data_11046 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; hsRad51-bound ssDNA ; _BMRB_accession_number 11046 _BMRB_flat_file_name bmr11046.str _Entry_type original _Submission_date 2008-05-15 _Accession_date 2008-05-15 _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 Shibata Takehiko . . 2 Ito Yutaka . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 37 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-09-20 update BMRB 'update sequence to DNA' 2010-01-25 update BMRB 'complete entry citation' 2009-10-15 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 11045 'Structure of d(TACG) bound to structurally distinct recombinase Mhr1p' 11047 'Structure of d(TACG) bound to structurally distinct recombinase ttRecO' 11048 'Structure of d(TACG) bound to structurally distinct recombinase ecRecT' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'A non-canonical DNA structure enables homologous recombination in various genetic systems.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19729448 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Masuda Tokiha . . 2 Ito Yutaka . . 3 Terada Tohru . . 4 Shibata Takehiko . . 5 Mikawa Tsutomu . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 284 _Journal_issue 44 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 30230 _Page_last 30239 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "5'-D(*DTP*DAP*DCP*DG)-3' 10 structures" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 1' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 2' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 3' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 4' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 5' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 6' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 7' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 8' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 9' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 10' $entity_1 hsRad51 $entity_2 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA (5'-D(*DTP*DAP*DCP*DG)-3')' _Molecular_mass 1231.30 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence TACG loop_ _Residue_seq_code _Residue_label 1 DT 2 DA 3 DC 4 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common hsRad51 _Molecular_mass . _Mol_thiol_state 'all free' _Details . _Residue_count 339 _Mol_residue_sequence ; MAMQMQLEANADTSVEEESF GPQPISRLEQCGINANDVKK LEEAGFHTVEAVAYAPKKEL INIKGISEAKADKILAEAAK LVPMGFTTATEFHQRRSEII QITTGSKELDKLLQGGIETG SITEMFGEFRTGKTQICHTL AVTCQLPIDRGGGEGKAMYI DTEGTFRPERLLAVAERYGL SGSDVLDNVAYARAFNTDHQ TQLLYQASAMMVESRYALLI VDSATALYRTDYSGRGELSA RQMHLARFLRMLLRLADEFG VAVVITNQVVAQVDGAAMFA ADPKKPIGGNIIAHASTTRL YLRKGRGETRICKIYDSPCL PEAEAMFAINADGVGDAKD ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ALA 3 MET 4 GLN 5 MET 6 GLN 7 LEU 8 GLU 9 ALA 10 ASN 11 ALA 12 ASP 13 THR 14 SER 15 VAL 16 GLU 17 GLU 18 GLU 19 SER 20 PHE 21 GLY 22 PRO 23 GLN 24 PRO 25 ILE 26 SER 27 ARG 28 LEU 29 GLU 30 GLN 31 CYS 32 GLY 33 ILE 34 ASN 35 ALA 36 ASN 37 ASP 38 VAL 39 LYS 40 LYS 41 LEU 42 GLU 43 GLU 44 ALA 45 GLY 46 PHE 47 HIS 48 THR 49 VAL 50 GLU 51 ALA 52 VAL 53 ALA 54 TYR 55 ALA 56 PRO 57 LYS 58 LYS 59 GLU 60 LEU 61 ILE 62 ASN 63 ILE 64 LYS 65 GLY 66 ILE 67 SER 68 GLU 69 ALA 70 LYS 71 ALA 72 ASP 73 LYS 74 ILE 75 LEU 76 ALA 77 