data_4B5I # _entry.id 4B5I # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4B5I PDBE EBI-53625 WWPDB D_1290053625 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 4B5F unspecified 'SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS (CRYSTAL FORM 1)' PDB 4B5G unspecified 'SUBSTRATE BOUND NEISSERIA AP ENDONUCLEASE IN ABSENCE OF METAL IONS (CRYSTAL FORM 2)' PDB 4B5H unspecified 'SUBSTATE BOUND INACTIVE MUTANT OF NEISSERIA AP ENDONUCLEASE IN PRESENCE OF METAL IONS' PDB 4B5J unspecified 'NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH AN ORPHAN ADENINE BASE' PDB 4B5M unspecified 'NEISSERIA AP ENDONUCLEASE BOUND TO THE SUBSTRATE WITH A CYTOSINE ORPHAN BASE' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4B5I _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2012-08-03 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Lu, D.' 1 'Silhan, J.' 2 'MacDonald, J.T.' 3 'Carpenter, E.P.' 4 'Jensen, K.' 5 'Tang, C.M.' 6 'Baldwin, G.S.' 7 'Freemont, P.S.' 8 # _citation.id primary _citation.title 'Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.' _citation.journal_abbrev 'Proc. Natl. Acad. Sci. U.S.A.' _citation.journal_volume 109 _citation.page_first 16852 _citation.page_last 16857 _citation.year 2012 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 1091-6490 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23035246 _citation.pdbx_database_id_DOI 10.1073/pnas.1206563109 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Lu, D.' 1 primary 'Silhan, J.' 2 primary 'MacDonald, J.T.' 3 primary 'Carpenter, E.P.' 4 primary 'Jensen, K.' 5 primary 'Tang, C.M.' 6 primary 'Baldwin, G.S.' 7 primary 'Freemont, P.S.' 8 # _cell.entry_id 4B5I _cell.length_a 69.090 _cell.length_b 69.090 _cell.length_c 119.670 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4B5I _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'PUTATIVE EXODEOXYRIBONUCLEASE' 29699.594 1 3.1.11.2 ? ? ? 2 polymer syn "5'-D(*GP*CP*TP*AP*CP)-3'" 1480.012 1 ? ? ? ? 3 polymer syn "5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'" 3414.234 1 ? ? ? ? 4 polymer syn "5'-D(*3DRP*CP*AP*TP*CP*GP)-3'" 1660.107 1 ? ? ? ? 5 non-polymer syn 'MANGANESE (II) ION' 54.938 1 ? ? ? ? 6 water nat water 18.015 32 ? ? ? ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 'NEISSERIA AP ENDONUCLEASE' 4 'DNA 6MER CONTAINING ABASIC RESIDUE' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNV QIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLK NWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYK DEKFSDHAPLVVEYDYAAE ; ;MLKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNV QIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLK NWKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYK DEKFSDHAPLVVEYDYAAE ; A ? 2 polydeoxyribonucleotide no no '(DG)(DC)(DT)(DA)(DC)' GCTAC U ? 3 polydeoxyribonucleotide no no '(DC)(DG)(DA)(DT)(DG)(DG)(DG)(DT)(DA)(DG)(DC)' CGATGGGTAGC V ? 4 polydeoxyribonucleotide no yes '(3DR)(DC)(DA)(DT)(DC)(DG)' NCATCG X ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 LEU n 1 3 LYS n 1 4 ILE n 1 5 ILE n 1 6 SER n 1 7 ALA n 1 8 ASN n 1 9 VAL n 1 10 ASN n 1 11 GLY n 1 12 ILE n 1 13 ARG n 1 14 SER n 1 15 ALA n 1 16 TYR n 1 17 LYS n 1 18 LYS n 1 19 GLY n 1 20 PHE n 1 21 TYR n 1 22 GLU n 1 23 TYR n 1 24 ILE n 1 25 ALA n 1 26 ALA n 1 27 SER n 1 28 GLY n 1 29 ALA n 1 30 ASP n 1 31 ILE n 1 32 VAL n 1 33 CYS n 1 34 VAL n 1 35 GLN n 1 36 GLU n 1 37 LEU n 1 38 LYS n 1 39 ALA n 1 40 GLN n 1 41 GLU n 1 42 ALA n 1 43 ASP n 1 44 LEU n 1 45 SER n 1 46 ALA n 1 47 ASP n 1 48 MET n 1 49 LYS n 1 50 ASN n 1 51 PRO n 1 52 HIS n 1 53 GLY n 1 54 MET n 1 55 HIS n 1 56 GLY n 1 57 HIS n 1 58 TRP n 1 59 HIS n 1 60 CYS n 1 61 ALA n 1 62 GLU n 1 63 LYS n 1 64 ARG n 1 65 GLY n 1 66 TYR n 1 67 SER n 1 68 GLY n 1 69 VAL n 1 70 ALA n 1 71 VAL n 1 72 TYR n 1 73 SER n 1 74 LYS n 1 75 ARG n 1 76 LYS n 1 77 PRO n 1 78 ASP n 1 79 ASN n 1 80 VAL n 1 81 GLN n 1 82 ILE n 1 83 GLY n 1 84 MET n 1 85 GLY n 1 86 ILE n 1 87 GLU n 1 88 GLU n 1 89 PHE n 1 90 ASP n 1 91 ARG n 1 92 GLU n 1 93 GLY n 1 94 ARG n 1 95 PHE n 1 96 VAL n 1 97 ARG n 1 98 CYS n 1 99 ASP n 1 100 PHE n 1 101 GLY n 1 102 ARG n 1 103 LEU n 1 104 SER n 1 105 VAL n 1 106 ILE n 1 107 SER n 1 108 LEU n 1 109 TYR n 1 110 LEU n 1 111 PRO n 1 112 SER n 1 113 GLY n 1 114 SER n 1 115 SER n 1 116 ALA n 1 117 GLU n 1 118 GLU n 1 119 ARG n 1 120 GLN n 1 121 GLN n 1 122 VAL n 1 123 LYS n 