data_4D81 # _entry.id 4D81 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4D81 PDBE EBI-62456 WWPDB D_1290062456 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4D82 _pdbx_database_related.content_type unspecified _pdbx_database_related.details 'METALLOSPHERA SEDULA VPS4 CRYSTAL STRUCTURE' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4D81 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2014-12-02 _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 'Caillat, C.' 1 'Macheboeuf, P.' 2 'Wu, Y.' 3 'McCarthy, A.A.' 4 'Boeri-Erba, E.' 5 'Effantin, G.' 6 'Gottlinger, H.G.' 7 'Weissenhorn, W.' 8 'Renesto, P.' 9 # _citation.id primary _citation.title 'Asymmetric Ring Structure of Vps4 Required for Escrt-III Disassembly.' _citation.journal_abbrev Nat.Commun. _citation.journal_volume 6 _citation.page_first 8781 _citation.page_last ? _citation.year 2015 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 2041-1723 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 26632262 _citation.pdbx_database_id_DOI 10.1038/NCOMMS9781 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Caillat, C.' 1 primary 'Macheboeuf, P.' 2 primary 'Wu, Y.' 3 primary 'Mccarthy, A.A.' 4 primary 'Boeri-Erba, E.' 5 primary 'Effantin, G.' 6 primary 'Gottlinger, H.G.' 7 primary 'Weissenhorn, W.' 8 primary 'Renesto, P.' 9 # _cell.entry_id 4D81 _cell.length_a 65.269 _cell.length_b 65.269 _cell.length_c 112.521 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D81 _symmetry.space_group_name_H-M 'P 65' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 # 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 'AAA ATPASE, CENTRAL DOMAIN PROTEIN' 32232.318 1 3.6.4.6 ? 'AAA, UNP RESIDUES 88-369' 'TRUNCATION OF THE RESIDUES 1-74' 2 non-polymer syn "ADENOSINE-5'-DIPHOSPHATE" 427.201 1 ? ? ? ? 3 water nat water 18.015 7 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name VPS4 # _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 ;GDIVMKEKPKVTLNEIVGLEDVKEALKEAVVYPSKRPDLFPLGWPRGILLYGPPGCGKTMIAAAVANELDSEFIHVDAAS IMSKWLGEAEKNVAKIFKTARELSKKENKPAIIFIDELDALLASYTSEVGGEARVRNQFLKEMDGLADKNEISKVYVIGA TNKPWRLDEPFLRRFQKRIYITLPDKAHRLELLKHYSSKVKLDPNVNLEELAELTDGYTASDIRDIVQSAHMRVVKEMFE KNLQEPRAINMDDFREVLKVRKPSVNQDMLKAYAAWHEKFKAL ; _entity_poly.pdbx_seq_one_letter_code_can ;GDIVMKEKPKVTLNEIVGLEDVKEALKEAVVYPSKRPDLFPLGWPRGILLYGPPGCGKTMIAAAVANELDSEFIHVDAAS IMSKWLGEAEKNVAKIFKTARELSKKENKPAIIFIDELDALLASYTSEVGGEARVRNQFLKEMDGLADKNEISKVYVIGA TNKPWRLDEPFLRRFQKRIYITLPDKAHRLELLKHYSSKVKLDPNVNLEELAELTDGYTASDIRDIVQSAHMRVVKEMFE KNLQEPRAINMDDFREVLKVRKPSVNQDMLKAYAAWHEKFKAL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 ASP n 1 3 ILE n 1 4 VAL n 1 5 MET n 1 6 LYS n 1 7 GLU n 1 8 LYS n 1 9 PRO n 1 10 LYS n 1 11 VAL n 1 12 THR n 1 13 LEU n 1 14 ASN n 1 15 GLU n 1 16 ILE n 1 17 VAL n 1 18 GLY n 1 19 LEU n 1 20 GLU n 1 21 ASP n 1 22 VAL n 1 23 LYS n 1 24 GLU n 1 25 ALA n 1 26 LEU n 1 27 LYS n 1 28 GLU n 1 29 ALA n 1 30 VAL n 1 31 VAL n 1 32 TYR n 1 33 PRO n 1 34 SER n 1 35 LYS n 1 36 ARG n 1 37 PRO n 1 38 ASP n 1 39 LEU n 1 40 PHE n 1 41 PRO n 1 42 LEU n 1 43 GLY n 1 44 TRP n 1 45 PRO n 1 46 ARG n 1 47 GLY n 1 48 ILE n 1 49 LEU n 1 50 LEU n 1 51 TYR n 1 52 GLY n 1 53 PRO n 1 54 PRO n 1 55 GLY n 1 56 CYS n 1 57 GLY n 1 58 LYS n 1 59 THR n 1 60 MET n 1 61 ILE n 1 62 ALA n 1 63 ALA n 1 64 ALA n 1 65 VAL n 1 66 ALA n 1 