data_5NFM # _entry.id 5NFM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 5NFM pdb_00005nfm 10.2210/pdb5nfm/pdb WWPDB D_1200004023 ? ? # 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 2018-10-10 2 'Structure model' 1 1 2020-11-04 3 'Structure model' 1 2 2024-01-17 # _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 ? _pdbx_audit_revision_details.details ? # 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 2 'Structure model' 'Derived calculations' 3 2 'Structure model' 'Structure summary' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 3 'Structure model' 'Refinement description' # 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 2 'Structure model' entity 4 2 'Structure model' pdbx_struct_conn_angle 5 2 'Structure model' struct_conn 6 3 'Structure model' chem_comp_atom 7 3 'Structure model' chem_comp_bond 8 3 'Structure model' database_2 9 3 'Structure model' pdbx_initial_refinement_model # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.journal_volume' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 'Structure model' '_citation.title' 9 2 'Structure model' '_citation.year' 10 2 'Structure model' '_entity.formula_weight' 11 2 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 12 2 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 2 'Structure model' '_pdbx_struct_conn_angle.value' 14 2 'Structure model' '_struct_conn.pdbx_dist_value' 15 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 3 'Structure model' '_database_2.pdbx_DOI' 17 3 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5NFM _pdbx_database_status.recvd_initial_deposition_date 2017-03-14 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Roret, T.' 1 0000-0003-2528-5789 'Didierjean, C.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Biosci.Rep. _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 0144-8463 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 40 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Sinorhizobium meliloti YrbA binds divalent metal cations using two conserved histidines.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1042/BSR20202956 _citation.pdbx_database_id_PubMed 32970113 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Roret, T.' 1 ? primary 'Alloing, G.' 2 ? primary 'Girardet, J.M.' 3 ? primary 'Perrot, T.' 4 ? primary 'Dhalleine, T.' 5 ? primary 'Couturier, J.' 6 ? primary 'Frendo, P.' 7 ? primary 'Didierjean, C.' 8 ? primary 'Rouhier, N.' 9 ? # 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 YrbA 7955.053 1 ? ? ? ? 2 non-polymer syn 'LITHIUM ION' 6.941 1 ? ? ? ? 3 non-polymer syn 'COPPER (II) ION' 63.546 1 ? ? ? ? 4 water nat water 18.015 150 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code MAPGDIEDMIKAGIPGARVTIRDLAGDGDHYAAEVVAEAFRGKTRVQQHQMVYNALKGNMGGILHALALQTSAPE _entity_poly.pdbx_seq_one_letter_code_can MAPGDIEDMIKAGIPGARVTIRDLAGDGDHYAAEVVAEAFRGKTRVQQHQMVYNALKGNMGGILHALALQTSAPE _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'LITHIUM ION' LI 3 'COPPER (II) ION' CU 4 water HOH # 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 ALA n 1 3 PRO n 1 4 GLY n 1 5 ASP n 1 6 ILE n 1 7 GLU n 1 8 ASP n 1 9 MET n 1 10 ILE n 1 11 LYS n 1 12 ALA n 1 13 GLY n 1 14 ILE n 1 15 PRO n 1 16 GLY n 1 17 ALA n 1 18 ARG n 1 19 VAL n 1 20 THR n 1 21 ILE n 1 22 ARG n 1 23 ASP n 1 24 LEU n 1 25 ALA n 1 26 GLY n 1 27 ASP n 1 28 GLY n 1 29 ASP n 1 30 HIS n 1 31 TYR n 1 32 ALA n 1 33 ALA n 1 34 GLU n 1 35 VAL n 1 36 VAL n 1 37 ALA n 1 38 GLU n 1 39 ALA n 1 40 PHE n 1 41 ARG n 1 42 GLY n 1 43 LYS n 1 44 THR n 1 45 ARG n 1 46 VAL n 1 47 GLN n 1 48 GLN n 1 49 HIS n 1 50 GLN n 1 51 MET n 1 52 VAL n 1 53 TYR n 1 54 ASN n 1 55 ALA n 1 56 LEU n 1 57 LYS n 1 58 GLY n 1 59 ASN n 1 60 MET n 1 61 GLY n 1 62 GLY n 1 63 ILE n 1 64 LEU n 1 65 HIS n 1 66 ALA n 1 67 LEU n 1 68 ALA n 1 69 LEU n 1 70 GLN n 1 71 THR n 1 72 SER n 1 73 ALA n 1 74 PRO n 1 75 GLU 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 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 75 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene SM2011_c00487 _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 'Sinorhizobium meliloti 2011' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1286640 _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_ _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 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 CU non-polymer . 'COPPER (II) ION' ? 'Cu 2' 63.546 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 LI non-polymer . 'LITHIUM ION' ? 