1 124 TYR n 1 125 ARG n 1 126 PHE n 1 127 LEU n 1 128 ASP n 1 129 ALA n 1 130 PHE n 1 131 TYR n 1 132 PRO n 1 133 MET n 1 134 LEU n 1 135 GLU n 1 136 ALA n 1 137 MET n 1 138 LYS n 1 139 ASN n 1 140 GLU n 1 141 GLY n 1 142 ARG n 1 143 ASP n 1 144 ILE n 1 145 VAL n 1 146 VAL n 1 147 CYS n 1 148 GLY n 1 149 ASP n 1 150 TRP n 1 151 ASN n 1 152 ILE n 1 153 ALA n 1 154 HIS n 1 155 GLN n 1 156 ASN n 1 157 ILE n 1 158 ASP n 1 159 LEU n 1 160 LYS n 1 161 ASN n 1 162 TRP n 1 163 LYS n 1 164 GLY n 1 165 ASN n 1 166 GLN n 1 167 LYS n 1 168 ASN n 1 169 SER n 1 170 GLY n 1 171 PHE n 1 172 LEU n 1 173 PRO n 1 174 GLU n 1 175 GLU n 1 176 ARG n 1 177 GLU n 1 178 TRP n 1 179 ILE n 1 180 GLY n 1 181 LYS n 1 182 VAL n 1 183 ILE n 1 184 HIS n 1 185 LYS n 1 186 LEU n 1 187 GLY n 1 188 TRP n 1 189 THR n 1 190 ASP n 1 191 MET n 1 192 TRP n 1 193 ARG n 1 194 THR n 1 195 LEU n 1 196 TYR n 1 197 PRO n 1 198 ASP n 1 199 VAL n 1 200 PRO n 1 201 GLY n 1 202 TYR n 1 203 THR n 1 204 TRP n 1 205 TRP n 1 206 SER n 1 207 ASN n 1 208 ARG n 1 209 GLY n 1 210 GLN n 1 211 ALA n 1 212 TYR n 1 213 ALA n 1 214 LYS n 1 215 ASP n 1 216 VAL n 1 217 GLY n 1 218 TRP n 1 219 ARG n 1 220 ILE n 1 221 ASP n 1 222 TYR n 1 223 GLN n 1 224 MET n 1 225 VAL n 1 226 THR n 1 227 PRO n 1 228 GLU n 1 229 LEU n 1 230 ALA n 1 231 ALA n 1 232 LYS n 1 233 ALA n 1 234 VAL n 1 235 SER n 1 236 ALA n 1 237 HIS n 1 238 VAL n 1 239 TYR n 1 240 LYS n 1 241 ASP n 1 242 GLU n 1 243 LYS n 1 244 PHE n 1 245 SER n 1 246 ASP n 1 247 HIS n 1 248 ALA n 1 249 PRO n 1 250 LEU n 1 251 VAL n 1 252 VAL n 1 253 GLU n 1 254 TYR n 1 255 ASP n 1 256 TYR n 1 257 ALA n 1 258 ALA n 1 259 GLU n 2 1 DG n 2 2 DC n 2 3 DT n 2 4 DA n 2 5 DC n 3 1 DC n 3 2 DG n 3 3 DA n 3 4 DT n 3 5 DG n 3 6 DG n 3 7 DG n 3 8 DT n 3 9 DA n 3 10 DG n 3 11 DC n 4 1 3DR n 4 2 DC n 4 3 DA n 4 4 DT n 4 5 DC n 4 6 DG n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'NEISSERIA MENINGITIDIS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 487 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 2 1 sample ? ? 'NEISSERIA MENINGITIDIS' ? 487 ? 3 1 sample ? ? 'NEISSERIA MENINGITIDIS' ? 487 ? 4 1 sample ? ? 'NEISSERIA MENINGITIDIS' ? 487 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 UNP C9X331_NEIM8 1 ? ? C9X331 ? 2 PDB 4B5I 2 ? ? 4B5I ? 3 PDB 4B5I 3 ? ? 4B5I ? 4 PDB 4B5I 4 ? ? 4B5I ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4B5I A 1 ? 259 ? C9X331 1 ? 259 ? 1 259 2 2 4B5I U 1 ? 5 ? 4B5I 31 ? 35 ? 31 35 3 3 4B5I V 1 ? 11 ? 4B5I 42 ? 52 ? 42 52 4 4 4B5I X 1 ? 6 ? 4B5I 36 ? 41 ? 36 41 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4B5I _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 101 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code C9X331 _struct_ref_seq_dif.db_mon_id ASP _struct_ref_seq_dif.pdbx_seq_db_seq_num 101 _struct_ref_seq_dif.details conflict _struct_ref_seq_dif.pdbx_auth_seq_num 101 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 3DR 'DNA linking' . "1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE" 'ABASIC DIDEOXYRIBOSE' 'C5 H11 O6 P' 198.111 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 4B5I _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.97 _exptl_crystal.density_percent_sol 37.55 _exptl_crystal.description NONE # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9797 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I03' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I03 _diffrn_source.pdbx_wavelength 0.9797 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4B5I _reflns.observed_criterion_sigma_I 1.2 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 59.80 _reflns.d_resolution_high 2.55 _reflns.number_obs 9098 _reflns.number_all ? _reflns.percent_possible_obs 99.2 _reflns.pdbx_Rmerge_I_obs 0.07 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.3 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4B5I _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 9098 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 45.231 _refine.ls_d_res_high 2.555 _refine.ls_percent_reflns_obs 91.49 _refine.ls_R_factor_obs 0.2070 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2047 _refine.ls_R_factor_R_free 0.2515 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.9 _refine.ls_number_reflns_R_free 448 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 2.4179 _refine.aniso_B[2][2] 2.4179 _refine.aniso_B[3][3] -4.8359 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.324 _refine.solvent_model_param_bsol 37.214 _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct OTHER _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.36 _refine.pdbx_overall_phase_error 25.86 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2072 _refine_hist.pdbx_number_atoms_nucleic_acid 438 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 32 _refine_hist.number_atoms_total 2543 _refine_hist.d_res_high 2.555 _refine_hist.d_res_low 45.231 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.003 ? ? 