67 ASN n 1 68 GLU n 1 69 LEU n 1 70 ASP n 1 71 SER n 1 72 GLU n 1 73 PHE n 1 74 ILE n 1 75 HIS n 1 76 VAL n 1 77 ASP n 1 78 ALA n 1 79 ALA n 1 80 SER n 1 81 ILE n 1 82 MET n 1 83 SER n 1 84 LYS n 1 85 TRP n 1 86 LEU n 1 87 GLY n 1 88 GLU n 1 89 ALA n 1 90 GLU n 1 91 LYS n 1 92 ASN n 1 93 VAL n 1 94 ALA n 1 95 LYS n 1 96 ILE n 1 97 PHE n 1 98 LYS n 1 99 THR n 1 100 ALA n 1 101 ARG n 1 102 GLU n 1 103 LEU n 1 104 SER n 1 105 LYS n 1 106 LYS n 1 107 GLU n 1 108 ASN n 1 109 LYS n 1 110 PRO n 1 111 ALA n 1 112 ILE n 1 113 ILE n 1 114 PHE n 1 115 ILE n 1 116 ASP n 1 117 GLU n 1 118 LEU n 1 119 ASP n 1 120 ALA n 1 121 LEU n 1 122 LEU n 1 123 ALA n 1 124 SER n 1 125 TYR n 1 126 THR n 1 127 SER n 1 128 GLU n 1 129 VAL n 1 130 GLY n 1 131 GLY n 1 132 GLU n 1 133 ALA n 1 134 ARG n 1 135 VAL n 1 136 ARG n 1 137 ASN n 1 138 GLN n 1 139 PHE n 1 140 LEU n 1 141 LYS n 1 142 GLU n 1 143 MET n 1 144 ASP n 1 145 GLY n 1 146 LEU n 1 147 ALA n 1 148 ASP n 1 149 LYS n 1 150 ASN n 1 151 GLU n 1 152 ILE n 1 153 SER n 1 154 LYS n 1 155 VAL n 1 156 TYR n 1 157 VAL n 1 158 ILE n 1 159 GLY n 1 160 ALA n 1 161 THR n 1 162 ASN n 1 163 LYS n 1 164 PRO n 1 165 TRP n 1 166 ARG n 1 167 LEU n 1 168 ASP n 1 169 GLU n 1 170 PRO n 1 171 PHE n 1 172 LEU n 1 173 ARG n 1 174 ARG n 1 175 PHE n 1 176 GLN n 1 177 LYS n 1 178 ARG n 1 179 ILE n 1 180 TYR n 1 181 ILE n 1 182 THR n 1 183 LEU n 1 184 PRO n 1 185 ASP n 1 186 LYS n 1 187 ALA n 1 188 HIS n 1 189 ARG n 1 190 LEU n 1 191 GLU n 1 192 LEU n 1 193 LEU n 1 194 LYS n 1 195 HIS n 1 196 TYR n 1 197 SER n 1 198 SER n 1 199 LYS n 1 200 VAL n 1 201 LYS n 1 202 LEU n 1 203 ASP n 1 204 PRO n 1 205 ASN n 1 206 VAL n 1 207 ASN n 1 208 LEU n 1 209 GLU n 1 210 GLU n 1 211 LEU n 1 212 ALA n 1 213 GLU n 1 214 LEU n 1 215 THR n 1 216 ASP n 1 217 GLY n 1 218 TYR n 1 219 THR n 1 220 ALA n 1 221 SER n 1 222 ASP n 1 223 ILE n 1 224 ARG n 1 225 ASP n 1 226 ILE n 1 227 VAL n 1 228 GLN n 1 229 SER n 1 230 ALA n 1 231 HIS n 1 232 MET n 1 233 ARG n 1 234 VAL n 1 235 VAL n 1 236 LYS n 1 237 GLU n 1 238 MET n 1 239 PHE n 1 240 GLU n 1 241 LYS n 1 242 ASN n 1 243 LEU n 1 244 GLN n 1 245 GLU n 1 246 PRO n 1 247 ARG n 1 248 ALA n 1 249 ILE n 1 250 ASN n 1 251 MET n 1 252 ASP n 1 253 ASP n 1 254 PHE n 1 255 ARG n 1 256 GLU n 1 257 VAL n 1 258 LEU n 1 259 LYS n 1 260 VAL n 1 261 ARG n 1 262 LYS n 1 263 PRO n 1 264 SER n 1 265 VAL n 1 266 ASN n 1 267 GLN n 1 268 ASP n 1 269 MET n 1 270 LEU n 1 271 LYS n 1 272 ALA n 1 273 TYR n 1 274 ALA n 1 275 ALA n 1 276 TRP n 1 277 HIS n 1 278 GLU n 1 279 LYS n 1 280 PHE n 1 281 LYS n 1 282 ALA n 1 283 LEU 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 'METALLOSPHAERA SEDULA' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 43687 _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 469008 _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 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant C41 _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 PLAMSID _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PDEST-17 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A4YHC5_METS5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession A4YHC5 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4D81 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 283 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A4YHC5 _struct_ref_seq.db_align_beg 