'Li 1' 6.941 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 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 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # 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 3 3 MET MET A . n A 1 2 ALA 2 4 4 ALA ALA A . n A 1 3 PRO 3 5 5 PRO PRO A . n A 1 4 GLY 4 6 6 GLY GLY A . n A 1 5 ASP 5 7 7 ASP ASP A . n A 1 6 ILE 6 8 8 ILE ILE A . n A 1 7 GLU 7 9 9 GLU GLU A . n A 1 8 ASP 8 10 10 ASP ASP A . n A 1 9 MET 9 11 11 MET MET A . n A 1 10 ILE 10 12 12 ILE ILE A . n A 1 11 LYS 11 13 13 LYS LYS A . n A 1 12 ALA 12 14 14 ALA ALA A . n A 1 13 GLY 13 15 15 GLY GLY A . n A 1 14 ILE 14 16 16 ILE ILE A . n A 1 15 PRO 15 17 17 PRO PRO A . n A 1 16 GLY 16 18 18 GLY GLY A . n A 1 17 ALA 17 19 19 ALA ALA A . n A 1 18 ARG 18 20 20 ARG ARG A . n A 1 19 VAL 19 21 21 VAL VAL A . n A 1 20 THR 20 22 22 THR THR A . n A 1 21 ILE 21 23 23 ILE ILE A . n A 1 22 ARG 22 24 24 ARG ARG A . n A 1 23 ASP 23 25 25 ASP ASP A . n A 1 24 LEU 24 26 26 LEU LEU A . n A 1 25 ALA 25 27 27 ALA ALA A . n A 1 26 GLY 26 28 28 GLY GLY A . n A 1 27 ASP 27 29 29 ASP ASP A . n A 1 28 GLY 28 30 30 GLY GLY A . n A 1 29 ASP 29 31 31 ASP ASP A . n A 1 30 HIS 30 32 32 HIS HIS A . n A 1 31 TYR 31 33 33 TYR TYR A . n A 1 32 ALA 32 34 34 ALA ALA A . n A 1 33 ALA 33 35 35 ALA ALA A . n A 1 34 GLU 34 36 36 GLU GLU A . n A 1 35 VAL 35 37 37 VAL VAL A . n A 1 36 VAL 36 38 38 VAL VAL A . n A 1 37 ALA 37 39 39 ALA ALA A . n A 1 38 GLU 38 40 40 GLU GLU A . n A 1 39 ALA 39 41 41 ALA ALA A . n A 1 40 PHE 40 42 42 PHE PHE A . n A 1 41 ARG 41 43 43 ARG ARG A . n A 1 42 GLY 42 44 44 GLY GLY A . n A 1 43 LYS 43 45 45 LYS LYS A . n A 1 44 THR 44 46 46 THR THR A . n A 1 45 ARG 45 47 47 ARG ARG A . n A 1 46 VAL 46 48 48 VAL VAL A . n A 1 47 GLN 47 49 49 GLN GLN A . n A 1 48 GLN 48 50 50 GLN GLN A . n A 1 49 HIS 49 51 51 HIS HIS A . n A 1 50 GLN 50 52 52 GLN GLN A . n A 1 51 MET 51 53 53 MET MET A . n A 1 52 VAL 52 54 54 VAL VAL A . n A 1 53 TYR 53 55 55 TYR TYR A . n A 1 54 ASN 54 56 56 ASN ASN A . n A 1 55 ALA 55 57 57 ALA ALA A . n A 1 56 LEU 56 58 58 LEU LEU A . n A 1 57 LYS 57 59 59 LYS LYS A . n A 1 58 GLY 58 60 60 GLY GLY A . n A 1 59 ASN 59 61 61 ASN ASN A . n A 1 60 MET 60 62 62 MET MET A . n A 1 61 GLY 61 63 63 GLY GLY A . n A 1 62 GLY 62 64 64 GLY GLY A . n A 1 63 ILE 63 65 65 ILE ILE A . n A 1 64 LEU 64 66 66 LEU LEU A . n A 1 65 HIS 65 67 67 HIS HIS A . n A 1 66 ALA 66 68 68 ALA ALA A . n A 1 67 LEU 67 69 69 LEU LEU A . n A 1 68 ALA 68 70 70 ALA ALA A . n A 1 69 LEU 69 71 71 LEU LEU A . n A 1 70 GLN 70 72 72 GLN GLN A . n A 1 71 THR 71 73 73 THR THR A . n A 1 72 SER 72 74 74 SER SER A . n A 1 73 ALA 73 75 75 ALA ALA A . n A 1 74 PRO 74 76 76 PRO PRO A . n A 1 75 GLU 75 77 77 GLU GLU A . 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 B 2 LI 1 101 80 LI LI A . C 3 CU 1 102 81 CU CU A . D 4 HOH 1 201 108 HOH HOH A . D 4 HOH 2 202 57 HOH HOH A . D 4 HOH 3 203 128 HOH HOH A . D 4 HOH 4 204 105 HOH HOH A . D 4 HOH 5 205 136 HOH HOH A . D 4 HOH 6 206 64 HOH HOH A . D 4 HOH 7 207 160 HOH HOH A . D 4 HOH 8 208 45 HOH HOH A . D 4 HOH 9 209 69 HOH HOH A . D 4 HOH 10 210 129 HOH HOH A . D 4 HOH 11 211 84 HOH HOH A . D 4 HOH 12 212 4 HOH HOH A . D 4 HOH 13 213 9 HOH HOH A . D 4 HOH 14 214 53 HOH HOH A . D 4 HOH 15 215 7 HOH HOH A . D 4 HOH 16 216 96 HOH HOH A . D 4 HOH 17 217 6 HOH HOH A . D 4 HOH 18 218 54 HOH HOH A . D 4 HOH 19 219 101 HOH HOH A . D 4 HOH 20 220 140 HOH HOH A . D 4 HOH 21 221 102 HOH HOH A . D 4 HOH 22 222 48 HOH HOH A . D 4 HOH 23 223 50 HOH HOH A . D 4 HOH 24 224 3 HOH HOH A . D 4 HOH 25 225 103 HOH HOH A . D 4 HOH 26 226 27 HOH HOH A . D 4 HOH 27 227 18 HOH HOH A . D 4 HOH 28 228 55 HOH HOH A . D 4 HOH 29 229 10 HOH HOH A . D 4 HOH 30 230 135 HOH HOH A . D 4 HOH 31 231 74 HOH HOH A . D 4 HOH 32 232 11 HOH HOH A . D 4 HOH 33 233 148 HOH HOH A . D 4 HOH 34 234 110 HOH HOH A . D 4 HOH 35 235 39 HOH HOH A . D 4 HOH 36 236 72 HOH HOH A . D 4 HOH 37 237 32 HOH HOH A . D 4 HOH 38 238 23 HOH HOH A . D 4 HOH 39 239 90 HOH HOH A . D 4 HOH 40 240 79 HOH HOH A . D 4 HOH 41 241 37 HOH HOH A . D 4 HOH 42 242 36 HOH HOH A . D 4 HOH 43 243 70 HOH HOH A . D 4 HOH 44 244 146 HOH HOH A . D 4 HOH 45 245 20 HOH HOH A . D 4 HOH 46 246 156 HOH HOH A . D 4 HOH 47 247 51 HOH HOH A . D 4 HOH 48 248 8 HOH HOH A . D 4 HOH 49 249 29 HOH HOH A . D 4 HOH 50 250 14 HOH HOH A . D 4 HOH 51 251 56 HOH HOH A . D 4 HOH 52 252 66 HOH HOH A . D 4 HOH 53 253 5 HOH HOH A . D 4 HOH 54 254 81 HOH HOH A . D 4 HOH 55 255 47 HOH HOH A . D 4 HOH 56 256 91 HOH HOH A . D 4 HOH 57 257 33 HOH HOH A . D 4 HOH 58 258 52 HOH HOH A . D 4 HOH 59 259 17 HOH HOH A . D 4 HOH 60 260 41 HOH HOH A . D 4 HOH 61 261 42 HOH HOH A . D 4 HOH 62 262 2 