2683 'X-RAY DIFFRACTION' ? f_angle_d 0.536 ? ? 3627 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 16.366 ? ? 987 'X-RAY DIFFRACTION' ? f_chiral_restr 0.035 ? ? 371 'X-RAY DIFFRACTION' ? f_plane_restr 0.001 ? ? 393 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all 'X-RAY DIFFRACTION' . 2.5548 2.9244 2538 0.2997 83.00 0.3701 . . 131 . . 'X-RAY DIFFRACTION' . 2.9244 3.6842 2894 0.2161 93.00 0.2872 . . 156 . . 'X-RAY DIFFRACTION' . 3.6842 45.2377 3218 0.1790 98.00 0.2100 . . 161 . . # _struct.entry_id 4B5I _struct.title 'Product complex of Neisseria AP endonuclease in presence of metal ions' _struct.pdbx_descriptor 'PUTATIVE EXODEOXYRIBONUCLEASE (E.C.3.1.11.2)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4B5I _struct_keywords.pdbx_keywords HYDROLASE/DNA _struct_keywords.text 'HYDROLASE-DNA COMPLEX' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 6 ? G N N 6 ? H N N 6 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLY A 11 ? LYS A 18 ? GLY A 11 LYS A 18 1 ? 8 HELX_P HELX_P2 2 GLY A 19 ? SER A 27 ? GLY A 19 SER A 27 1 ? 9 HELX_P HELX_P3 3 SER A 45 ? ASN A 50 ? SER A 45 ASN A 50 1 ? 6 HELX_P HELX_P4 4 PRO A 51 ? MET A 54 ? PRO A 51 MET A 54 5 ? 4 HELX_P HELX_P5 5 ILE A 86 ? ARG A 91 ? ILE A 86 ARG A 91 1 ? 6 HELX_P HELX_P6 6 ALA A 116 ? GLU A 140 ? ALA A 116 GLU A 140 1 ? 25 HELX_P HELX_P7 7 GLN A 155 ? ASP A 158 ? GLN A 155 ASP A 158 5 ? 4 HELX_P HELX_P8 8 LEU A 172 ? LYS A 185 ? LEU A 172 LYS A 185 1 ? 14 HELX_P HELX_P9 9 MET A 191 ? TYR A 196 ? MET A 191 TYR A 196 1 ? 6 HELX_P HELX_P10 10 GLN A 210 ? ASP A 215 ? GLN A 210 ASP A 215 1 ? 6 HELX_P HELX_P11 11 THR A 226 ? ALA A 231 ? THR A 226 ALA A 231 1 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc1 metalc ? ? E MN . MN ? ? ? 1_555 A GLU 36 OE2 ? ? A MN 1257 A GLU 36 1_555 ? ? ? ? ? ? ? 2.517 ? metalc2 metalc ? ? E MN . MN ? ? ? 1_555 A GLU 36 OE1 ? ? A MN 1257 A GLU 36 1_555 ? ? ? ? ? ? ? 2.631 ? metalc3 metalc ? ? E MN . MN ? ? ? 1_555 B DC 5 "O3'" ? ? A MN 1257 U DC 35 1_555 ? ? ? ? ? ? ? 2.569 ? covale1 covale ? ? D 3DR 1 "O3'" ? ? ? 1_555 D DC 2 P ? ? X 3DR 36 X DC 37 1_555 ? ? ? ? ? ? ? 1.607 ? metalc4 metalc ? ? D 3DR 1 OP1 ? ? ? 1_555 E MN . MN ? ? X 3DR 36 A MN 1257 1_555 ? ? ? ? ? ? ? 2.543 ? hydrog1 hydrog ? ? B DG 1 N1 ? ? ? 1_555 C DC 11 N3 ? ? U DG 31 V DC 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? B DG 1 N2 ? ? ? 1_555 C DC 11 O2 ? ? U DG 31 V DC 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? B DG 1 O6 ? ? ? 1_555 C DC 11 N4 ? ? U DG 31 V DC 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? B DC 2 O2 ? ? ? 1_555 C DG 10 N2 ? ? U DC 32 V DG 51 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? hydrog5 hydrog ? ? B DT 3 N3 ? ? ? 1_555 C DA 9 N1 ? ? U DT 33 V DA 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? B DT 3 O4 ? ? ? 1_555 C DA 9 N6 ? ? U DT 33 V DA 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? B DA 4 N1 ? ? ? 1_555 C DT 8 N3 ? ? U DA 34 V DT 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? B DA 4 N6 ? ? ? 1_555 C DT 8 O4 ? ? U DA 34 V DT 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? B DC 5 N3 ? ? ? 1_555 C DG 7 N1 ? ? U DC 35 V DG 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? B DC 5 N4 ? ? ? 1_555 C DG 7 O6 ? ? U DC 35 V DG 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? B DC 5 O2 ? ? ? 1_555 C DG 7 N2 ? ? U DC 35 V DG 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? C DC 1 N3 ? ? ? 1_555 D DG 6 N1 ? ? V DC 42 X DG 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? C DC 1 N4 ? ? ? 1_555 D DG 6 O6 ? ? V DC 42 X DG 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? C DC 1 O2 ? ? ? 1_555 D DG 6 N2 ? ? V DC 42 X DG 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? C DG 2 N1 ? ? ? 1_555 D DC 5 N3 ? ? V DG 43 X DC 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? C DG 2 N2 ? ? ? 