88 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 369 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 88 _struct_ref_seq.pdbx_auth_seq_align_end 369 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4D81 _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _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 A4YHC5 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 87 _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 ADP non-polymer n "ADENOSINE-5'-DIPHOSPHATE" ? 'C10 H15 N5 O10 P2' 427.201 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 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 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 4D81 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 42.78 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.8 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '40% (W/V) POLYETHYLENE GLYCOL 200 (PEG200) 100 MM TRIS-HCL BUFFER (PH 8.8)' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2013-11-11 _diffrn_detector.details ? # _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 0.973750 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength 0.973750 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4D81 _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 56.50 _reflns.d_resolution_high 2.40 _reflns.number_obs 12935 _reflns.number_all ? _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.70 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.1 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.40 _reflns_shell.d_res_low 2.49 _reflns_shell.percent_possible_all 99.7 _reflns_shell.Rmerge_I_obs 0.63 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.30 _reflns_shell.pdbx_redundancy 4.2 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4D81 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 10038 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 56.52 _refine.ls_d_res_high 2.40 _refine.ls_percent_reflns_obs 99.63 _refine.ls_R_factor_obs 0.20971 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20665 _refine.ls_R_factor_R_free 0.26283 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.3 _refine.ls_number_reflns_R_free 565 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.951 _refine.correlation_coeff_Fo_to_Fc_free 0.921 _refine.B_iso_mean 55.263 _refine.aniso_B[1][1] 0.66 _refine.aniso_B[2][2] 0.66 _refine.aniso_B[3][3] -2.13 _refine.aniso_B[1][2] 0.33 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.614 _refine.pdbx_overall_ESU_R_Free 0.297 _refine.overall_SU_ML 0.256 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 11.263 _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 2111 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 27 _refine_hist.number_atoms_solvent 7 _refine_hist.number_atoms_total 2145 _refine_hist.d_res_high 2.40 _refine_hist.d_res_low 56.52 # 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 r_bond_refined_d 0.012 0.019 ? 2181 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 2144 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.572 1.993 ? 2950 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.830 3.000 ? 4944 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.806 5.000 ? 261 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 39.621 24.286 ? 98 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 16.628 15.000 ? 