HOH HOH A . D 4 HOH 63 263 15 HOH HOH A . D 4 HOH 64 264 49 HOH HOH A . D 4 HOH 65 265 22 HOH HOH A . D 4 HOH 66 266 62 HOH HOH A . D 4 HOH 67 267 38 HOH HOH A . D 4 HOH 68 268 77 HOH HOH A . D 4 HOH 69 269 126 HOH HOH A . D 4 HOH 70 270 68 HOH HOH A . D 4 HOH 71 271 80 HOH HOH A . D 4 HOH 72 272 43 HOH HOH A . D 4 HOH 73 273 67 HOH HOH A . D 4 HOH 74 274 89 HOH HOH A . D 4 HOH 75 275 71 HOH HOH A . D 4 HOH 76 276 60 HOH HOH A . D 4 HOH 77 277 24 HOH HOH A . D 4 HOH 78 278 21 HOH HOH A . D 4 HOH 79 279 28 HOH HOH A . D 4 HOH 80 280 112 HOH HOH A . D 4 HOH 81 281 76 HOH HOH A . D 4 HOH 82 282 30 HOH HOH A . D 4 HOH 83 283 75 HOH HOH A . D 4 HOH 84 284 44 HOH HOH A . D 4 HOH 85 285 147 HOH HOH A . D 4 HOH 86 286 65 HOH HOH A . D 4 HOH 87 287 31 HOH HOH A . D 4 HOH 88 288 107 HOH HOH A . D 4 HOH 89 289 143 HOH HOH A . D 4 HOH 90 290 88 HOH HOH A . D 4 HOH 91 291 19 HOH HOH A . D 4 HOH 92 292 144 HOH HOH A . D 4 HOH 93 293 111 HOH HOH A . D 4 HOH 94 294 93 HOH HOH A . D 4 HOH 95 295 85 HOH HOH A . D 4 HOH 96 296 141 HOH HOH A . D 4 HOH 97 297 98 HOH HOH A . D 4 HOH 98 298 114 HOH HOH A . D 4 HOH 99 299 92 HOH HOH A . D 4 HOH 100 300 104 HOH HOH A . D 4 HOH 101 301 159 HOH HOH A . D 4 HOH 102 302 16 HOH HOH A . D 4 HOH 103 303 151 HOH HOH A . D 4 HOH 104 304 116 HOH HOH A . D 4 HOH 105 305 97 HOH HOH A . D 4 HOH 106 306 125 HOH HOH A . D 4 HOH 107 307 1 HOH HOH A . D 4 HOH 108 308 113 HOH HOH A . D 4 HOH 109 309 127 HOH HOH A . D 4 HOH 110 310 123 HOH HOH A . D 4 HOH 111 311 87 HOH HOH A . D 4 HOH 112 312 118 HOH HOH A . D 4 HOH 113 313 115 HOH HOH A . D 4 HOH 114 314 149 HOH HOH A . D 4 HOH 115 315 13 HOH HOH A . D 4 HOH 116 316 155 HOH HOH A . D 4 HOH 117 317 142 HOH HOH A . D 4 HOH 118 318 78 HOH HOH A . D 4 HOH 119 319 133 HOH HOH A . D 4 HOH 120 320 83 HOH HOH A . D 4 HOH 121 321 139 HOH HOH A . D 4 HOH 122 322 100 HOH HOH A . D 4 HOH 123 323 94 HOH HOH A . D 4 HOH 124 324 124 HOH HOH A . D 4 HOH 125 325 59 HOH HOH A . D 4 HOH 126 326 157 HOH HOH A . D 4 HOH 127 327 61 HOH HOH A . D 4 HOH 128 328 82 HOH HOH A . D 4 HOH 129 329 26 HOH HOH A . D 4 HOH 130 330 46 HOH HOH A . D 4 HOH 131 331 154 HOH HOH A . D 4 HOH 132 332 119 HOH HOH A . D 4 HOH 133 333 12 HOH HOH A . D 4 HOH 134 334 122 HOH HOH A . D 4 HOH 135 335 106 HOH HOH A . D 4 HOH 136 336 40 HOH HOH A . D 4 HOH 137 337 58 HOH HOH A . D 4 HOH 138 338 158 HOH HOH A . D 4 HOH 139 339 73 HOH HOH A . D 4 HOH 140 340 34 HOH HOH A . D 4 HOH 141 341 109 HOH HOH A . D 4 HOH 142 342 131 HOH HOH A . D 4 HOH 143 343 138 HOH HOH A . D 4 HOH 144 344 95 HOH HOH A . D 4 HOH 145 345 99 HOH HOH A . D 4 HOH 146 346 63 HOH HOH A . D 4 HOH 147 347 25 HOH HOH A . D 4 HOH 148 348 145 HOH HOH A . D 4 HOH 149 349 153 HOH HOH A . D 4 HOH 150 350 121 HOH HOH A . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.11.1_2575: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALA ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? MOLREP ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 5NFM _cell.details ? _cell.formula_units_Z ? _cell.length_a 30.752 _cell.length_a_esd ? _cell.length_b 32.159 _cell.length_b_esd ? _cell.length_c 62.575 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NFM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5NFM _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.94 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 36.75 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method MICROBATCH _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;0.7 M lithium sulfate 0.02 M copper acetate 0.1 M Tris-HCl, pH 8.5 ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-11-15 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.722307 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'ESRF BEAMLINE BM30A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.722307 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BM30A _diffrn_source.pdbx_synchrotron_site ESRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5NFM _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 0.80 _reflns.d_resolution_low 32.16 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all 465091 _reflns.number_obs 66196 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 7.0 _reflns.pdbx_Rmerge_I_obs 0.084 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 15.0 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.091 _reflns.pdbx_Rpim_I_all 0.034 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 0.80 _reflns_shell.d_res_low 0.81 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 2.4 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs 21702 _reflns_shell.number_possible ? _reflns_shell.number_unique_all 3201 _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 99.0 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.856 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 6.8 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 0.927 _reflns_shell.pdbx_Rpim_I_all 0.352 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.727 _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5NFM _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 0.800 _refine.ls_d_res_low 22.425 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 66112 _refine.ls_number_reflns_R_free 3301 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.90 _refine.ls_percent_reflns_R_free 4.99 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1222 _refine.ls_R_factor_R_free 0.1320 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1217 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 5NFK _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 11.44 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.05 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 556 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 150 _refine_hist.number_atoms_total 708 _refine_hist.d_res_high 0.800 _refine_hist.d_res_low 22.425 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.032 ? 594 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.898 ? 790 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 16.425 ? 220 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.083 ? 86 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.005 ? 108 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 0.8004 0.8118 . . 147 2530 99.00 . . . 0.2497 . 0.2163 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.8118 0.8239 . . 105 2636 100.00 . . . 0.2036 . 0.1968 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.8239 0.8368 . . 134 2592 100.00 . . . 0.2317 . 0.1892 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.8368 0.8505 . . 142 2565 100.00 . . . 0.1939 . 0.1881 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.8505 0.8652 . . 145 2577 100.00 . . . 0.1848 . 0.1703 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.8652 0.8809 . . 140 2593 100.00 . . . 0.1722 . 0.1556 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.8809 0.8979 . . 142 2567 100.00 . . . 0.1505 . 0.1502 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.8979 0.9162 . . 154 2589 100.00 . . . 0.1815 . 0.1522 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.9162 0.9361 . . 142 2590 100.00 . . . 0.1621 . 0.1326 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.9361 0.9579 . . 130 2587 100.00 . . . 0.1539 . 0.1190 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.9579 0.9819 . . 143 2581 100.00 . . . 0.1514 . 0.1216 . . . . . . . . . . 'X-RAY DIFFRACTION' 0.9819 1.0084 . . 131 2635 100.00 . . . 0.1164 . 0.1150 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.0084 1.0381 . . 136 2610 100.00 . . . 0.1194 . 0.1113 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.0381 1.0716 . . 116 2585 100.00 . . . 0.0965 . 0.1011 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.0716 1.1099 . . 116 2661 100.00 . . . 0.0910 . 0.0977 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.1099 1.1543 . . 143 2590 100.00 . . . 0.1236 . 0.0923 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.1543 1.2069 . . 121 2629 100.00 . . . 0.1192 . 0.0981 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.2069 1.2705 . . 183 2585 100.00 . . . 0.1056 . 0.1024 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.2705 1.3501 . . 134 2644 100.00 . . . 0.1142 . 0.1009 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.3501 1.4543 . . 152 2615 100.00 . . . 0.1155 . 0.1101 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.4543 1.6006 . . 146 2652 100.00 . . . 0.1137 . 0.1138 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.6006 1.8321 . . 160 2650 100.00 . . . 0.1294 . 0.1194 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.8321 2.3079 . . 128 2715 100.00 . . . 0.1038 . 0.1108 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.3079 22.4342 . . 111 2833 99.00 . . . 0.1383 . 0.1254 . . . . . . . . . . # _struct.entry_id 5NFM _struct.title 'Crystal structure of YrbA from Sinorhizobium meliloti in complex with copper.' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 5NFM _struct_keywords.text 'BolA, YrbA, histidyl ligation, ligase' _struct_keywords.pdbx_keywords LIGASE # 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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code M4MWA0_SINM2 _struct_ref.pdbx_db_accession M4MWA0 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code MAPGDIEDMIKAGIPGARVTIRDLAGDGDHYAAEVVAEAFRGKTRVQQHQMVYNALKGNMGGILHALALQTSAPE _struct_ref.pdbx_align_begin 3 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5NFM _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 75 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession M4MWA0 _struct_ref_seq.db_align_beg 3 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 77 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 3 _struct_ref_seq.pdbx_auth_seq_align_end 77 # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # 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)' 120 ? 1 MORE -9 ? 1 'SSA (A^2)' 4650 ? # _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 # loop_ _pdbx_struct_assembly_auth_evidence.id _pdbx_struct_assembly_auth_evidence.assembly_id _pdbx_struct_assembly_auth_evidence.experimental_support _pdbx_struct_assembly_auth_evidence.details 1 1 'mass spectrometry' Monomeric 2 1 'gel filtration' Monomeric # _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_ _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 AA1 GLY A 4 ? ILE A 14 ? GLY A 6 ILE A 16 1 ? 11 HELX_P HELX_P2 AA2 ALA A 25 ? ASP A 27 ? ALA A 27 ASP A 29 5 ? 3 HELX_P HELX_P3 AA3 GLU A 38 ? ARG A 41 ? GLU A 40 ARG A 43 5 ? 4 HELX_P HELX_P4 AA4 THR A 44 ? LYS A 57 ? THR A 46 LYS A 59 1 ? 14 HELX_P HELX_P5 AA5 GLY A 62 ? ALA A 66 ? GLY A 64 ALA A 68 1 ? 5 # _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 _struct_conn.pdbx_role metalc1 metalc ? ? A ASP 23 OD1 ? ? ? 1_555 B LI . LI ? ? A ASP 25 A LI 101 1_555 ? ? ? ? ? ? ? 1.819 ? ? metalc2 metalc ? ? A LEU 24 O ? ? ? 1_555 B LI . LI ? ? A LEU 26 A LI 101 1_555 ? ? ? ? ? ? ? 1.935 ? ? metalc3 metalc ? ? A ASP 27 OD1 ? ? ? 1_555 B LI . LI ? ? A ASP 29 A LI 101 1_555 ? ? ? ? ? ? ? 1.907 ? ? metalc4 metalc ? ? A HIS 30 O ? ? ? 1_555 B LI . LI ? ? A HIS 32 A LI 101 1_555 ? ? ? ? ? ? ? 1.930 ? ? metalc5 metalc ? ? A HIS 30 NE2 ? ? ? 1_555 C CU . CU ? ? A HIS 32 A CU 102 1_555 ? ? ? ? ? ? ? 2.004 ? ? metalc6 metalc ? ? A HIS 65 NE2 ? ? ? 1_555 C CU . CU ? ? A HIS 67 A CU 102 1_555 ? ? ? ? ? ? ? 2.022 ? ? metalc7 metalc ? ? C CU . CU ? ? ? 1_555 D HOH . O ? ? A CU 102 A HOH 204 1_555 ? ? ? ? ? ? ? 2.021 ? ? metalc8 metalc ? ? C CU . CU ? ? ? 1_555 D HOH . O ? ? A CU 102 A HOH 210 1_555 ? ? ? ? ? ? ? 2.413 ? ? metalc9 metalc ? ? C CU . CU ? ? ? 1_555 D HOH . O ? ? A CU 102 A HOH 289 1_555 ? ? ? ? ? ? ? 2.024 ? ? metalc10 metalc ? ? C CU . CU ? ? ? 1_555 D HOH . O ? ? A CU 102 A HOH 295 1_555 ? ? ? ? ? ? ? 2.432 ? ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 OD1 ? A ASP 23 ? A ASP 25 ? 1_555 LI ? B LI . ? A LI 101 ? 1_555 O ? A LEU 24 ? A LEU 26 ? 1_555 104.1 ? 2 OD1 ? A ASP 23 ? A ASP 25 ? 1_555 LI ? B LI . ? A LI 101 ? 1_555 OD1 ? A ASP 27 ? A ASP 29 ? 1_555 110.1 ? 3 O ? A LEU 24 ? A LEU 26 ? 1_555 LI ? B LI . ? A LI 101 ? 1_555 OD1 ? A ASP 27 ? A ASP 29 ? 1_555 96.1 ? 4 OD1 ? A ASP 23 ? A ASP 25 ? 1_555 LI ? B LI . ? A LI 101 ? 1_555 O ? A HIS 30 ? A HIS 32 ? 1_555 104.8 ? 5 O ? A LEU 24 ? A LEU 26 ? 1_555 LI ? B LI . ? A LI 101 ? 1_555 O ? A HIS 30 ? A HIS 32 ? 1_555 120.3 ? 6 OD1 ? A ASP 27 ? A ASP 29 ? 1_555 LI ? B LI . ? A LI 101 ? 1_555 O ? A HIS 30 ? A HIS 32 ? 1_555 120.3 ? 7 NE2 ? A HIS 30 ? A HIS 32 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 NE2 ? A HIS 65 ? A HIS 67 ? 1_555 94.4 ? 8 NE2 ? A HIS 30 ? A HIS 32 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 89.4 ? 9 NE2 ? A HIS 65 ? A HIS 67 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 173.5 ? 10 NE2 ? A HIS 30 ? A HIS 32 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 210 ? 1_555 96.4 ? 11 NE2 ? A HIS 65 ? A HIS 67 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 210 ? 1_555 103.9 ? 12 O ? D HOH . ? A HOH 204 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 210 ? 1_555 80.8 ? 13 NE2 ? A HIS 30 ? A HIS 32 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 289 ? 1_555 169.7 ? 14 NE2 ? A HIS 65 ? A HIS 67 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 289 ? 1_555 95.3 ? 15 O ? D HOH . ? A HOH 204 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 289 ? 1_555 81.2 ? 16 O ? D HOH . ? A HOH 210 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 289 ? 1_555 78.0 ? 17 NE2 ? A HIS 30 ? A HIS 32 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 94.9 ? 18 NE2 ? A HIS 65 ? A HIS 67 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 94.3 ? 19 O ? D HOH . ? A HOH 204 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 80.1 ? 