1_555 D DC 5 O2 ? ? V DG 43 X DC 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? C DG 2 O6 ? ? ? 1_555 D DC 5 N4 ? ? V DG 43 X DC 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? C DA 3 N1 ? ? ? 1_555 D DT 4 N3 ? ? V DA 44 X DT 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? C DA 3 N6 ? ? ? 1_555 D DT 4 O4 ? ? V DA 44 X DT 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? C DT 4 N3 ? ? ? 1_555 D DA 3 N1 ? ? V DT 45 X DA 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? C DT 4 O4 ? ? ? 1_555 D DA 3 N6 ? ? V DT 45 X DA 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? C DG 5 N2 ? ? ? 1_555 D DC 2 O2 ? ? V DG 46 X DC 37 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? covale ? ? hydrog ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 6 ? AB ? 6 ? AC ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA 1 2 ? anti-parallel AA 2 3 ? anti-parallel AA 3 4 ? parallel AA 4 5 ? anti-parallel AA 5 6 ? anti-parallel AB 1 2 ? anti-parallel AB 2 3 ? anti-parallel AB 3 4 ? parallel AB 4 5 ? anti-parallel AB 5 6 ? anti-parallel AC 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA 1 HIS A 55 ? HIS A 59 ? HIS A 55 HIS A 59 AA 2 VAL A 69 ? SER A 73 ? VAL A 69 SER A 73 AA 3 ILE A 31 ? GLN A 35 ? ILE A 31 GLN A 35 AA 4 LEU A 2 ? ASN A 8 ? LEU A 2 ASN A 8 AA 5 LEU A 250 ? TYR A 254 ? LEU A 250 TYR A 254 AA 6 ALA A 233 ? VAL A 238 ? ALA A 233 VAL A 238 AB 1 ASN A 79 ? ILE A 82 ? ASN A 79 ILE A 82 AB 2 PHE A 95 ? PHE A 100 ? PHE A 95 PHE A 100 AB 3 LEU A 103 ? TYR A 109 ? LEU A 103 TYR A 109 AB 4 ASP A 143 ? ASP A 149 ? ASP A 143 ASP A 149 AB 5 ASP A 221 ? VAL A 225 ? ASP A 221 VAL A 225 AB 6 THR A 189 ? ASP A 190 ? THR A 189 ASP A 190 AC 1 TRP A 204 ? TRP A 205 ? TRP A 204 TRP A 205 AC 2 GLY A 217 ? TRP A 218 ? GLY A 217 TRP A 218 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA 1 2 N HIS A 59 ? N HIS A 59 O VAL A 69 ? O VAL A 69 AA 2 3 N TYR A 72 ? N TYR A 72 O VAL A 32 ? O VAL A 32 AA 3 4 N CYS A 33 ? N CYS A 33 O ILE A 5 ? O ILE A 5 AA 4 5 N SER A 6 ? N SER A 6 O LEU A 250 ? O LEU A 250 AA 5 6 O GLU A 253 ? O GLU A 253 N VAL A 234 ? N VAL A 234 AB 1 2 N GLN A 81 ? N GLN A 81 O ARG A 97 ? O ARG A 97 AB 2 3 N PHE A 100 ? N PHE A 100 O LEU A 103 ? O LEU A 103 AB 3 4 N SER A 104 ? N SER A 104 O ASP A 143 ? O ASP A 143 AB 4 5 N GLY A 148 ? N GLY A 148 O TYR A 222 ? O TYR A 222 AB 5 6 N VAL A 225 ? N VAL A 225 O THR A 189 ? O THR A 189 AC 1 2 O TRP A 204 ? O TRP A 204 N TRP A 218 ? N TRP A 218 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE MN A 1257' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 GLU A 36 ? GLU A 36 . ? 1_555 ? 2 AC1 4 ASP A 246 ? ASP A 246 . ? 1_555 ? 3 AC1 4 DC B 5 ? DC U 35 . ? 1_555 ? 4 AC1 4 3DR D 1 ? 3DR X 36 . ? 1_555 ? # _database_PDB_matrix.entry_id 4B5I _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 4B5I _atom_sites.fract_transf_matrix[1][1] 0.014474 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.014474 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.008356 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MN N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 1 MET MET A . n A 1 2 LEU 2 2 2 LEU LEU A . n A 1 3 LYS 3 3 3 LYS LYS A . n A 1 4 ILE 4 4 4 ILE ILE A . n A 1 5 ILE 5 5 5 ILE ILE A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 ALA 7 7 7 ALA ALA A . n A 1 8 ASN 8 8 8 ASN ASN A . n A 1 9 VAL 9 9 9 VAL VAL A . n A 1 10 ASN 10 10 10 ASN ASN A . n A 1 11 GLY 11 11 11 GLY GLY A . n A 1 12 ILE 12 12 12 ILE ILE A . n A 1 13 ARG 13 13 13 ARG ARG A . n A 1 14 SER 14 14 14 SER SER A . n A 1 15 ALA 15 15 15 ALA ALA A . n A 1 16 TYR 16 16 16 TYR TYR A . n A 1 17 LYS 17 17 17 LYS LYS A . n A 1 18 LYS 18 18 18 LYS LYS A . n A 1 19 GLY 19 19 19 GLY GLY A . n A 1 20 PHE 20 20 20 PHE PHE A . n A 1 21 TYR 21 21 21 TYR TYR A . n A 1 22 GLU 22 22 22 GLU GLU A . n A 1 23 TYR 23 23 23 TYR TYR A . n A 1 24 ILE 24 24 24 ILE ILE A . n A 1 25 ALA 25 25 25 ALA ALA A . n A 1 26 ALA 26 26 26 ALA ALA A . n A 1 27 SER 27 27 27 SER SER A . n A 1 28 GLY 28 28 28 GLY GLY A . n A 1 29 ALA 29 29 29 ALA ALA A . n A 1 30 ASP 30 30 30 ASP ASP A . n A 1 31 ILE 31 31 31 ILE ILE A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 CYS 33 33 33 CYS CYS A . n A 1 34 VAL 34 34 34 VAL VAL A . n A 1 35 GLN 35 35 35 GLN GLN A . n A 1 36 GLU 36 36 36 GLU GLU A . n A 1 37 LEU 37 37 37 LEU LEU A . n A 1 38 LYS 