405 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 10.494 15.000 ? 15 'X-RAY DIFFRACTION' ? r_chiral_restr 0.085 0.200 ? 328 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.021 ? 2387 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 469 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 3.867 5.168 ? 1050 'X-RAY DIFFRACTION' ? r_mcbond_other 3.857 5.166 ? 1049 'X-RAY DIFFRACTION' ? r_mcangle_it 5.630 7.737 ? 1309 'X-RAY DIFFRACTION' ? r_mcangle_other 5.630 7.739 ? 1310 'X-RAY DIFFRACTION' ? r_scbond_it 4.646 5.771 ? 1131 'X-RAY DIFFRACTION' ? r_scbond_other 4.644 5.771 ? 1132 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other 7.200 8.427 ? 1642 'X-RAY DIFFRACTION' ? r_long_range_B_refined 9.434 42.115 ? 2527 'X-RAY DIFFRACTION' ? r_long_range_B_other 9.434 42.114 ? 2527 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.401 _refine_ls_shell.d_res_low 2.463 _refine_ls_shell.number_reflns_R_work 731 _refine_ls_shell.R_factor_R_work 0.250 _refine_ls_shell.percent_reflns_obs 99.49 _refine_ls_shell.R_factor_R_free 0.361 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 48 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 4D81 _struct.title 'Metallosphera sedula Vps4 crystal structure' _struct.pdbx_descriptor 'AAA ATPASE, CENTRAL DOMAIN PROTEIN (E.C.3.6.4.6)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4D81 _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.text 'HYDROLASE, VPS4' # 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 ? # _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 THR A 12 ? ILE A 16 ? THR A 98 ILE A 102 5 ? 5 HELX_P HELX_P2 2 LEU A 19 ? VAL A 30 ? LEU A 105 VAL A 116 1 ? 12 HELX_P HELX_P3 3 VAL A 30 ? ARG A 36 ? VAL A 116 ARG A 122 1 ? 7 HELX_P HELX_P4 4 PRO A 37 ? PHE A 40 ? PRO A 123 PHE A 126 5 ? 4 HELX_P HELX_P5 5 GLY A 57 ? ASP A 70 ? GLY A 143 ASP A 156 1 ? 14 HELX_P HELX_P6 6 ALA A 78 ? MET A 82 ? ALA A 164 MET A 168 1 ? 5 HELX_P HELX_P7 7 GLU A 88 ? ASN A 108 ? GLU A 174 ASN A 194 1 ? 21 HELX_P HELX_P8 8 GLU A 117 ? ALA A 123 ? GLU A 203 ALA A 209 5 ? 7 HELX_P HELX_P9 9 GLU A 132 ? ASP A 148 ? GLU A 218 ASP A 234 1 ? 17 HELX_P HELX_P10 10 LYS A 163 ? LEU A 167 ? LYS A 249 LEU A 253 5 ? 5 HELX_P HELX_P11 11 ASP A 168 ? ARG A 174 ? ASP A 254 ARG A 260 1 ? 7 HELX_P HELX_P12 12 ASP A 185 ? SER A 198 ? ASP A 271 SER A 284 1 ? 14 HELX_P HELX_P13 13 ASN A 207 ? THR A 215 ? ASN A 293 THR A 301 1 ? 9 HELX_P HELX_P14 14 THR A 219 ? LYS A 241 ? THR A 305 LYS A 327 1 ? 23 HELX_P HELX_P15 15 ASN A 250 ? ARG A 261 ? ASN A 336 ARG A 347 1 ? 12 HELX_P HELX_P16 16 ASP A 268 ? HIS A 277 ? ASP A 354 HIS A 363 1 ? 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_sheet.id AA _struct_sheet.type ? _struct_sheet.number_strands 5 _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 AA 1 2 ? parallel AA 2 3 ? parallel AA 3 4 ? parallel AA 4 5 ? 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 GLU A 72 ? ASP A 77 ? GLU A 158 ASP A 163 AA 2 ALA A 111 ? ASP A 116 ? ALA A 197 ASP A 202 AA 3 VAL A 155 ? THR A 161 ? VAL A 241 THR A 247 AA 4 GLY A 47 ? TYR A 51 ? GLY A 133 TYR A 137 AA 5 LYS A 177 ? TYR A 180 ? LYS A 263 TYR A 266 # 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 ILE A 74 ? N ILE A 160 O ILE A 112 ? O ILE A 198 AA 2 3 N ILE A 113 ? N ILE A 199 O TYR A 156 ? O TYR A 242 AA 3 4 N GLY A 159 ? N GLY A 245 O ILE A 48 ? O ILE A 134 AA 4 5 N LEU A 49 ? N LEU A 135 O LYS A 177 ? O LYS A 263 # _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 13 _struct_site.details 'BINDING SITE FOR RESIDUE ADP A 1364' # 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 13 ILE A 16 ? ILE A 102 . ? 