data_4J3H # _entry.id 4J3H # _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 4J3H RCSB RCSB077548 WWPDB D_1000077548 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3T98 . unspecified PDB 3T97 . unspecified PDB 2OSZ . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4J3H _pdbx_database_status.recvd_initial_deposition_date 2013-02-05 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Solmaz, S.R.' 1 'Blobel, G.' 2 'Melcak, I.' 3 # _citation.id primary _citation.title 'Ring cycle for dilating and constricting the nuclear pore.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 110 _citation.page_first 5858 _citation.page_last 5863 _citation.year 2013 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23479651 _citation.pdbx_database_id_DOI 10.1073/pnas.1302655110 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Solmaz, S.R.' 1 primary 'Blobel, G.' 2 primary 'Melcak, I.' 3 # _cell.entry_id 4J3H _cell.length_a 41.320 _cell.length_b 41.320 _cell.length_c 198.410 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4J3H _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? # 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 'Nuclear pore complex protein Nup54' 5619.972 2 ? 'I458M I481M' 'UNP Residues 453-494' ? 2 non-polymer syn 'CALCIUM ION' 40.078 3 ? ? ? ? 3 water nat water 18.015 80 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name '54 kDa nucleoporin, Nucleoporin Nup54, nucleoporin p54' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GSH(MSE)EEKYY(MSE)DADLLREIKQHLKQQQEGLSHL(MSE)SIIKDDLEDIKLV' _entity_poly.pdbx_seq_one_letter_code_can GSHMEEKYYMDADLLREIKQHLKQQQEGLSHLMSIIKDDLEDIKLV _entity_poly.pdbx_strand_id A,B _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 SER n 1 3 HIS n 1 4 MSE n 1 5 GLU n 1 6 GLU n 1 7 LYS n 1 8 TYR n 1 9 TYR n 1 10 MSE n 1 11 ASP n 1 12 ALA n 1 13 ASP n 1 14 LEU n 1 15 LEU n 1 16 ARG n 1 17 GLU n 1 18 ILE n 1 19 LYS n 1 20 GLN n 1 21 HIS n 1 22 LEU n 1 23 LYS n 1 24 GLN n 1 25 GLN n 1 26 GLN n 1 27 GLU n 1 28 GLY n 1 29 LEU n 1 30 SER n 1 31 HIS n 1 32 LEU n 1 33 MSE n 1 34 SER n 1 35 ILE n 1 36 ILE n 1 37 LYS n 1 38 ASP n 1 39 ASP n 1 40 LEU n 1 41 GLU n 1 42 ASP n 1 43 ILE n 1 44 LYS n 1 45 LEU n 1 46 VAL 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 'brown rat,rat,rats' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Nup54 _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 'Rattus norvegicus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10116 _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)RIL' _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 Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET28a _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code NUP54_RAT _struct_ref.pdbx_db_accession P70582 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code EEKYYIDADLLREIKQHLKQQQEGLSHLISIIKDDLEDIKLV _struct_ref.pdbx_align_begin 453 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4J3H A 5 ? 46 ? P70582 453 ? 494 ? 453 494 2 1 4J3H B 5 ? 46 ? P70582 453 ? 494 ? 453 494 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 4J3H GLY A 1 ? UNP P70582 ? ? 'EXPRESSION TAG' 449 1 1 4J3H SER A 2 ? UNP P70582 ? ? 'EXPRESSION TAG' 450 2 1 4J3H HIS A 3 ? UNP P70582 ? ? 'EXPRESSION TAG' 451 3 1 4J3H MSE A 4 ? UNP P70582 ? ? 'EXPRESSION TAG' 452 4 1 4J3H MSE A 10 ? UNP P70582 ILE 458 'ENGINEERED MUTATION' 458 5 1 4J3H MSE A 33 ? UNP P70582 ILE 481 'ENGINEERED MUTATION' 481 6 2 4J3H GLY B 1 ? UNP P70582 ? ? 'EXPRESSION TAG' 449 7 2 4J3H SER B 2 ? UNP P70582 ? ? 