38 38 38 LYS LYS A . n A 1 39 ALA 39 39 39 ALA ALA A . n A 1 40 GLN 40 40 40 GLN GLN A . n A 1 41 GLU 41 41 41 GLU GLU A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 ASP 43 43 43 ASP ASP A . n A 1 44 LEU 44 44 44 LEU LEU A . n A 1 45 SER 45 45 45 SER SER A . n A 1 46 ALA 46 46 46 ALA ALA A . n A 1 47 ASP 47 47 47 ASP ASP A . n A 1 48 MET 48 48 48 MET MET A . n A 1 49 LYS 49 49 49 LYS LYS A . n A 1 50 ASN 50 50 50 ASN ASN A . n A 1 51 PRO 51 51 51 PRO PRO A . n A 1 52 HIS 52 52 52 HIS HIS A . n A 1 53 GLY 53 53 53 GLY GLY A . n A 1 54 MET 54 54 54 MET MET A . n A 1 55 HIS 55 55 55 HIS HIS A . n A 1 56 GLY 56 56 56 GLY GLY A . n A 1 57 HIS 57 57 57 HIS HIS A . n A 1 58 TRP 58 58 58 TRP TRP A . n A 1 59 HIS 59 59 59 HIS HIS A . n A 1 60 CYS 60 60 60 CYS CYS A . n A 1 61 ALA 61 61 61 ALA ALA A . n A 1 62 GLU 62 62 62 GLU GLU A . n A 1 63 LYS 63 63 63 LYS LYS A . n A 1 64 ARG 64 64 64 ARG ARG A . n A 1 65 GLY 65 65 65 GLY GLY A . n A 1 66 TYR 66 66 66 TYR TYR A . n A 1 67 SER 67 67 67 SER SER A . n A 1 68 GLY 68 68 68 GLY GLY A . n A 1 69 VAL 69 69 69 VAL VAL A . n A 1 70 ALA 70 70 70 ALA ALA A . n A 1 71 VAL 71 71 71 VAL VAL A . n A 1 72 TYR 72 72 72 TYR TYR A . n A 1 73 SER 73 73 73 SER SER A . n A 1 74 LYS 74 74 74 LYS LYS A . n A 1 75 ARG 75 75 75 ARG ARG A . n A 1 76 LYS 76 76 76 LYS LYS A . n A 1 77 PRO 77 77 77 PRO PRO A . n A 1 78 ASP 78 78 78 ASP ASP A . n A 1 79 ASN 79 79 79 ASN ASN A . n A 1 80 VAL 80 80 80 VAL VAL A . n A 1 81 GLN 81 81 81 GLN GLN A . n A 1 82 ILE 82 82 82 ILE ILE A . n A 1 83 GLY 83 83 83 GLY GLY A . n A 1 84 MET 84 84 84 MET MET A . n A 1 85 GLY 85 85 85 GLY GLY A . n A 1 86 ILE 86 86 86 ILE ILE A . n A 1 87 GLU 87 87 87 GLU GLU A . n A 1 88 GLU 88 88 88 GLU GLU A . n A 1 89 PHE 89 89 89 PHE PHE A . n A 1 90 ASP 90 90 90 ASP ASP A . n A 1 91 ARG 91 91 91 ARG ARG A . n A 1 92 GLU 92 92 92 GLU GLU A . n A 1 93 GLY 93 93 93 GLY GLY A . n A 1 94 ARG 94 94 94 ARG ARG A . n A 1 95 PHE 95 95 95 PHE PHE A . n A 1 96 VAL 96 96 96 VAL VAL A . n A 1 97 ARG 97 97 97 ARG ARG A . n A 1 98 CYS 98 98 98 CYS CYS A . n A 1 99 ASP 99 99 99 ASP ASP A . n A 1 100 PHE 100 100 100 PHE PHE A . n A 1 101 GLY 101 101 101 GLY GLY A . n A 1 102 ARG 102 102 102 ARG ARG A . n A 1 103 LEU 103 103 103 LEU LEU A . n A 1 104 SER 104 104 104 SER SER A . n A 1 105 VAL 105 105 105 VAL VAL A . n A 1 106 ILE 106 106 106 ILE ILE A . n A 1 107 SER 107 107 107 SER SER A . n A 1 108 LEU 108 108 108 LEU LEU A . n A 1 109 TYR 109 109 109 TYR TYR A . n A 1 110 LEU 110 110 110 LEU LEU A . n A 1 111 PRO 111 111 111 PRO PRO A . n A 1 112 SER 112 112 112 SER SER A . n A 1 113 GLY 113 113 113 GLY GLY A . n A 1 114 SER 114 114 114 SER SER A . n A 1 115 SER 115 115 115 SER SER A . n A 1 116 ALA 116 116 116 ALA ALA A . n A 1 117 GLU 117 117 117 GLU GLU A . n A 1 118 GLU 118 118 118 GLU GLU A . n A 1 119 ARG 119 119 119 ARG ARG A . n A 1 120 GLN 120 120 120 GLN GLN A . n A 1 121 GLN 121 121 121 GLN GLN A . n A 1 122 VAL 122 122 122 VAL VAL A . n A 1 123 LYS 123 123 123 LYS LYS A . n A 1 124 TYR 124 124 124 TYR TYR A . n A 1 125 ARG 125 125 125 ARG ARG A . n A 1 126 PHE 126 126 126 PHE PHE A . n A 1 127 LEU 127 127 127 LEU LEU A . n A 1 128 ASP 128 128 128 ASP ASP A . n A 1 129 ALA 129 129 129 ALA ALA A . n A 1 130 PHE 130 130 130 PHE PHE A . n A 1 131 TYR 131 131 131 TYR TYR A . n A 1 132 PRO 132 132 132 PRO PRO A . n A 1 133 MET 133 133 133 MET MET A . n A 1 134 LEU 134 134 134 LEU LEU A . n A 1 135 GLU 135 135 135 GLU GLU A . n A 1 136 ALA 136 136 136 ALA ALA A . n A 1 137 MET 137 137 137 MET MET A . n A 1 138 LYS 138 138 138 LYS LYS A . n A 1 139 ASN 139 139 139 ASN ASN A . n A 1 140 GLU 140 140 140 GLU GLU A . n A 1 141 GLY 141 141 141 GLY GLY A . n A 1 142 ARG 142 142 142 ARG ARG A . n A 1 143 ASP 143 143 143 ASP ASP A . n A 1 144 ILE 144 144 144 ILE ILE A . n A 1 145 VAL 145 145 145 VAL VAL A . n A 1 146 VAL 146 146 146 VAL VAL A . n A 1 147 CYS 147 147 147 CYS CYS A . n A 1 148 GLY 148 148 148 GLY GLY A . n A 1 149 ASP 149 149 149 ASP ASP A . n A 1 150 TRP 150 150 150 TRP TRP A . n A 1 151 ASN 151 151 151 ASN ASN A . n A 1 152 ILE 152 152 152 ILE ILE A . n A 1 153 ALA 153 153 153 ALA ALA A . n A 1 154 HIS 154 154 154 HIS HIS A . n A 1 155 GLN 155 155 155 GLN GLN A . n A 1 156 ASN 156 156 156 ASN ASN A . n A 1 157 ILE 157 157 157 ILE ILE A . n A 1 158 ASP 158 158 158 ASP ASP A . n A 1 159 LEU 159 159 159 LEU LEU A . n A 1 