data_27410 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Ile and Met methyl 1H and 13C chemical shifts of DNA polymerase beta, 1-nucleotide gapped double hairpin DNA and dAMPCPP ternary complex ; _BMRB_accession_number 27410 _BMRB_flat_file_name bmr27410.str _Entry_type original _Submission_date 2018-02-23 _Accession_date 2018-02-23 _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 DeRose Eugene F. . 2 Kirby Thomas W. . 3 Mueller Geoffrey A. . 4 Beard William A. . 5 Wilson Samuel H. . 6 London Robert E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 29 "13C chemical shifts" 29 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-11-14 update BMRB 'update entry citation' 2018-06-20 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 27407 'Ile and Met methyl 1H and 13C chemical shifts of DNA polymerase beta' 27409 'Ile and Met methyl 1H and 13C chemical shifts of DNA polymerase beta and 1-nucleotide gapped double hairpin DNA binary complex' stop_ _Original_release_date 2018-02-23 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Transitions in DNA polymerase beta microsecond-millisecond dynamics related to substrate binding and catalysis ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 29917149 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 DeRose Eugene F. . 2 Kirby Thomas W. . 3 Mueller Geoffrey A. . 4 Beard William A. . 5 Wilson Samuel H. . 6 London Robert E. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 46 _Journal_issue 14 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 7309 _Page_last 7322 _Year 2018 _Details . loop_ _Keyword 'micro-millisecond dynamics' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA polymerase beta ternary complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA polymerase beta' $DNA_polymerase_beta_polypeptide 'hairpin DNA' $1-nucleotide_gapped_double_hairpin_DNA dAMPCPP $dAMPCPP 'metal ion' $entity_MG 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_DNA_polymerase_beta_polypeptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common DNA_polymerase_beta_polypeptide _Molecular_mass . _Mol_thiol_state 'all free' loop_ _Biological_function 'dRP lyase' nucleotidyltransferase stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 335 _Mol_residue_sequence ; MSKRKAPQETLNGGITDMLV ELANFEKNVSQAIHKYNAYR KAASVIAKYPHKIKSGAEAK KLPGVGTKIAEKIDEFLATG KLRKLEKIRQDDTSSSINFL TRVTGIGPSAARKLVDEGIK TLEDLRKNEDKLNHHQRIGL KYFEDFEKRIPREEMLQMQD IVLNEVKKLDPEYIATVCGS FRRGAESSGDMDVLLTHPNF TSESSKQPKLLHRVVEQLQK VRFITDTLSKGETKFMGVCQ LPSENDENEYPHRRIDIRLI PKDQYYAGVLYFTGSDIFNK NMRAHALEKGFTINEYTIRP LGVTGVAGEPLPVDSEQDIF DYIQWRYREPKDRSE ; loop_ _Residue_seq_code _Residue_label 1 MET 2 SER 3 LYS 4 ARG 5 LYS 6 ALA 7 PRO 8 GLN 9 GLU 10 THR 11 LEU 12 ASN 13 GLY 14 GLY 15 ILE 16 THR 17 ASP 18 MET 19 LEU 20 VAL 21 GLU 22 LEU 23 ALA 24 ASN 25 PHE 26 GLU 27 LYS 28 ASN 29 VAL 30 SER 31 GLN 32 ALA 33 ILE 34 