1_555 ? 2 AC1 13 VAL A 17 ? VAL A 103 . ? 1_555 ? 3 AC1 13 PRO A 54 ? PRO A 140 . ? 1_555 ? 4 AC1 13 GLY A 55 ? GLY A 141 . ? 1_555 ? 5 AC1 13 CYS A 56 ? CYS A 142 . ? 1_555 ? 6 AC1 13 GLY A 57 ? GLY A 143 . ? 1_555 ? 7 AC1 13 LYS A 58 ? LYS A 144 . ? 1_555 ? 8 AC1 13 THR A 59 ? THR A 145 . ? 1_555 ? 9 AC1 13 MET A 60 ? MET A 146 . ? 1_555 ? 10 AC1 13 TYR A 196 ? TYR A 282 . ? 1_555 ? 11 AC1 13 ALA A 220 ? ALA A 306 . ? 1_555 ? 12 AC1 13 SER A 221 ? SER A 307 . ? 1_555 ? 13 AC1 13 ARG A 224 ? ARG A 310 . ? 1_555 ? # _database_PDB_matrix.entry_id 4D81 _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 4D81 _atom_sites.fract_transf_matrix[1][1] 0.015321 _atom_sites.fract_transf_matrix[1][2] 0.008846 _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] 0.017691 _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] 0.008887 _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 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 GLY 1 87 ? ? ? A . n A 1 2 ASP 2 88 ? ? ? A . n A 1 3 ILE 3 89 ? ? ? A . n A 1 4 VAL 4 90 ? ? ? A . n A 1 5 MET 5 91 ? ? ? A . n A 1 6 LYS 6 92 ? ? ? A . n A 1 7 GLU 7 93 ? ? ? A . n A 1 8 LYS 8 94 ? ? ? A . n A 1 9 PRO 9 95 ? ? ? A . n A 1 10 LYS 10 96 ? ? ? A . n A 1 11 VAL 11 97 97 VAL VAL A . n A 1 12 THR 12 98 98 THR THR A . n A 1 13 LEU 13 99 99 LEU LEU A . n A 1 14 ASN 14 100 100 ASN ASN A . n A 1 15 GLU 15 101 101 GLU GLU A . n A 1 16 ILE 16 102 102 ILE ILE A . n A 1 17 VAL 17 103 103 VAL VAL A . n A 1 18 GLY 18 104 104 GLY GLY A . n A 1 19 LEU 19 105 105 LEU LEU A . n A 1 20 GLU 20 106 106 GLU GLU A . n A 1 21 ASP 21 107 107 ASP ASP A . n A 1 22 VAL 22 108 108 VAL VAL A . n A 1 23 LYS 23 109 109 LYS LYS A . n A 1 24 GLU 24 110 110 GLU GLU A . n A 1 25 ALA 25 111 111 ALA ALA A . n A 1 26 LEU 26 112 112 LEU LEU A . n A 1 27 LYS 27 113 113 LYS LYS A . n A 1 28 GLU 28 114 114 GLU GLU A . n A 1 29 ALA 29 115 115 ALA ALA A . n A 1 30 VAL 30 116 116 VAL VAL A . n A 1 31 VAL 31 117 117 VAL VAL A . n A 1 32 TYR 32 118 118 TYR TYR A . n A 1 33 PRO 33 119 119 PRO PRO A . n A 1 34 SER 34 120 120 SER SER A . n A 1 35 LYS 35 121 121 LYS LYS A . n A 1 36 ARG 36 122 122 ARG ARG A . n A 1 37 PRO 37 123 123 PRO PRO A . n A 1 38 ASP 38 124 124 ASP ASP A . n A 1 39 LEU 39 125 125 LEU LEU A . n A 1 40 PHE 40 126 126 PHE PHE A . n A 1 41 PRO 41 127 127 PRO PRO A . n A 1 42 LEU 42 128 128 LEU LEU A . n A 1 43 GLY 43 129 129 GLY GLY A . n A 1 44 TRP 44 130 130 TRP TRP A . n A 1 45 PRO 45 131 131 PRO PRO A . n A 1 46 ARG 46 132 132 ARG ARG A . n A 1 47 GLY 47 133 133 GLY GLY A . n A 1 48 ILE 48 134 134 ILE ILE A . n A 1 49 LEU 49 135 135 LEU LEU A . n A 1 50 LEU 50 136 136 LEU LEU A . n A 1 51 TYR 51 137 137 TYR TYR A . n A 1 52 GLY 52 138 138 GLY GLY A . n A 1 53 PRO 53 139 139 PRO PRO A . n A 1 54 PRO 54 140 140 PRO PRO A . n A 1 55 GLY 55 141 141 GLY GLY A . n A 1 56 CYS 56 142 142 CYS CYS A . n A 1 57 GLY 57 143 143 GLY GLY A . n A 1 58 LYS 58 144 144 LYS LYS A . n A 1 59 THR 59 145 145 THR THR A . n A 1 60 MET 60 146 146 