1 248 24 24 G H5' H 4.489 0.000 1 249 24 24 G H8 H 7.202 0.000 1 250 24 24 G H21 H 8.670 0.000 1 251 24 24 G C1' C 92.527 0.000 1 252 24 24 G C8 C 135.587 0.000 1 253 25 25 U H1' H 5.631 0.000 1 254 25 25 U H2' H 4.419 0.000 1 255 25 25 U H3 H 14.340 0.000 1 256 25 25 U H3' H 4.481 0.000 1 257 25 25 U H4' H 4.419 0.000 1 258 25 25 U H5 H 4.980 0.000 1 259 25 25 U H5' H 4.449 0.000 1 260 25 25 U H6 H 7.840 0.000 1 261 25 25 U C1' C 94.387 0.000 1 262 25 25 U C6 C 141.640 0.000 1 263 25 25 U N1 N 192.140 0.000 1 264 25 25 U N3 N 163.3 0.000 1 265 26 26 C H1' H 5.639 0.000 1 266 26 26 C H2' H 3.891 0.000 1 267 26 26 C H3' H 4.111 0.000 1 268 26 26 C H4' H 4.411 0.000 1 269 26 26 C H5 H 5.601 0.000 1 270 26 26 C H5' H 4.342 0.000 1 271 26 26 C H6 H 7.701 0.000 1 272 26 26 C H41 H 8.500 0.000 1 273 26 26 C H42 H 6.950 0.000 1 274 26 26 C C1' C 90.113 0.000 1 275 26 26 C C5 C 94.952 0.000 1 276 26 26 C C6 C 139.932 0.000 1 277 27 27 C H1' H 5.491 0.000 1 278 27 27 C H2' H 4.280 0.000 1 279 27 27 C H3' H 4.342 0.000 1 280 27 27 C H4' H 4.342 0.000 1 281 27 27 C H5 H 5.462 0.000 1 282 27 27 C H5' H 4.420 0.000 1 283 27 27 C H6 H 7.658 0.000 1 284 27 27 C H41 H 8.400 0.000 1 285 27 27 C H42 H 6.970 0.000 1 286 27 27 C C1' C 91.126 0.000 1 287 27 27 C C6 C 138.565 0.000 1 stop_ save_