GLU 78 ALA 79 ALA 80 LYS 81 LEU 82 VAL 83 PRO 84 MET 85 GLY 86 PHE 87 THR 88 THR 89 ALA 90 THR 91 GLU 92 PHE 93 HIS 94 GLN 95 ARG 96 ARG 97 SER 98 GLU 99 ILE 100 ILE 101 GLN 102 ILE 103 THR 104 THR 105 GLY 106 SER 107 LYS 108 GLU 109 LEU 110 ASP 111 LYS 112 LEU 113 LEU 114 GLN 115 GLY 116 GLY 117 ILE 118 GLU 119 THR 120 GLY 121 SER 122 ILE 123 THR 124 GLU 125 MET 126 PHE 127 GLY 128 GLU 129 PHE 130 ARG 131 THR 132 GLY 133 LYS 134 THR 135 GLN 136 ILE 137 CYS 138 HIS 139 THR 140 LEU 141 ALA 142 VAL 143 THR 144 CYS 145 GLN 146 LEU 147 PRO 148 ILE 149 ASP 150 ARG 151 GLY 152 GLY 153 GLY 154 GLU 155 GLY 156 LYS 157 ALA 158 MET 159 TYR 160 ILE 161 ASP 162 THR 163 GLU 164 GLY 165 THR 166 PHE 167 ARG 168 PRO 169 GLU 170 ARG 171 LEU 172 LEU 173 ALA 174 VAL 175 ALA 176 GLU 177 ARG 178 TYR 179 GLY 180 LEU 181 SER 182 GLY 183 SER 184 ASP 185 VAL 186 LEU 187 ASP 188 ASN 189 VAL 190 ALA 191 TYR 192 ALA 193 ARG 194 ALA 195 PHE 196 ASN 197 THR 198 ASP 199 HIS 200 GLN 201 THR 202 GLN 203 LEU 204 LEU 205 TYR 206 GLN 207 ALA 208 SER 209 ALA 210 MET 211 MET 212 VAL 213 GLU 214 SER 215 ARG 216 TYR 217 ALA 218 LEU 219 LEU 220 ILE 221 VAL 222 ASP 223 SER 224 ALA 225 THR 226 ALA 227 LEU 228 TYR 229 ARG 230 THR 231 ASP 232 TYR 233 SER 234 GLY 235 ARG 236 GLY 237 GLU 238 LEU 239 SER 240 ALA 241 ARG 242 GLN 243 MET 244 HIS 245 LEU 246 ALA 247 ARG 248 PHE 249 LEU 250 ARG 251 MET 252 LEU 253 LEU 254 ARG 255 LEU 256 ALA 257 ASP 258 GLU 259 PHE 260 GLY 261 VAL 262 ALA 263 VAL 264 VAL 265 ILE 266 THR 267 ASN 268 GLN 269 VAL 270 VAL 271 ALA 272 GLN 273 VAL 274 ASP 275 GLY 276 ALA 277 ALA 278 MET 279 PHE 280 ALA 281 ALA 282 ASP 283 PRO 284 LYS 285 LYS 286 PRO 287 ILE 288 GLY 289 GLY 290 ASN 291 ILE 292 ILE 293 ALA 294 HIS 295 ALA 296 SER 297 THR 298 THR 299 ARG 300 LEU 301 TYR 302 LEU 303 ARG 304 LYS 305 GLY 306 ARG 307 GLY 308 GLU 309 THR 310 ARG 311 ILE 312 CYS 313 LYS 314 ILE 315 TYR 316 ASP 317 SER 318 PRO 319 CYS 320 LEU 321 PRO 322 GLU 323 ALA 324 GLU 325 ALA 326 MET 327 PHE 328 ALA 329 ILE 330 ASN 331 ALA 332 ASP 333 GLY 334 VAL 335 GLY 336 ASP 337 ALA 338 LYS 339 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-10-07 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value DBJ BAA02718 "Rad51 protein [Mus musculus]" 100.00 339 98.82 99.41 0.00e+00 DBJ BAA02961 "MmRad51 [Mus musculus]" 100.00 339 98.82 99.41 0.00e+00 DBJ BAA02962 "HsRad51 [Homo sapiens]" 100.00 339 99.71 100.00 0.00e+00 DBJ BAA03189 "RAD51 [Homo sapiens]" 100.00 339 100.00 100.00 0.00e+00 DBJ BAB27489 "unnamed protein product [Mus musculus]" 100.00 339 98.82 99.41 0.00e+00 EMBL CAA69384 "rad51 [Cricetulus griseus]" 100.00 339 98.82 99.41 0.00e+00 EMBL CAG38796 "RAD51 [Homo sapiens]" 100.00 339 100.00 100.00 0.00e+00 GB AAC28561 "Rad51 [Oryctolagus cuniculus]" 100.00 339 98.53 98.82 0.00e+00 GB AAD49705 "Rad51 [Homo sapiens]" 100.00 339 100.00 100.00 0.00e+00 GB AAF69145 "RAD51 [Homo sapiens]" 100.00 339 100.00 100.00 0.00e+00 GB AAH27384 "RAD51 homolog (S. cerevisiae) [Mus musculus]" 100.00 339 98.82 99.41 0.00e+00 GB AAI05459 "RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae) [Bos taurus]" 100.00 339 99.41 99.41 0.00e+00 PRF 2102359A "RAD51-like protein" 100.00 339 98.82 99.41 0.00e+00 REF NP_001003043 "DNA repair protein RAD51 homolog 1 [Canis lupus familiaris]" 100.00 339 99.12 99.41 0.00e+00 REF NP_001039644 "DNA repair protein RAD51 homolog 1 [Bos taurus]" 100.00 339 99.41 99.41 0.00e+00 REF NP_001075493 "DNA repair protein RAD51 homolog 1 [Oryctolagus cuniculus]" 100.00 339 98.53 98.82 0.00e+00 REF NP_001102674 "DNA repair protein RAD51 homolog 1 [Rattus norvegicus]" 100.00 339 99.41 99.71 0.00e+00 REF NP_001116653 "DNA repair protein RAD51 homolog 1 [Sus scrofa]" 100.00 339 98.82 99.71 0.00e+00 SP O77507 "RecName: Full=DNA repair protein RAD51 homolog 1" 100.00 339 98.53 98.82 0.00e+00 SP P70099 "RecName: Full=DNA repair protein RAD51 homolog 1" 100.00 339 98.82 99.41 0.00e+00 SP Q06609 "RecName: Full=DNA repair protein RAD51 homolog 1; Short=HsRAD51; Short=hRAD51; AltName: Full=RAD51 homolog A" 100.00 339 100.00 100.00 0.00e+00 SP Q08297 "RecName: Full=DNA repair protein RAD51 homolog 1; AltName: Full=RAD51 homolog A" 100.00 339 98.82 99.41 0.00e+00 SP Q2KJ94 "RecName: Full=DNA repair protein RAD51 homolog 1" 100.00 339 99.41 99.41 0.00e+00 TPG DAA25435 "TPA: DNA repair protein RAD51 homolog 1 [Bos taurus]" 100.00 339 99.41 99.41 0.00e+00 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 . . . . . . $entity_2 human 9606 Eukaryota Metazoa . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $entity_1 'obtained from a vendor' . . . . . . $entity_2 'recombinant technology' . . . K12 plasmid pET15b 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 $entity_1 0.5 mM 'natural abundance' $entity_2 0.05 mM 'natural abundance' AMP-PNP 10 mM 'natural abundance' MgCl2 5 mM 'natural abundance' NaCl 100 mM 'natural abundance' D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _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_transferred_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'transferred NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ save_ROESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name ROESY _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 7.1 . pH pressure 1 . atm 'ionic strength' 100 . 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 0.0 . indirect . . . 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' 'transferred NOESY' DQF-COSY TOCSY ROESY 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 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 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 DT H1' H 5.91 0.01 1 2 1 1 DT H2' H 1.60 0.01 2 3 1 1 DT H2'' H 2.15 0.01 2 4 1 1 DT H3' H 4.57 0.01 1 5 1 1 DT H4' H 3.99 0.01 1 6 1 1 DT H5' H 3.61 0.01 2 7 1 1 DT H5'' H 3.61 0.01 2 8 1 1 DT H6 H 7.29 0.01 1 9 1 1 DT H71 H 1.79 0.01 1 10 1 1 DT H72 H 1.79 0.01 1 11 1 1 DT H73 H 1.79 0.01 1 12 2 2 DA H1' H 6.24 0.01 1 13 2 2 DA H2 H 8.04 0.01 1 14 2 2 DA H2' H 2.79 0.01 1 15 2 2 DA H2'' H 2.69 0.01 1 16 2 2 DA H3' H 4.96 0.01 1 17 2 2 DA H4' H 4.36 0.01 1 18 2 2 DA H5' H 4.01 0.01 2 19 2 2 DA H5'' H 4.01 0.01 2 20 2 2 DA H8 H 8.31 0.01 1 21 3 3 DC H1' H 6.03 0.01 1 22 3 3 DC H2' H 1.88 0.01 1 23 3 3 DC H2'' H 2.32 0.01 1 24 3 3 DC H3' H 4.73 0.01 1 25 3 3 DC H4' H 4.16 0.01 1 26 3 3 DC H5 H 5.76 0.01 1 27 3 3 DC H5' H 4.03 0.01 2 28 3 3 DC H5'' H 4.03 0.01 2 29 3 3 DC H6 H 7.50 0.01 1 30 4 4 DG H1' H 6.13 0.01 1 31 4 4 DG H2' H 2.69 0.01 1 32 4 4 DG H2'' H 2.43 0.01 1 33 4 4 DG H3' H 4.66 0.01 1 34 4 4 DG H4' H 4.15 0.01 1 35 4 4 DG H5' H 4.05 0.01 2 36 4 4 DG H5'' H 4.05 0.01 2 37 4 4 DG H8 H 7.93 0.01 1 stop_ save_