HIS 35 LYS 36 TYR 37 ASN 38 ALA 39 TYR 40 ARG 41 LYS 42 ALA 43 ALA 44 SER 45 VAL 46 ILE 47 ALA 48 LYS 49 TYR 50 PRO 51 HIS 52 LYS 53 ILE 54 LYS 55 SER 56 GLY 57 ALA 58 GLU 59 ALA 60 LYS 61 LYS 62 LEU 63 PRO 64 GLY 65 VAL 66 GLY 67 THR 68 LYS 69 ILE 70 ALA 71 GLU 72 LYS 73 ILE 74 ASP 75 GLU 76 PHE 77 LEU 78 ALA 79 THR 80 GLY 81 LYS 82 LEU 83 ARG 84 LYS 85 LEU 86 GLU 87 LYS 88 ILE 89 ARG 90 GLN 91 ASP 92 ASP 93 THR 94 SER 95 SER 96 SER 97 ILE 98 ASN 99 PHE 100 LEU 101 THR 102 ARG 103 VAL 104 THR 105 GLY 106 ILE 107 GLY 108 PRO 109 SER 110 ALA 111 ALA 112 ARG 113 LYS 114 LEU 115 VAL 116 ASP 117 GLU 118 GLY 119 ILE 120 LYS 121 THR 122 LEU 123 GLU 124 ASP 125 LEU 126 ARG 127 LYS 128 ASN 129 GLU 130 ASP 131 LYS 132 LEU 133 ASN 134 HIS 135 HIS 136 GLN 137 ARG 138 ILE 139 GLY 140 LEU 141 LYS 142 TYR 143 PHE 144 GLU 145 ASP 146 PHE 147 GLU 148 LYS 149 ARG 150 ILE 151 PRO 152 ARG 153 GLU 154 GLU 155 MET 156 LEU 157 GLN 158 MET 159 GLN 160 ASP 161 ILE 162 VAL 163 LEU 164 ASN 165 GLU 166 VAL 167 LYS 168 LYS 169 LEU 170 ASP 171 PRO 172 GLU 173 TYR 174 ILE 175 ALA 176 THR 177 VAL 178 CYS 179 GLY 180 SER 181 PHE 182 ARG 183 ARG 184 GLY 185 ALA 186 GLU 187 SER 188 SER 189 GLY 190 ASP 191 MET 192 ASP 193 VAL 194 LEU 195 LEU 196 THR 197 HIS 198 PRO 199 ASN 200 PHE 201 THR 202 SER 203 GLU 204 SER 205 SER 206 LYS 207 GLN 208 PRO 209 LYS 210 LEU 211 LEU 212 HIS 213 ARG 214 VAL 215 VAL 216 GLU 217 GLN 218 LEU 219 GLN 220 LYS 221 VAL 222 ARG 223 PHE 224 ILE 225 THR 226 ASP 227 THR 228 LEU 229 SER 230 LYS 231 GLY 232 GLU 233 THR 234 LYS 235 PHE 236 MET 237 GLY 238 VAL 239 CYS 240 GLN 241 LEU 242 PRO 243 SER 244 GLU 245 ASN 246 ASP 247 GLU 248 ASN 249 GLU 250 TYR 251 PRO 252 HIS 253 ARG 254 ARG 255 ILE 256 ASP 257 ILE 258 ARG 259 LEU 260 ILE 261 PRO 262 LYS 263 ASP 264 GLN 265 TYR 266 TYR 267 ALA 268 GLY 269 VAL 270 LEU 271 TYR 272 PHE 273 THR 274 GLY 275 SER 276 ASP 277 ILE 278 PHE 279 ASN 280 LYS 281 ASN 282 MET 283 ARG 284 ALA 285 HIS 286 ALA 287 LEU 288 GLU 289 LYS 290 GLY 291 PHE 292 THR 293 ILE 294 ASN 295 GLU 296 TYR 297 THR 298 ILE 299 ARG 300 PRO 301 LEU 302 GLY 303 VAL 304 THR 305 GLY 306 VAL 307 ALA 308 GLY 309 GLU 310 PRO 311 LEU 312 PRO 313 VAL 314 ASP 315 SER 316 GLU 317 GLN 318 ASP 319 ILE 320 PHE 321 ASP 322 TYR 323 ILE 324 GLN 325 TRP 326 ARG 327 TYR 328 ARG 329 GLU 330 PRO 331 LYS 332 ASP 333 ARG 334 SER 335 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_1-nucleotide_gapped_double_hairpin_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 1-nucleotide_gapped_double_hairpin_DNA _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 23 _Mol_residue_sequence ; GGCGAAGCCTGGTGCGAAGC ACC ; loop_ _Residue_seq_code _Residue_label 1 DG 2 DG 3 DC 4 DG 5 DA 6 DA 7 DG 8 DC 9 DC 10 DT 11 DG 12 DG 13 DT 14 DG 15 DC 16 DG 17 DA 18 DA 19 DG 20 DC 21 DA 22 DC 23 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_dAMPCPP _Saveframe_category monomeric_polymer _Mol_type polymer _Name_common dAMPCPP _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count . _Mol_residue_sequence ; X ; loop_ _Residue_seq_code _Residue_label 1 X stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_MG _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_MG (MAGNESIUM ION)" _BMRB_code MG _PDB_code MG _Molecular_mass 24.305 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons MG MG MG . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_polymerase_beta_polypeptide Rat 10116 Eukaryota Metazoa Rattus norvegicus $1-nucleotide_gapped_double_hairpin_DNA Rat 10116 Eukaryota Metazoa Rattus norvegicus 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 $DNA_polymerase_beta_polypeptide 'recombinant technology' . . . . pET30 $1-nucleotide_gapped_double_hairpin_DNA '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 $DNA_polymerase_beta_polypeptide 400 uM 'Ile CD1-[13CH3],Leu,Val-[13CH3,12CD3],[U-13C; U-15N; U-2H]' 'potassium phosphate' 100 mM 'natural abundance' DTT 1 mM 'natural abundance' 'sodium azide' 10 mM 'natural abundance' DSS 80 uM 'natural abundance' $1-nucleotide_gapped_double_hairpin_DNA 453 uM 'natural abundance' MgCl2 10 mM 'natural abundance' $dAMPCPP 600 uM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_polymerase_beta_polypeptide 200 uM 'Ile CD1-[13CH3],Leu,Val-[13CH3,12CD3],Met-[13CH3],[U-15N; U-2H]' 'potassium chloride' 150 mM 'natural abundance' TRIS 40 mM '[U-100% 2H]' CDTA 1 mM 'natural abundance' DTT 1 mM 'natural abundance' 'AEBSF protease inhibitor' 0.1 mM 'natural abundance' 'sodium azide' 0.04 % 'natural abundance' DSS 50 uM 'natural abundance' $1-nucleotide_gapped_double_hairpin_DNA 220 uM 'natural abundance' MgCl2 5 mM 'natural abundance' $dAMPCPP 280 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMRJ _Saveframe_category software _Name VNMRJ _Version 4.2/2.2 loop_ _Vendor _Address _Electronic_address Agilent/Varian . . stop_ loop_ _Task collection stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRViewJ _Saveframe_category software _Name NMRViewJ _Version . loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model DD2 _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model DD2 _Field_strength 600 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 _Details . save_ save_spectrometer_4 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HMQC_methyl_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC methyl' _Sample_label $sample_1 save_ save_2D_1H-13C_HMQC_methyl_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMQC methyl' _Sample_label $sample_1 save_ save_2D_1H-13C-HMQC_methyl_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C-HMQC methyl' _Sample_label $sample_2 save_ save_2D_1H-13C-HMQC_methyl_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C-HMQC methyl' _Sample_label $sample_2 save_ save_3D_HMCM[CG]CBCA_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HMCM[CG]CBCA' _Sample_label $sample_1 save_ save_3D_HMCM(CGCBCA)CO_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HMCM(CGCBCA)CO' _Sample_label $sample_1 save_ save_4D_methyl_1H-13C-13C-1H_NOESY/3D_F2F3F4_cube_7 _Saveframe_category NMR_applied_experiment _Experiment_name '4D methyl 1H-13C-13C-1H NOESY/3D F2F3F4 cube' _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 6.7 . pH pressure 1 . atm temperature 308 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 150 . mM pH 7.6 . pH pressure 1 . atm temperature 308 . 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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_ _Software_label $VNMRJ $NMRPipe $NMRViewJ stop_ loop_ _Experiment_label '2D 1H-13C HMQC methyl' '2D 1H-13C-HMQC methyl' '3D HMCM[CG]CBCA' '3D HMCM(CGCBCA)CO' '4D methyl 1H-13C-13C-1H NOESY/3D F2F3F4 cube' 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 polymerase beta' _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 15 15 ILE HD1 H 0.988 0.05 1 2 15 15 ILE CD1 C 14.839 0.2 1 3 18 18 MET HE H 1.669 0.05 1 4 18 18 MET CE C 16.335 0.2 1 5 33 33 ILE HD1 H 0.696 0.05 1 6 33 33 ILE CD1 C 12.989 0.2 1 7 46 46 ILE HD1 H 0.589 0.05 1 8 46 46 ILE CD1 C 13.586 0.2 1 9 53 53 ILE HD1 H 0.694 0.05 1 10 53 53 ILE CD1 C 13.315 0.2 1 11 69 69 ILE HD1 H 0.772 0.05 1 12 69 69 ILE CD1 C 13.947 0.2 1 13 73 73 ILE HD1 H 0.676 0.05 1 14 73 73 ILE CD1 C 15.004 0.2 1 15 88 88 ILE HD1 H 0.049 0.05 1 16 88 88 ILE CD1 C 13.973 0.2 1 17 97 97 ILE HD1 H 0.859 0.05 1 18 97 97 ILE CD1 C 13.916 0.2 1 19 106 106 ILE HD1 H 0.637 0.05 1 20 106 106 ILE CD1 C 11.853 0.2 1 21 119 119 ILE HD1 H 0.714 0.05 1 22 119 119 ILE CD1 C 14.054 0.2 1 23 138 138 ILE HD1 H 0.537 0.05 1 24 138 138 ILE CD1 C 10.184 0.2 1 25 150 150 ILE HD1 H 0.596 0.05 1 26 150 150 ILE CD1 C 13.050 0.2 1 27 155 155 MET HE H 2.017 0.05 1 28 155 155 MET CE C 17.707 0.2 1 29 158 158 MET HE H 2.042 0.05 1 30 158 158 MET CE C 17.485 0.2 1 31 161 161 ILE HD1 H 0.651 0.05 1 32 161 161 ILE CD1 C 14.042 0.2 1 33 174 174 ILE HD1 H 0.592 0.05 1 34 174 174 ILE CD1 C 13.141 0.2 1 35 191 191 MET HE H 1.815 0.05 1 36 191 191 MET CE C 18.450 0.2 1 37 224 224 ILE HD1 H 0.724 0.05 1 38 224 224 ILE CD1 C 14.023 0.2 1 39 236 236 MET HE H 2.106 0.05 1 40 236 236 MET CE C 16.440 0.2 1 41 255 255 ILE HD1 H 0.829 0.05 1 42 255 255 ILE CD1 C 13.909 0.2 1 43 257 257 ILE HD1 H 0.526 0.05 1 44 257 257 ILE CD1 C 12.310 0.2 1 45 260 260 ILE HD1 H 0.784 0.05 1 46 260 260 ILE CD1 C 12.281 0.2 1 47 277 277 ILE HD1 H 0.581 0.05 1 48 277 277 ILE CD1 C 11.209 0.2 1 49 282 282 MET HE H 1.082 0.05 1 50 282 282 MET CE C 17.548 0.2 1 51 293 293 ILE HD1 H 0.513 0.05 1 52 293 293 ILE CD1 C 15.114 0.2 1 53 298 298 ILE HD1 H 0.348 0.05 1 54 298 298 ILE CD1 C 13.693 0.2 1 55 319 319 ILE HD1 H 0.949 0.05 1 56 319 319 ILE CD1 C 12.791 0.2 1 57 323 323 ILE HD1 H 0.122 0.05 1 58 323 323 ILE CD1 C 14.767 0.2 1 stop_ save_