MET MET A . n A 1 61 ILE 61 147 147 ILE ILE A . n A 1 62 ALA 62 148 148 ALA ALA A . n A 1 63 ALA 63 149 149 ALA ALA A . n A 1 64 ALA 64 150 150 ALA ALA A . n A 1 65 VAL 65 151 151 VAL VAL A . n A 1 66 ALA 66 152 152 ALA ALA A . n A 1 67 ASN 67 153 153 ASN ASN A . n A 1 68 GLU 68 154 154 GLU GLU A . n A 1 69 LEU 69 155 155 LEU LEU A . n A 1 70 ASP 70 156 156 ASP ASP A . n A 1 71 SER 71 157 157 SER SER A . n A 1 72 GLU 72 158 158 GLU GLU A . n A 1 73 PHE 73 159 159 PHE PHE A . n A 1 74 ILE 74 160 160 ILE ILE A . n A 1 75 HIS 75 161 161 HIS HIS A . n A 1 76 VAL 76 162 162 VAL VAL A . n A 1 77 ASP 77 163 163 ASP ASP A . n A 1 78 ALA 78 164 164 ALA ALA A . n A 1 79 ALA 79 165 165 ALA ALA A . n A 1 80 SER 80 166 166 SER SER A . n A 1 81 ILE 81 167 167 ILE ILE A . n A 1 82 MET 82 168 168 MET MET A . n A 1 83 SER 83 169 169 SER SER A . n A 1 84 LYS 84 170 170 LYS LYS A . n A 1 85 TRP 85 171 171 TRP TRP A . n A 1 86 LEU 86 172 172 LEU LEU A . n A 1 87 GLY 87 173 173 GLY GLY A . n A 1 88 GLU 88 174 174 GLU GLU A . n A 1 89 ALA 89 175 175 ALA ALA A . n A 1 90 GLU 90 176 176 GLU GLU A . n A 1 91 LYS 91 177 177 LYS LYS A . n A 1 92 ASN 92 178 178 ASN ASN A . n A 1 93 VAL 93 179 179 VAL VAL A . n A 1 94 ALA 94 180 180 ALA ALA A . n A 1 95 LYS 95 181 181 LYS LYS A . n A 1 96 ILE 96 182 182 ILE ILE A . n A 1 97 PHE 97 183 183 PHE PHE A . n A 1 98 LYS 98 184 184 LYS LYS A . n A 1 99 THR 99 185 185 THR THR A . n A 1 100 ALA 100 186 186 ALA ALA A . n A 1 101 ARG 101 187 187 ARG ARG A . n A 1 102 GLU 102 188 188 GLU GLU A . n A 1 103 LEU 103 189 189 LEU LEU A . n A 1 104 SER 104 190 190 SER SER A . n A 1 105 LYS 105 191 191 LYS LYS A . n A 1 106 LYS 106 192 192 LYS LYS A . n A 1 107 GLU 107 193 193 GLU GLU A . n A 1 108 ASN 108 194 194 ASN ASN A . n A 1 109 LYS 109 195 195 LYS LYS A . n A 1 110 PRO 110 196 196 PRO PRO A . n A 1 111 ALA 111 197 197 ALA ALA A . n A 1 112 ILE 112 198 198 ILE ILE A . n A 1 113 ILE 113 199 199 ILE ILE A . n A 1 114 PHE 114 200 200 PHE PHE A . n A 1 115 ILE 115 201 201 ILE ILE A . n A 1 116 ASP 116 202 202 ASP ASP A . n A 1 117 GLU 117 203 203 GLU GLU A . n A 1 118 LEU 118 204 204 LEU LEU A . n A 1 119 ASP 119 205 205 ASP ASP A . n A 1 120 ALA 120 206 206 ALA ALA A . n A 1 121 LEU 121 207 207 LEU LEU A . n A 1 122 LEU 122 208 208 LEU LEU A . n A 1 123 ALA 123 209 209 ALA ALA A . n A 1 124 SER 124 210 210 SER SER A . n A 1 125 TYR 125 211 211 TYR TYR A . n A 1 126 THR 126 212 212 THR THR A . n A 1 127 SER 127 213 ? ? ? A . n A 1 128 GLU 128 214 ? ? ? A . n A 1 129 VAL 129 215 ? ? ? A . n A 1 130 GLY 130 216 ? ? ? A . n A 1 131 GLY 131 217 217 GLY GLY A . n A 1 132 GLU 132 218 218 GLU GLU A . n A 1 133 ALA 133 219 219 ALA ALA A . n A 1 134 ARG 134 220 220 ARG ARG A . n A 1 135 VAL 135 221 221 VAL VAL A . n A 1 136 ARG 136 222 222 ARG ARG A . n A 1 137 ASN 137 223 223 ASN ASN A . n A 1 138 GLN 138 224 224 GLN GLN A . n A 1 139 PHE 139 225 225 PHE PHE A . n A 1 140 LEU 140 226 226 LEU LEU A . n A 1 141 LYS 141 227 227 LYS LYS A . n A 1 142 GLU 142 228 228 GLU GLU A . n A 1 143 MET 143 229 229 MET MET A . n A 1 144 ASP 144 230 230 ASP ASP A . n A 1 145 GLY 145 231 231 GLY GLY A . n A 1 146 LEU 146 232 232 LEU LEU A . n A 1 147 ALA 147 233 233 ALA ALA A . n A 1 148 ASP 148 234 234 ASP ASP A . n A 1 149 LYS 149 235 235 LYS LYS A . n A 1 150 ASN 150 236 236 ASN ASN A . n