'EXPRESSION TAG' 450 8 2 4J3H HIS B 3 ? UNP P70582 ? ? 'EXPRESSION TAG' 451 9 2 4J3H MSE B 4 ? UNP P70582 ? ? 'EXPRESSION TAG' 452 10 2 4J3H MSE B 10 ? UNP P70582 ILE 458 'ENGINEERED MUTATION' 458 11 2 4J3H MSE B 33 ? UNP P70582 ILE 481 'ENGINEERED MUTATION' 481 12 # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 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 4J3H _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_percent_sol 43.45 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.3 _exptl_crystal_grow.pdbx_details '22-26% PEG 400, 0.1 M Na Hepes buffer pH 7.1 - 8.1, 0.2 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range ? # _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 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2011-10-20 _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 'Double silicon(111) crystal' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9792 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X29A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X29A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9792 # _reflns.entry_id 4J3H _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F -3.0 _reflns.d_resolution_low 35 _reflns.d_resolution_high 1.5 _reflns.number_obs 30293 _reflns.number_all 30293 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.053 _reflns.pdbx_netI_over_sigmaI 38.4 _reflns.B_iso_Wilson_estimate 26 _reflns.pdbx_redundancy 24 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.5 _reflns_shell.d_res_low 1.7 _reflns_shell.percent_possible_all 99.4 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.252 _reflns_shell.meanI_over_sigI_obs 13.3 _reflns_shell.pdbx_redundancy 22 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 9434 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4J3H _refine.ls_number_reflns_obs 30293 _refine.ls_number_reflns_all 30293 _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 33.661 _refine.ls_d_res_high 1.5002 _refine.ls_percent_reflns_obs 99.77 _refine.ls_R_factor_obs 0.1949 _refine.ls_R_factor_all 0.1949 _refine.ls_R_factor_R_work 0.1919 _refine.ls_R_factor_R_free 0.2227 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.05 _refine.ls_number_reflns_R_free 3044 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 0.1764 _refine.aniso_B[2][2] 0.1764 _refine.aniso_B[3][3] -0.3529 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] -0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.360 _refine.solvent_model_param_bsol 41.117 _refine.pdbx_solvent_vdw_probe_radii 1.30 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 1.11 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model Anisotropic _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details Random _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.34 _refine.pdbx_overall_phase_error 17.69 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _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 675 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 80 _refine_hist.number_atoms_total 758 _refine_hist.d_res_high 1.5002 _refine_hist.d_res_low 33.661 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.010 ? ? 701 ? 'X-RAY DIFFRACTION' f_angle_d 1.240 ? ? 937 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 13.461 ? ? 286 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.076 ? ? 101 ? 'X-RAY DIFFRACTION' f_plane_restr 0.005 ? ? 123 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id . 1.5002 1.5236 1264 0.2564 99.00 0.2620 . . 