20 O ? D HOH . ? A HOH 210 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 157.6 ? 21 O ? D HOH . ? A HOH 289 ? 1_555 CU ? C CU . ? A CU 102 ? 1_555 O ? D HOH . ? A HOH 295 ? 1_555 87.7 ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 3 _struct_sheet.details ? # 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 AA1 1 2 ? anti-parallel AA1 2 3 ? 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 AA1 1 ARG A 18 ? ASP A 23 ? ARG A 20 ASP A 25 AA1 2 TYR A 31 ? VAL A 36 ? TYR A 33 VAL A 38 AA1 3 LEU A 67 ? SER A 72 ? LEU A 69 SER A 74 # 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 AA1 1 2 N ARG A 18 ? N ARG A 20 O VAL A 36 ? O VAL A 38 AA1 2 3 N ALA A 33 ? N ALA A 35 O ALA A 68 ? O ALA A 70 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _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 _struct_site.details AC1 Software A LI 101 ? 4 'binding site for residue LI A 101' AC2 Software A CU 102 ? 6 'binding site for residue CU A 102' # 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 ASP A 23 ? ASP A 25 . ? 1_555 ? 2 AC1 4 LEU A 24 ? LEU A 26 . ? 1_555 ? 3 AC1 4 ASP A 27 ? ASP A 29 . ? 1_555 ? 4 AC1 4 HIS A 30 ? HIS A 32 . ? 1_555 ? 5 AC2 6 HIS A 30 ? HIS A 32 . ? 1_555 ? 6 AC2 6 HIS A 65 ? HIS A 67 . ? 1_555 ? 7 AC2 6 HOH D . ? HOH A 204 . ? 1_555 ? 8 AC2 6 HOH D . ? HOH A 210 . ? 1_555 ? 9 AC2 6 HOH D . ? HOH A 289 . ? 1_555 ? 10 AC2 6 HOH D . ? HOH A 295 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 246 ? ? O A HOH 319 ? ? 1.88 2 1 O A HOH 230 ? ? O A HOH 314 ? ? 1.89 3 1 O A HOH 314 ? ? O A HOH 332 ? ? 1.94 4 1 O A HOH 206 ? ? O A HOH 279 ? ? 2.02 5 1 O A HOH 321 ? ? O A HOH 324 ? ? 2.03 6 1 O A HOH 296 ? ? O A HOH 314 ? ? 2.08 7 1 O A HOH 271 ? ? O A HOH 317 ? ? 2.13 8 1 O A HOH 316 ? ? O A HOH 321 ? ? 2.13 9 1 O A HOH 327 ? ? O A HOH 344 ? ? 2.16 10 1 O A HOH 234 ? ? O A HOH 280 ? ? 2.17 11 1 O A HOH 288 ? ? O A HOH 308 ? ? 2.17 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 276 ? ? 1_555 O A HOH 293 ? ? 4_455 2.01 2 1 O A HOH 315 ? ? 1_555 O A HOH 317 ? ? 3_554 2.12 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ASP _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 31 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -131.35 _pdbx_validate_torsion.psi -62.32 # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 348 ? 6.20 . 2 1 O A A HOH 349 ? 6.77 . 3 1 O ? A HOH 350 ? 6.82 . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 CU CU CU N N 74 GLN N N N N 75 GLN CA C N S 76 GLN C C N N 77 GLN O O N N 78 GLN CB C N N 79 GLN CG C N N 80 GLN CD C N N 81 GLN OE1 O N N 82 GLN NE2 N N N 83 GLN OXT O N N 84 GLN H H N N 85 GLN H2 H N N 86 GLN HA H N N 87 GLN HB2 H N N 88 GLN HB3 H N N 89 GLN HG2 H N N 90 GLN HG3 H N N 91 GLN HE21 H N N 92 GLN HE22 H N N 93 GLN HXT H N N 94 GLU N N N N 95 GLU CA C N S 96 GLU C C N N 97 GLU O O N N 98 GLU CB C N N 99 GLU CG C N N 100 GLU CD C N N 101 GLU OE1 O N N 102 GLU OE2 O N N 103 GLU OXT O N N 104 GLU H H N N 105 GLU H2 H N N 106 GLU HA H N N 107 GLU HB2 H N N 108 GLU HB3 H N N 109 GLU HG2 H N N 110 GLU HG3 H N N 111 GLU HE2 H N N 112 GLU HXT H N N 113 GLY N N N N 114 GLY CA C N N 115 GLY C C N N 116 GLY O O N N 117 GLY OXT O N N 118 GLY H H N N 119 GLY H2 H N N 120 GLY HA2 H N N 121 GLY HA3 H N N 122 GLY HXT H N N 123 HIS N N N N 124 HIS CA C N S 125 HIS C C N N 126 HIS O O N N 127 HIS CB C N N 128 HIS CG C Y N 129 HIS ND1 N Y N 130 HIS CD2 C Y N 131 HIS CE1 C Y N 132 HIS NE2 N Y N 133 HIS OXT O N N 134 HIS H H N N 135 HIS H2 H N N 136 HIS HA H N N 137 HIS HB2 H N N 138 HIS HB3 H N N 139 HIS HD1 H N N 140 HIS HD2 H N N 141 HIS HE1 H N N 142 HIS HE2 H N N 143 HIS HXT H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 ILE N N N N 148 ILE CA C N S 149 ILE C C N N 150 ILE O O N N 151 ILE CB C N S 152 ILE CG1 C N N 153 ILE CG2 C N N 154 ILE CD1 C N N 155 ILE OXT O N N 156 ILE H H N N 157 ILE H2 H N N 158 ILE HA H N N 159 ILE HB H N N 160 ILE HG12 H N N 161 ILE HG13 H N N 162 ILE HG21 H N N 163 ILE HG22 H N N 164 ILE HG23 H N N 165 ILE HD11 H N N 166 ILE HD12 H N N 167 ILE HD13 H N N 168 ILE HXT H N N 169 LEU N N N N 170 LEU CA C N S 171 LEU C C N N 172 LEU O O N N 173 LEU CB C N N 174 LEU CG C N N 175 LEU CD1 C N N 176 LEU CD2 C N N 177 LEU OXT O N N 178 LEU H H N N 179 LEU H2 H N N 180 LEU HA H N N 181 LEU HB2 H N N 182 LEU HB3 H N N 183 LEU HG H N N 184 LEU HD11 H N N 185 LEU HD12 H N N 186 LEU HD13 H N N 187 LEU HD21 H N N 188 LEU HD22 H N N 189 LEU HD23 H N N 190 LEU HXT H N N 191 LI LI LI N N 192 LYS N N N N 193 LYS CA C N S 194 LYS C C N N 195 LYS O O N N 196 LYS CB C N N 197 LYS CG C N N 198 LYS CD C N N 199 LYS CE C N N 200 LYS NZ N N N 201 LYS OXT O