A 1 151 GLU 151 237 237 GLU GLU A . n A 1 152 ILE 152 238 238 ILE ILE A . n A 1 153 SER 153 239 239 SER SER A . n A 1 154 LYS 154 240 240 LYS LYS A . n A 1 155 VAL 155 241 241 VAL VAL A . n A 1 156 TYR 156 242 242 TYR TYR A . n A 1 157 VAL 157 243 243 VAL VAL A . n A 1 158 ILE 158 244 244 ILE ILE A . n A 1 159 GLY 159 245 245 GLY GLY A . n A 1 160 ALA 160 246 246 ALA ALA A . n A 1 161 THR 161 247 247 THR THR A . n A 1 162 ASN 162 248 248 ASN ASN A . n A 1 163 LYS 163 249 249 LYS LYS A . n A 1 164 PRO 164 250 250 PRO PRO A . n A 1 165 TRP 165 251 251 TRP TRP A . n A 1 166 ARG 166 252 252 ARG ARG A . n A 1 167 LEU 167 253 253 LEU LEU A . n A 1 168 ASP 168 254 254 ASP ASP A . n A 1 169 GLU 169 255 255 GLU GLU A . n A 1 170 PRO 170 256 256 PRO PRO A . n A 1 171 PHE 171 257 257 PHE PHE A . n A 1 172 LEU 172 258 258 LEU LEU A . n A 1 173 ARG 173 259 259 ARG ARG A . n A 1 174 ARG 174 260 260 ARG ARG A . n A 1 175 PHE 175 261 261 PHE PHE A . n A 1 176 GLN 176 262 262 GLN GLN A . n A 1 177 LYS 177 263 263 LYS LYS A . n A 1 178 ARG 178 264 264 ARG ARG A . n A 1 179 ILE 179 265 265 ILE ILE A . n A 1 180 TYR 180 266 266 TYR TYR A . n A 1 181 ILE 181 267 267 ILE ILE A . n A 1 182 THR 182 268 268 THR THR A . n A 1 183 LEU 183 269 269 LEU LEU A . n A 1 184 PRO 184 270 270 PRO PRO A . n A 1 185 ASP 185 271 271 ASP ASP A . n A 1 186 LYS 186 272 272 LYS LYS A . n A 1 187 ALA 187 273 273 ALA ALA A . n A 1 188 HIS 188 274 274 HIS HIS A . n A 1 189 ARG 189 275 275 ARG ARG A . n A 1 190 LEU 190 276 276 LEU LEU A . n A 1 191 GLU 191 277 277 GLU GLU A . n A 1 192 LEU 192 278 278 LEU LEU A . n A 1 193 LEU 193 279 279 LEU LEU A . n A 1 194 LYS 194 280 280 LYS LYS A . n A 1 195 HIS 195 281 281 HIS HIS A . n A 1 196 TYR 196 282 282 TYR TYR A . n A 1 197 SER 197 283 283 SER SER A . n A 1 198 SER 198 284 284 SER SER A . n A 1 199 LYS 199 285 285 LYS LYS A . n A 1 200 VAL 200 286 286 VAL VAL A . n A 1 201 LYS 201 287 287 LYS LYS A . n A 1 202 LEU 202 288 288 LEU LEU A . n A 1 203 ASP 203 289 289 ASP ASP A . n A 1 204 PRO 204 290 290 PRO PRO A . n A 1 205 ASN 205 291 291 ASN ASN A . n A 1 206 VAL 206 292 292 VAL VAL A . n A 1 207 ASN 207 293 293 ASN ASN A . n A 1 208 LEU 208 294 294 LEU LEU A . n A 1 209 GLU 209 295 295 GLU GLU A . n A 1 210 GLU 210 296 296 GLU GLU A . n A 1 211 LEU 211 297 297 LEU LEU A . n A 1 212 ALA 212 298 298 ALA ALA A . n A 1 213 GLU 213 299 299 GLU GLU A . n A 1 214 LEU 214 300 300 LEU LEU A . n A 1 215 THR 215 301 301 THR THR A . n A 1 216 ASP 216 302 302 ASP ASP A . n A 1 217 GLY 217 303 303 GLY GLY A . n A 1 218 TYR 218 304 304 TYR TYR A . n A 1 219 THR 219 305 305 THR THR A . n A 1 220 ALA 220 306 306 ALA ALA A . n A 1 221 SER 221 307 307 SER SER A . n A 1 222 ASP 222 308 308 ASP ASP A . n A 1 223 ILE 223 309 309 ILE ILE A . n A 1 224 ARG 224 310 310 ARG ARG A . n A 1 225 ASP 225 311 311 ASP ASP A . n A 1 226 ILE 226 312 312 ILE ILE A . n A 1 227 VAL 227 313 313 VAL VAL A . n A 1 228 GLN 228 314 314 GLN GLN A . n A 1 229 SER 229 315 315 SER SER A . n A 1 230 ALA 230 316 316 ALA ALA A . n A 1 231 HIS 231 317 317 HIS HIS A . n A 1 232 MET 232 318 318 MET MET A . n A 1 233 ARG 233 319 319 ARG ARG A . n A 1 234 VAL 234 320 320 VAL VAL A . n A 1 235 VAL 235 321 321 VAL VAL A . n A 1 236 LYS 236 322 322 LYS LYS A . n A 1 237 GLU 237 323 323 GLU GLU A . n A 1 238 MET 238 324 324 