160 LYS 160 160 160 LYS LYS A . n A 1 161 ASN 161 161 161 ASN ASN A . n A 1 162 TRP 162 162 162 TRP TRP A . n A 1 163 LYS 163 163 163 LYS LYS A . n A 1 164 GLY 164 164 164 GLY GLY A . n A 1 165 ASN 165 165 165 ASN ASN A . n A 1 166 GLN 166 166 166 GLN GLN A . n A 1 167 LYS 167 167 167 LYS LYS A . n A 1 168 ASN 168 168 168 ASN ASN A . n A 1 169 SER 169 169 169 SER SER A . n A 1 170 GLY 170 170 170 GLY GLY A . n A 1 171 PHE 171 171 171 PHE PHE A . n A 1 172 LEU 172 172 172 LEU LEU A . n A 1 173 PRO 173 173 173 PRO PRO A . n A 1 174 GLU 174 174 174 GLU GLU A . n A 1 175 GLU 175 175 175 GLU GLU A . n A 1 176 ARG 176 176 176 ARG ARG A . n A 1 177 GLU 177 177 177 GLU GLU A . n A 1 178 TRP 178 178 178 TRP TRP A . n A 1 179 ILE 179 179 179 ILE ILE A . n A 1 180 GLY 180 180 180 GLY GLY A . n A 1 181 LYS 181 181 181 LYS LYS A . n A 1 182 VAL 182 182 182 VAL VAL A . n A 1 183 ILE 183 183 183 ILE ILE A . n A 1 184 HIS 184 184 184 HIS HIS A . n A 1 185 LYS 185 185 185 LYS LYS A . n A 1 186 LEU 186 186 186 LEU LEU A . n A 1 187 GLY 187 187 187 GLY GLY A . n A 1 188 TRP 188 188 188 TRP TRP A . n A 1 189 THR 189 189 189 THR THR A . n A 1 190 ASP 190 190 190 ASP ASP A . n A 1 191 MET 191 191 191 MET MET A . n A 1 192 TRP 192 192 192 TRP TRP A . n A 1 193 ARG 193 193 193 ARG ARG A . n A 1 194 THR 194 194 194 THR THR A . n A 1 195 LEU 195 195 195 LEU LEU A . n A 1 196 TYR 196 196 196 TYR TYR A . n A 1 197 PRO 197 197 197 PRO PRO A . n A 1 198 ASP 198 198 198 ASP ASP A . n A 1 199 VAL 199 199 199 VAL VAL A . n A 1 200 PRO 200 200 200 PRO PRO A . n A 1 201 GLY 201 201 201 GLY GLY A . n A 1 202 TYR 202 202 202 TYR TYR A . n A 1 203 THR 203 203 203 THR THR A . n A 1 204 TRP 204 204 204 TRP TRP A . n A 1 205 TRP 205 205 205 TRP TRP A . n A 1 206 SER 206 206 206 SER SER A . n A 1 207 ASN 207 207 207 ASN ASN A . n A 1 208 ARG 208 208 208 ARG ARG A . n A 1 209 GLY 209 209 209 GLY GLY A . n A 1 210 GLN 210 210 210 GLN GLN A . n A 1 211 ALA 211 211 211 ALA ALA A . n A 1 212 TYR 212 212 212 TYR TYR A . n A 1 213 ALA 213 213 213 ALA ALA A . n A 1 214 LYS 214 214 214 LYS LYS A . n A 1 215 ASP 215 215 215 ASP ASP A . n A 1 216 VAL 216 216 216 VAL VAL A . n A 1 217 GLY 217 217 217 GLY GLY A . n A 1 218 TRP 218 218 218 TRP TRP A . n A 1 219 ARG 219 219 219 ARG ARG A . n A 1 220 ILE 220 220 220 ILE ILE A . n A 1 221 ASP 221 221 221 ASP ASP A . n A 1 222 TYR 222 222 222 TYR TYR A . n A 1 223 GLN 223 223 223 GLN GLN A . n A 1 224 MET 224 224 224 MET MET A . n A 1 225 VAL 225 225 225 VAL VAL A . n A 1 226 THR 226 226 226 THR THR A . n A 1 227 PRO 227 227 227 PRO PRO A . n A 1 228 GLU 228 228 228 GLU GLU A . n A 1 229 LEU 229 229 229 LEU LEU A . n A 1 230 ALA 230 230 230 ALA ALA A . n A 1 231 ALA 231 231 231 ALA ALA A . n A 1 232 LYS 232 232 232 LYS LYS A . n A 1 233 ALA 233 233 233 ALA ALA A . n A 1 234 VAL 234 234 234 VAL VAL A . n A 1 235 SER 235 235 235 SER SER A . n A 1 236 ALA 236 236 236 ALA ALA A . n A 1 237 HIS 237 237 237 HIS HIS A . n A 1 238 VAL 238 238 238 VAL VAL A . n A 1 239 TYR 239 239 239 TYR TYR A . n A 1 240 LYS 240 240 240 LYS LYS A . n A 1 241 ASP 241 241 241 ASP ASP A . n A 1 242 GLU 242 242 242 GLU GLU A . n A 1 243 LYS 243 243 243 LYS LYS A . n A 1 244 PHE 244 244 244 PHE PHE A . n A 1 245 SER 245 245 245 SER SER A . n A 1 246 ASP 246 246 246 ASP ASP A . n A 1 247 HIS 247 247 247 HIS HIS A . n A 1 248 ALA 248 248 248 ALA ALA A . n A 1 249 PRO 249 249 249 PRO PRO A . n A 1 250 LEU 250 250 250 LEU LEU A . n A 1 251 VAL 251 251 251 VAL VAL A . n A 1 252 VAL 252 252 252 VAL VAL A . n A 1 253 GLU 253 253 253 GLU GLU A . n A 1 254 TYR 254 254 254 TYR TYR A . n A 1 255 ASP 255 255 255 ASP ASP A . n A 1 256 TYR 256 256 256 TYR TYR A . n A 1 257 ALA 257 257 ? ? ? A . n A 1 258 ALA 258 258 ? ? ? A . n A 1 259 GLU 259 259 ? ? ? A . n B 2 1 DG 1 31 31 DG DG U . n B 2 2 DC 2 32 32 DC DC U . n B 2 3 DT 3 33 33 DT DT U . n B 2 4 DA 4 34 34 DA DA U . n B 2 5 DC 5 35 35 DC DC U . n C 3 1 DC 1 42 42 DC DC V . n C 3 2 DG 2 43 43 DG DG V . n C 3 3 DA 3 44 44 DA DA V . n C 3 4 DT 4 45 45 DT DT V . n C 3 5 DG 5 46 46 DG DG V . n C 3 6 DG 6 47 47 DG DG V . n C 3 7 DG 7 48 48 DG DG V . n C 3 8 DT 8 49 49 DT DT V . n C 3 9 DA 9 50 50 DA DA V . n C 3 10 DG 10 51 51 DG DG V . n C 3 11 DC 11 52 52 DC DC V . n D 4 1 3DR 1 36 36 3DR 3DR X . n D 4 2 DC 2 37 37 DC DC X . n D 4 3 DA 3 38 38 DA DA X . n D 4 4 DT 4 39 39 DT DT X . n D 4 5 DC 5 40 40 DC DC X . n D 4 6 DG 6 41 41 DG DG X . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 5 MN 1 1257 1257 MN MN A . F 6 HOH 1 2001 2001 HOH HOH A . F 6 HOH 2 2002 2002 HOH HOH A . F 6 HOH 3 2003 2003 HOH HOH A . F 6 HOH 4 2004 2004 HOH HOH A . F 6 HOH 5 2005 2005 HOH HOH A . F 6 HOH 6 2006 2006 HOH HOH A . F 6 HOH 7 2007 2007 HOH HOH A . F 6 HOH 8 2008 2008 HOH HOH A . F 6 HOH 9 2009 2009 HOH HOH A . F 6 HOH 10 2010 2010 HOH HOH A . F 6 HOH 11 2011 2011 HOH HOH A . F 6 HOH 12 2012 2012 HOH HOH A . F 6 HOH 13 2013 2013 HOH HOH A . F 6 HOH 14 2014 2014 HOH HOH A . F 6 HOH 15 2015 2015 HOH HOH A . F 6 HOH 16 2016 2016 HOH HOH A . F 6 HOH 17 2017 2017 HOH HOH A . F 6 HOH 18 2018 2018 HOH HOH A . F 6 HOH 19 2019 2019 HOH HOH A . F 6 HOH 20 2020 2020 HOH HOH A . F 6 HOH 21 2021 2021 HOH HOH A . F 6 HOH 22 2022 2022 HOH HOH A . F 6 HOH 23 2023 2023 HOH HOH A . F 6 HOH 24 2024 2024 HOH HOH A . F 6 HOH 25 2025 2025 HOH HOH A . F 6 HOH 26 2026 2026 HOH HOH A . F 6 HOH 27 2027 2027 HOH HOH A . F 6 HOH 28 2028 2028 HOH HOH A . F 6 HOH 29 2029 2029 HOH HOH A . F 6 HOH 30 2030 2030 HOH HOH A . G 6 HOH 1 2001 2001 HOH HOH U . H 6 HOH 1 2001 2001 HOH HOH X . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3840 ? 1 MORE -18.5 ? 1 'SSA (A^2)' 12620 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OE2 ? A GLU 36 ? A GLU 36 ? 1_555 MN ? E MN . ? A MN 1257 ? 1_555 OE1 ? A GLU 36 ? A GLU 36 ? 1_555 50.4 ? 2 OE2 ? A GLU 36 ? A GLU 36 ? 1_555 MN ? E MN . ? A MN 1257 ? 1_555 "O3'" ? B DC 5 ? U DC 35 ? 1_555 64.7 ? 3 OE1 ? A GLU 36 ? A GLU 36 ? 1_555 MN ? E MN . ? A MN 1257 ? 1_555 "O3'" ? B DC 5 ? U DC 35 ? 1_555 105.0 ? 4 OE2 ? A GLU 36 ? A GLU 36 ? 1_555 MN ? E MN . ? A MN 1257 ? 1_555 OP1 ? D 3DR 1 ? X 3DR 36 ? 1_555 84.4 ? 5 OE1 ? A GLU 36 ? A GLU 36 ? 1_555 MN ? E MN . ? A MN 1257 ? 1_555 OP1 ? D 3DR 1 ? X 3DR 36 ? 1_555 130.7 ? 6 "O3'" ? B DC 5 ? U DC 35 ? 1_555 MN ? E MN . ? A MN 1257 ? 1_555 OP1 ? D 3DR 1 ? X 3DR 36 ? 1_555 61.8 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-10-17 2 'Structure model' 1 1 2012-10-31 3 'Structure model' 1 2 2018-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' citation 2 3 'Structure model' citation_author # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_citation.journal_abbrev' 2 3 'Structure model' '_citation.journal_id_ISSN' 3 3 'Structure model' '_citation.page_last' 4 3 'Structure model' '_citation.pdbx_database_id_DOI' 5 3 'Structure model' '_citation.title' 6 3 'Structure model' '_citation_author.name' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -13.4889 29.1915 14.2242 0.2822 0.3077 0.1131 0.1041 -0.0600 -0.0733 1.5170 2.9216 1.3782 -1.4469 -0.3893 1.1930 -0.4045 -0.4548 0.2783 0.7962 0.5422 -0.1919 0.0752 -0.1413 0.0524 'X-RAY DIFFRACTION' 2 ? refined -21.8563 37.0527 8.0559 0.3465 0.3605 0.4093 0.1351 0.0146 0.0109 0.2950 0.5076 0.1889 -0.3889 -0.1874 0.1643 -0.2017 -0.4670 -0.4742 0.2581 -0.0788 0.1421 -0.4416 -0.3748 0.0001 'X-RAY DIFFRACTION' 3 ? refined -25.6829 23.5509 8.1398 0.0455 0.3041 0.1328 0.0014 0.1486 0.0346 2.0593 1.2718 1.7643 -0.0414 0.5502 1.0261 -0.3194 -0.3924 -0.0683 0.0176 -0.2282 0.1855 -0.0421 -0.4349 -0.6748 'X-RAY DIFFRACTION' 4 ? refined -31.0458 17.8872 2.0998 0.1791 0.2835 0.4941 -0.0849 0.0265 -0.0566 0.2223 0.4292 3.0281 -0.0904 -0.2631 1.1305 -0.1320 0.0978 0.1145 0.2373 0.0360 0.3243 0.8270 -0.2615 -0.0168 'X-RAY DIFFRACTION' 5 ? refined -28.9139 33.3065 -5.7231 0.1245 0.4311 0.3560 0.0162 -0.2071 -0.0947 1.0469 1.8183 3.6570 1.3158 -0.6418 -0.0786 0.7060 -0.2861 -0.7002 -0.1490 -0.2934 0.4528 0.0356 -0.0227 0.1846 'X-RAY DIFFRACTION' 6 ? refined -18.9941 15.1237 -4.6916 0.3420 0.2141 0.2898 0.0043 -0.0269 -0.0349 1.1846 1.9110 1.6040 0.0453 -0.3329 -0.2359 -0.1167 0.1713 -0.5277 -0.7471 0.0838 0.5124 0.6665 -0.3535 0.0006 'X-RAY DIFFRACTION' 7 ? refined -9.1240 20.5485 0.1825 0.1245 0.2731 0.2406 0.0701 -0.0435 -0.0888 0.5965 4.7540 1.9290 -0.6561 -0.7686 1.0186 -0.2160 -0.0270 -0.2011 -0.1861 0.5648 -0.5320 0.3097 0.0827 0.1967 'X-RAY DIFFRACTION' 8 ? refined -18.8886 9.2359 22.9656 1.2308 0.6506 0.8651 -0.1127 0.3704 0.0896 0.0496 0.0413 -0.0006 -0.0459 0.0031 -0.0007 0.1516 1.4777 0.2202 0.5065 0.5780 -0.1415 0.6407 -0.2818 0.0020 'X-RAY DIFFRACTION' 9 ? refined -14.1052 -7.7495 6.8885 0.8918 1.2329 1.0189 0.1077 0.0870 0.6312 0.0616 0.0629 0.0152 -0.0646 -0.0064 -0.0019 0.4130 0.5403 -0.6861 -0.1155 0.0529 0.1906 