N N 202 LYS H H N N 203 LYS H2 H N N 204 LYS HA H N N 205 LYS HB2 H N N 206 LYS HB3 H N N 207 LYS HG2 H N N 208 LYS HG3 H N N 209 LYS HD2 H N N 210 LYS HD3 H N N 211 LYS HE2 H N N 212 LYS HE3 H N N 213 LYS HZ1 H N N 214 LYS HZ2 H N N 215 LYS HZ3 H N N 216 LYS HXT H N N 217 MET N N N N 218 MET CA C N S 219 MET C C N N 220 MET O O N N 221 MET CB C N N 222 MET CG C N N 223 MET SD S N N 224 MET CE C N N 225 MET OXT O N N 226 MET H H N N 227 MET H2 H N N 228 MET HA H N N 229 MET HB2 H N N 230 MET HB3 H N N 231 MET HG2 H N N 232 MET HG3 H N N 233 MET HE1 H N N 234 MET HE2 H N N 235 MET HE3 H N N 236 MET HXT H N N 237 PHE N N N N 238 PHE CA C N S 239 PHE C C N N 240 PHE O O N N 241 PHE CB C N N 242 PHE CG C Y N 243 PHE CD1 C Y N 244 PHE CD2 C Y N 245 PHE CE1 C Y N 246 PHE CE2 C Y N 247 PHE CZ C Y N 248 PHE OXT O N N 249 PHE H H N N 250 PHE H2 H N N 251 PHE HA H N N 252 PHE HB2 H N N 253 PHE HB3 H N N 254 PHE HD1 H N N 255 PHE HD2 H N N 256 PHE HE1 H N N 257 PHE HE2 H N N 258 PHE HZ H N N 259 PHE HXT H N N 260 PRO N N N N 261 PRO CA C N S 262 PRO C C N N 263 PRO O O N N 264 PRO CB C N N 265 PRO CG C N N 266 PRO CD C N N 267 PRO OXT O N N 268 PRO H H N N 269 PRO HA H N N 270 PRO HB2 H N N 271 PRO HB3 H N N 272 PRO HG2 H N N 273 PRO HG3 H N N 274 PRO HD2 H N N 275 PRO HD3 H N N 276 PRO HXT H N N 277 SER N N N N 278 SER CA C N S 279 SER C C N N 280 SER O O N N 281 SER CB C N N 282 SER OG O N N 283 SER OXT O N N 284 SER H H N N 285 SER H2 H N N 286 SER HA H N N 287 SER HB2 H N N 288 SER HB3 H N N 289 SER HG H N N 290 SER HXT H N N 291 THR N N N N 292 THR CA C N S 293 THR C C N N 294 THR O O N N 295 THR CB C N R 296 THR OG1 O N N 297 THR CG2 C N N 298 THR OXT O N N 299 THR H H N N 300 THR H2 H N N 301 THR HA H N N 302 THR HB H N N 303 THR HG1 H N N 304 THR HG21 H N N 305 THR HG22 H N N 306 THR HG23 H N N 307 THR HXT H N N 308 TYR N N N N 309 TYR CA C N S 310 TYR C C N N 311 TYR O O N N 312 TYR CB C N N 313 TYR CG C Y N 314 TYR CD1 C Y N 315 TYR CD2 C Y N 316 TYR CE1 C Y N 317 TYR CE2 C Y N 318 TYR CZ C Y N 319 TYR OH O N N 320 TYR OXT O N N 321 TYR H H N N 322 TYR H2 H N N 323 TYR HA H N N 324 TYR HB2 H N N 325 TYR HB3 H N N 326 TYR HD1 H N N 327 TYR HD2 H N N 328 TYR HE1 H N N 329 TYR HE2 H N N 330 TYR HH H N N 331 TYR HXT H N N 332 VAL N N N N 333 VAL CA C N S 334 VAL C C N N 335 VAL O O N N 336 VAL CB C N N 337 VAL CG1 C N N 338 VAL CG2 C N N 339 VAL OXT O N N 340 VAL H H N N 341 VAL H2 H N N 342 VAL HA H N N 343 VAL HB H N N 344 VAL HG11 H N N 345 VAL HG12 H N N 346 VAL HG13 H N N 347 VAL HG21 H N N 348 VAL HG22 H N N 349 VAL HG23 H N N 350 VAL HXT H N N 351 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 GLN N CA sing N N 70 GLN N H sing N N 71 GLN N H2 sing N N 72 GLN CA C sing N N 73 GLN CA CB sing N N 74 GLN CA HA sing N N 75 GLN C O doub N N 76 GLN C OXT sing N N 77 GLN CB CG sing N N 78 GLN CB HB2 sing N N 79 GLN CB HB3 sing N N 80 GLN CG CD sing N N 81 GLN CG HG2 sing N N 82 GLN CG HG3 sing N N 83 GLN CD OE1 doub N N 84 GLN CD NE2 sing N N 85 GLN NE2 HE21 sing N N 86 GLN NE2 HE22 sing N N 87 GLN OXT HXT sing N N 88 GLU N CA sing N N 89 GLU N H sing N N 90 GLU N H2 sing N N 91 GLU CA C sing N N 92 GLU CA CB sing N N 93 GLU CA HA sing N N 94 GLU C O doub N N 95 GLU C OXT sing N N 96 GLU CB CG sing N N 97 GLU CB HB2 sing N N 98 GLU CB HB3 sing N N 99 GLU CG CD sing N N 100 GLU CG HG2 sing N N 101 GLU CG HG3 sing N N 102 GLU CD OE1 doub N N 103 GLU CD OE2 sing N N 104 GLU OE2 HE2 sing N N 105 GLU OXT HXT sing N N 106 GLY N CA sing N N 107 GLY N H sing N N 108 GLY N H2 sing N N 109 GLY CA C sing N N 110 GLY CA HA2 sing N N 111 GLY CA HA3 sing N N 112 GLY C O doub N N 113 GLY C OXT sing N N 114 GLY OXT HXT sing N N 115 HIS N CA sing N N 116 HIS N H sing N N 117 HIS N H2 sing N N 118 HIS CA C sing N N 119 HIS CA CB sing N N 120 HIS CA HA sing N N 121 HIS C O doub N N 122 HIS C OXT sing N N 123 HIS CB CG sing N N 124 HIS CB HB2 sing N N 125 HIS CB HB3 sing N N 126 HIS CG ND1 sing Y N 127 HIS CG CD2 doub Y N 128 HIS ND1 CE1 doub Y N 129 HIS ND1 HD1 sing N N 130 HIS CD2 NE2 sing Y N 131 HIS CD2 HD2 sing N N 132 HIS CE1 NE2 sing Y N 133 HIS CE1 HE1 sing N N 134 HIS NE2 HE2 sing N N 135 HIS OXT HXT sing N N 136 HOH O H1 sing N N 137 HOH O H2 sing N N 138 ILE N CA sing N N 139 ILE N H sing N N 140 ILE N H2 sing N N 141 ILE CA C sing N N 142 ILE CA CB sing N N 143 ILE CA HA sing N N 144 ILE C O doub N N 145 ILE C OXT sing N N 146 ILE CB CG1 sing N N 147 ILE CB CG2 sing N N 148 ILE CB HB sing N N 149 ILE CG1 CD1 sing N N 150 ILE CG1 HG12 sing N N 151 ILE CG1 HG13 sing N N 152 ILE CG2 HG21 sing N N 153 ILE CG2 HG22 sing N N 154 