MET MET A . n A 1 239 PHE 239 325 325 PHE PHE A . n A 1 240 GLU 240 326 326 GLU GLU A . n A 1 241 LYS 241 327 327 LYS LYS A . n A 1 242 ASN 242 328 328 ASN ASN A . n A 1 243 LEU 243 329 329 LEU LEU A . n A 1 244 GLN 244 330 330 GLN GLN A . n A 1 245 GLU 245 331 331 GLU GLU A . n A 1 246 PRO 246 332 332 PRO PRO A . n A 1 247 ARG 247 333 333 ARG ARG A . n A 1 248 ALA 248 334 334 ALA ALA A . n A 1 249 ILE 249 335 335 ILE ILE A . n A 1 250 ASN 250 336 336 ASN ASN A . n A 1 251 MET 251 337 337 MET MET A . n A 1 252 ASP 252 338 338 ASP ASP A . n A 1 253 ASP 253 339 339 ASP ASP A . n A 1 254 PHE 254 340 340 PHE PHE A . n A 1 255 ARG 255 341 341 ARG ARG A . n A 1 256 GLU 256 342 342 GLU GLU A . n A 1 257 VAL 257 343 343 VAL VAL A . n A 1 258 LEU 258 344 344 LEU LEU A . n A 1 259 LYS 259 345 345 LYS LYS A . n A 1 260 VAL 260 346 346 VAL VAL A . n A 1 261 ARG 261 347 347 ARG ARG A . n A 1 262 LYS 262 348 348 LYS LYS A . n A 1 263 PRO 263 349 349 PRO PRO A . n A 1 264 SER 264 350 350 SER SER A . n A 1 265 VAL 265 351 351 VAL VAL A . n A 1 266 ASN 266 352 352 ASN ASN A . n A 1 267 GLN 267 353 353 GLN GLN A . n A 1 268 ASP 268 354 354 ASP ASP A . n A 1 269 MET 269 355 355 MET MET A . n A 1 270 LEU 270 356 356 LEU LEU A . n A 1 271 LYS 271 357 357 LYS LYS A . n A 1 272 ALA 272 358 358 ALA ALA A . n A 1 273 TYR 273 359 359 TYR TYR A . n A 1 274 ALA 274 360 360 ALA ALA A . n A 1 275 ALA 275 361 361 ALA ALA A . n A 1 276 TRP 276 362 362 TRP TRP A . n A 1 277 HIS 277 363 363 HIS HIS A . n A 1 278 GLU 278 364 ? ? ? A . n A 1 279 LYS 279 365 ? ? ? A . n A 1 280 PHE 280 366 ? ? ? A . n A 1 281 LYS 281 367 ? ? ? A . n A 1 282 ALA 282 368 ? ? ? A . n A 1 283 LEU 283 369 ? ? ? 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 ADP 1 1364 1364 ADP ADP A . C 3 HOH 1 2001 2001 HOH HOH A . C 3 HOH 2 2002 2002 HOH HOH A . C 3 HOH 3 2003 2003 HOH HOH A . C 3 HOH 4 2004 2004 HOH HOH A . C 3 HOH 5 2005 2005 HOH HOH A . C 3 HOH 6 2006 2006 HOH HOH A . C 3 HOH 7 2007 2007 HOH HOH A . # _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 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _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_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 2015-11-25 2 'Structure model' 1 1 2015-12-16 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.8.0073 ? 1 XDS 'data reduction' . ? 2 SCALA 'data scaling' . ? 3 PHASER phasing . ? 4 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id VAL _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 116 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -120.20 _pdbx_validate_torsion.psi -53.14 # 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 GLY 87 ? A GLY 1 2 1 Y 1 A ASP 88 ? A ASP 2 3 1 Y 1 A ILE 89 ? A ILE 3 4 1 Y 1 A VAL 90 ? A VAL 4 5 1 Y 1 A MET 91 ? A MET 5 6 1 Y 1 A LYS 92 ? A LYS 6 7 1 Y 1 A GLU 93 ? A GLU 7 8 1 Y 1 A LYS 94 ? A LYS 8 9 1 Y 1 A PRO 95 ? A PRO 9 10 1 Y 1 A LYS 96 ? A LYS 10 11 1 Y 1 A SER 213 ? A SER 127 12 1 Y 1 A GLU 214 ? A GLU 128 13 1 Y 1 A VAL 215 ? A VAL 129 14 1 Y 1 A GLY 216 ? A GLY 130 15 1 Y 1 A GLU 364 ? A GLU 278 16 1 Y 1 A LYS 365 ? A LYS 279 17 1 Y 1 A PHE 366 ? A PHE 280 18 1 Y 1 A LYS 367 ? A LYS 281 19 1 Y 1 A ALA 368 ? A ALA 282 20 1 Y 1 A LEU 369 ? A LEU 283 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 "ADENOSINE-5'-DIPHOSPHATE" ADP 3 water HOH #