0.3295 -0.2236 0.0016 'X-RAY DIFFRACTION' 10 ? refined -11.5310 11.2620 20.6194 0.8654 0.7224 0.6601 0.3377 0.0032 -0.2358 0.2630 0.1366 0.0198 0.1964 -0.0774 -0.0578 0.3052 -0.6113 -1.2532 0.9066 -0.6885 0.3011 -0.2996 -0.0313 0.0012 'X-RAY DIFFRACTION' 11 ? refined -9.7163 -1.0349 6.2878 0.9054 0.5113 0.7564 0.2610 -0.0676 -0.0027 0.5031 0.2145 0.3190 0.2903 0.1247 -0.0630 0.3411 -0.2499 -0.4939 0.0980 -0.2982 -0.6108 0.2172 0.3943 -0.0006 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 1:70)' 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 71:85)' 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 86:119)' 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 120:136)' 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 137:142)' 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 143:196)' 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 197:256)' 'X-RAY DIFFRACTION' 8 8 ? ? ? ? ? ? ? ? ? '(CHAIN U AND RESID 31:35)' 'X-RAY DIFFRACTION' 9 9 ? ? ? ? ? ? ? ? ? '(CHAIN V AND RESID 42:46)' 'X-RAY DIFFRACTION' 10 10 ? ? ? ? ? ? ? ? ? '(CHAIN V AND RESID 47:52)' 'X-RAY DIFFRACTION' 11 11 ? ? ? ? ? ? ? ? ? '(CHAIN X AND RESID 36:41)' # _software.name PHENIX _software.classification refinement _software.version '(PHENIX.REFINE)' _software.citation_id ? _software.pdbx_ordinal 1 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU A 36 ? ? 60.56 64.60 2 1 SER A 67 ? ? 52.30 -150.06 3 1 PHE A 171 ? ? -141.51 32.10 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A ALA 257 ? A ALA 257 2 1 Y 1 A ALA 258 ? A ALA 258 3 1 Y 1 A GLU 259 ? A GLU 259 # _ndb_struct_conf_na.entry_id 4B5I _ndb_struct_conf_na.feature 'double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 B DG 1 1_555 C DC 11 1_555 -0.885 -0.240 -0.649 0.587 -31.733 2.842 1 U_DG31:DC52_V U 31 ? V 52 ? 19 1 1 B DC 2 1_555 C DG 10 1_555 -0.539 0.721 0.833 -27.603 -20.834 16.571 2 U_DC32:DG51_V U 32 ? V 51 ? ? 1 1 B DT 3 1_555 C DA 9 1_555 0.464 0.134 0.366 -18.784 -1.756 13.127 3 U_DT33:DA50_V U 33 ? V 50 ? 20 1 1 B DA 4 1_555 C DT 8 1_555 0.158 0.042 0.679 0.148 -1.435 9.463 4 U_DA34:DT49_V U 34 ? V 49 ? 20 1 1 B DC 5 1_555 C DG 7 1_555 0.352 0.287 0.326 0.630 1.838 6.002 5 U_DC35:DG48_V U 35 ? V 48 ? 19 1 1 C DC 1 1_555 D DG 6 1_555 -0.710 0.190 0.511 3.937 -23.195 10.136 6 V_DC42:DG41_X V 42 ? X 41 ? 19 1 1 C DG 2 1_555 D DC 5 1_555 -0.849 -0.271 0.644 8.438 -18.024 0.775 7 V_DG43:DC40_X V 43 ? X 40 ? 19 1 1 C DA 3 1_555 D DT 4 1_555 -0.147 -0.221 0.350 0.269 -14.393 -3.062 8 V_DA44:DT39_X V 44 ? X 39 ? 20 1 1 C DT 4 1_555 D DA 3 1_555 0.237 -0.017 0.833 -8.862 -22.779 5.004 9 V_DT45:DA38_X V 45 ? X 38 ? 20 1 1 C DG 5 1_555 D DC 2 1_555 -1.841 0.132 -0.290 12.691 32.318 14.980 10 V_DG46:DC37_X V 46 ? X 37 ? ? 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 B DG 1 1_555 C DC 11 1_555 B DC 2 1_555 C DG 10 1_555 1.232 -0.575 3.810 -1.920 0.148 42.392 -0.811 -1.928 3.752 0.204 2.653 42.434 1 UU_DG31DC32:DG51DC52_VV U 31 ? V 52 ? U 32 ? V 51 ? 1 B DC 2 1_555 C DG 10 1_555 B DT 3 1_555 C DA 9 1_555 -0.249 -0.231 3.107 3.472 10.399 32.276 -1.948 0.944 2.857 18.067 -6.032 34.040 2 UU_DC32DT33:DA50DG51_VV U 32 ? V 51 ? U 33 ? V 50 ? 1 B DT 3 1_555 C DA 9 1_555 B DA 4 1_555 C DT 8 1_555 0.423 -0.129 2.637 -1.191 10.801 29.963 -1.812 -0.945 2.428 20.078 2.214 31.830 3 UU_DT33DA34:DT49DA50_VV U 33 ? V 50 ? U 34 ? V 49 ? 1 B DA 4 1_555 C DT 8 1_555 B DC 5 1_555 C DG 7 1_555 -0.234 -0.814 3.421 0.619 -3.745 32.901 -0.760 0.521 3.485 -6.584 -1.088 33.113 4 UU_DA34DC35:DG48DT49_VV U 34 ? V 49 ? U 35 ? V 48 ? 1 C DC 1 1_555 D DG 6 1_555 C DG 2 1_555 D DC 5 1_555 0.625 0.168 2.921 0.830 13.672 38.139 -1.148 -0.819 2.828 20.146 -1.223 40.438 5 VV_DC42DG43:DC40DG41_XX V 42 ? X 41 ? V 43 ? X 40 ? 1 C DG 2 1_555 D DC 5 1_555 C DA 3 1_555 D DT 4 1_555 -0.126 -0.525 3.168 1.438 -1.261 42.422 -0.601 0.315 3.176 -1.742 -1.987 42.463 6 VV_DG43DA44:DT39DC40_XX V 43 ? X 40 ? V 44 ? X 39 ? 1 C DA 3 1_555 D DT 4 1_555 C DT 4 1_555 D DA 3 1_555 0.390 -0.690 3.442 -0.944 -5.758 34.629 -0.223 -0.797 3.496 -9.589 1.571 35.102 7 VV_DA44DT45:DA38DT39_XX V 44 ? X 39 ? V 45 ? X 38 ? 1 C DT 4 1_555 D DA 3 1_555 C DG 5 1_555 D DC 2 1_555 1.409 0.374 3.154 6.416 -13.019 30.496 2.738 -1.399 2.983 -23.174 -11.420 33.700 8 VV_DT45DG46:DC37DA38_XX V 45 ? X 38 ? V 46 ? X 37 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 5 'MANGANESE (II) ION' MN 6 water HOH #