ILE CG2 HG23 sing N N 155 ILE CD1 HD11 sing N N 156 ILE CD1 HD12 sing N N 157 ILE CD1 HD13 sing N N 158 ILE OXT HXT sing N N 159 LEU N CA sing N N 160 LEU N H sing N N 161 LEU N H2 sing N N 162 LEU CA C sing N N 163 LEU CA CB sing N N 164 LEU CA HA sing N N 165 LEU C O doub N N 166 LEU C OXT sing N N 167 LEU CB CG sing N N 168 LEU CB HB2 sing N N 169 LEU CB HB3 sing N N 170 LEU CG CD1 sing N N 171 LEU CG CD2 sing N N 172 LEU CG HG sing N N 173 LEU CD1 HD11 sing N N 174 LEU CD1 HD12 sing N N 175 LEU CD1 HD13 sing N N 176 LEU CD2 HD21 sing N N 177 LEU CD2 HD22 sing N N 178 LEU CD2 HD23 sing N N 179 LEU OXT HXT sing N N 180 LYS N CA sing N N 181 LYS N H sing N N 182 LYS N H2 sing N N 183 LYS CA C sing N N 184 LYS CA CB sing N N 185 LYS CA HA sing N N 186 LYS C O doub N N 187 LYS C OXT sing N N 188 LYS CB CG sing N N 189 LYS CB HB2 sing N N 190 LYS CB HB3 sing N N 191 LYS CG CD sing N N 192 LYS CG HG2 sing N N 193 LYS CG HG3 sing N N 194 LYS CD CE sing N N 195 LYS CD HD2 sing N N 196 LYS CD HD3 sing N N 197 LYS CE NZ sing N N 198 LYS CE HE2 sing N N 199 LYS CE HE3 sing N N 200 LYS NZ HZ1 sing N N 201 LYS NZ HZ2 sing N N 202 LYS NZ HZ3 sing N N 203 LYS OXT HXT sing N N 204 MET N CA sing N N 205 MET N H sing N N 206 MET N H2 sing N N 207 MET CA C sing N N 208 MET CA CB sing N N 209 MET CA HA sing N N 210 MET C O doub N N 211 MET C OXT sing N N 212 MET CB CG sing N N 213 MET CB HB2 sing N N 214 MET CB HB3 sing N N 215 MET CG SD sing N N 216 MET CG HG2 sing N N 217 MET CG HG3 sing N N 218 MET SD CE sing N N 219 MET CE HE1 sing N N 220 MET CE HE2 sing N N 221 MET CE HE3 sing N N 222 MET OXT HXT sing N N 223 PHE N CA sing N N 224 PHE N H sing N N 225 PHE N H2 sing N N 226 PHE CA C sing N N 227 PHE CA CB sing N N 228 PHE CA HA sing N N 229 PHE C O doub N N 230 PHE C OXT sing N N 231 PHE CB CG sing N N 232 PHE CB HB2 sing N N 233 PHE CB HB3 sing N N 234 PHE CG CD1 doub Y N 235 PHE CG CD2 sing Y N 236 PHE CD1 CE1 sing Y N 237 PHE CD1 HD1 sing N N 238 PHE CD2 CE2 doub Y N 239 PHE CD2 HD2 sing N N 240 PHE CE1 CZ doub Y N 241 PHE CE1 HE1 sing N N 242 PHE CE2 CZ sing Y N 243 PHE CE2 HE2 sing N N 244 PHE CZ HZ sing N N 245 PHE OXT HXT sing N N 246 PRO N CA sing N N 247 PRO N CD sing N N 248 PRO N H sing N N 249 PRO CA C sing N N 250 PRO CA CB sing N N 251 PRO CA HA sing N N 252 PRO C O doub N N 253 PRO C OXT sing N N 254 PRO CB CG sing N N 255 PRO CB HB2 sing N N 256 PRO CB HB3 sing N N 257 PRO CG CD sing N N 258 PRO CG HG2 sing N N 259 PRO CG HG3 sing N N 260 PRO CD HD2 sing N N 261 PRO CD HD3 sing N N 262 PRO OXT HXT sing N N 263 SER N CA sing N N 264 SER N H sing N N 265 SER N H2 sing N N 266 SER CA C sing N N 267 SER CA CB sing N N 268 SER CA HA sing N N 269 SER C O doub N N 270 SER C OXT sing N N 271 SER CB OG sing N N 272 SER CB HB2 sing N N 273 SER CB HB3 sing N N 274 SER OG HG sing N N 275 SER OXT HXT sing N N 276 THR N CA sing N N 277 THR N H sing N N 278 THR N H2 sing N N 279 THR CA C sing N N 280 THR CA CB sing N N 281 THR CA HA sing N N 282 THR C O doub N N 283 THR C OXT sing N N 284 THR CB OG1 sing N N 285 THR CB CG2 sing N N 286 THR CB HB sing N N 287 THR OG1 HG1 sing N N 288 THR CG2 HG21 sing N N 289 THR CG2 HG22 sing N N 290 THR CG2 HG23 sing N N 291 THR OXT HXT sing N N 292 TYR N CA sing N N 293 TYR N H sing N N 294 TYR N H2 sing N N 295 TYR CA C sing N N 296 TYR CA CB sing N N 297 TYR CA HA sing N N 298 TYR C O doub N N 299 TYR C OXT sing N N 300 TYR CB CG sing N N 301 TYR CB HB2 sing N N 302 TYR CB HB3 sing N N 303 TYR CG CD1 doub Y N 304 TYR CG CD2 sing Y N 305 TYR CD1 CE1 sing Y N 306 TYR CD1 HD1 sing N N 307 TYR CD2 CE2 doub Y N 308 TYR CD2 HD2 sing N N 309 TYR CE1 CZ doub Y N 310 TYR CE1 HE1 sing N N 311 TYR CE2 CZ sing Y N 312 TYR CE2 HE2 sing N N 313 TYR CZ OH sing N N 314 TYR OH HH sing N N 315 TYR OXT HXT sing N N 316 VAL N CA sing N N 317 VAL N H sing N N 318 VAL N H2 sing N N 319 VAL CA C sing N N 320 VAL CA CB sing N N 321 VAL CA HA sing N N 322 VAL C O doub N N 323 VAL C OXT sing N N 324 VAL CB CG1 sing N N 325 VAL CB CG2 sing N N 326 VAL CB HB sing N N 327 VAL CG1 HG11 sing N N 328 VAL CG1 HG12 sing N N 329 VAL CG1 HG13 sing N N 330 VAL CG2 HG21 sing N N 331 VAL CG2 HG22 sing N N 332 VAL CG2 HG23 sing N N 333 VAL OXT HXT sing N N 334 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 5NFK _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 5NFM _atom_sites.fract_transf_matrix[1][1] 0.032518 _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] 0.031095 _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] 0.015981 _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 CU H LI N O S # loop_