140 . . . . 'X-RAY DIFFRACTION' . 1.5236 1.5486 1193 0.2418 100.00 0.2658 . . 147 . . . . 'X-RAY DIFFRACTION' . 1.5486 1.5753 1232 0.2163 99.00 0.2382 . . 139 . . . . 'X-RAY DIFFRACTION' . 1.5753 1.6039 1236 0.2164 100.00 0.2796 . . 139 . . . . 'X-RAY DIFFRACTION' . 1.6039 1.6348 1242 0.2087 100.00 0.2098 . . 133 . . . . 'X-RAY DIFFRACTION' . 1.6348 1.6681 1235 0.2060 100.00 0.2349 . . 135 . . . . 'X-RAY DIFFRACTION' . 1.6681 1.7044 1257 0.2042 100.00 0.1961 . . 144 . . . . 'X-RAY DIFFRACTION' . 1.7044 1.7441 1221 0.1913 100.00 0.2120 . . 139 . . . . 'X-RAY DIFFRACTION' . 1.7441 1.7877 1245 0.1812 100.00 0.2281 . . 140 . . . . 'X-RAY DIFFRACTION' . 1.7877 1.8360 1221 0.1848 100.00 0.1902 . . 131 . . . . 'X-RAY DIFFRACTION' . 1.8360 1.8900 1252 0.1822 100.00 0.2481 . . 138 . . . . 'X-RAY DIFFRACTION' . 1.8900 1.9510 1246 0.1780 100.00 0.1757 . . 139 . . . . 'X-RAY DIFFRACTION' . 1.9510 2.0208 1221 0.1742 100.00 0.2245 . . 134 . . . . 'X-RAY DIFFRACTION' . 2.0208 2.1017 1261 0.1827 100.00 0.1945 . . 134 . . . . 'X-RAY DIFFRACTION' . 2.1017 2.1973 1233 0.1825 100.00 0.1913 . . 142 . . . . 'X-RAY DIFFRACTION' . 2.1973 2.3131 1247 0.1748 100.00 0.2476 . . 138 . . . . 'X-RAY DIFFRACTION' . 2.3131 2.4580 1237 0.1731 100.00 0.2140 . . 136 . . . . 'X-RAY DIFFRACTION' . 2.4580 2.6477 1237 0.1929 100.00 0.2755 . . 134 . . . . 'X-RAY DIFFRACTION' . 2.6477 2.9140 1252 0.2161 100.00 0.2362 . . 142 . . . . 'X-RAY DIFFRACTION' . 2.9140 3.3354 1220 0.2071 100.00 0.2534 . . 142 . . . . 'X-RAY DIFFRACTION' . 3.3354 4.2009 1262 0.1684 100.00 0.1865 . . 139 . . . . 'X-RAY DIFFRACTION' . 4.2009 33.6697 1235 0.2061 100.00 0.2287 . . 139 . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 4J3H _struct.title 'Ring cycle for dilating and constricting the nuclear pore: structure of a Nup54 homo-tetramer.' _struct.pdbx_descriptor 'Nuclear pore complex protein Nup54' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4J3H _struct_keywords.pdbx_keywords 'TRANSPORT PROTEIN' _struct_keywords.text ;FG-repeat, mid-plane ring, gating, nup, Helical bundle, four helix bundle, transport channel, Nucleoporin, transport, nucleo-cytoplasmic transport, mRNP export, Nup58, Nup62, Karyopherin, Nup45, Nuclear envelope, nuclear pore complex, nucleus, NPC, TRANSPORT PROTEIN ; # 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 1 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 3 ? G N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # 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 ASP A 11 ? GLU A 41 ? ASP A 459 GLU A 489 1 ? 31 HELX_P HELX_P2 2 ASP B 11 ? ASP B 42 ? ASP B 459 ASP B 490 1 ? 32 # _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 covale1 covale ? ? A TYR 9 C ? ? ? 1_555 A MSE 10 N ? ? A TYR 457 A MSE 458 1_555 ? ? ? ? ? ? ? 1.327 ? covale2 covale ? ? A MSE 10 C ? ? ? 1_555 A ASP 11 N ? ? A MSE 458 A ASP 459 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A LEU 32 C ? ? ? 1_555 A MSE 33 N ? ? A LEU 480 A MSE 481 1_555 ? ? ? ? ? ? ? 1.329 ? covale4 covale ? ? A MSE 33 C ? ? ? 1_555 A SER 34 N ? ? A MSE 481 A SER 482 1_555 ? ? ? ? ? ? ? 1.329 ? covale5 covale ? ? B TYR 9 C ? ? ? 1_555 B MSE 10 N ? ? B TYR 457 B MSE 458 1_555 ? ? ? ? ? ? ? 1.333 ? covale6 covale ? ? B MSE 10 C ? ? ? 1_555 B ASP 11 N ? ? B MSE 458 B ASP 459 1_555 ? ? ? ? ? ? ? 1.320 ? covale7 covale ? ? B LEU 32 C ? ? ? 1_555 B MSE 33 N ? ? B LEU 480 B MSE 481 1_555 ? ? ? ? ? ? ? 1.336 ? covale8 covale ? ? B MSE 33 C ? ? ? 1_555 B SER 34 N ? ? B MSE 481 B SER 482 1_555 ? ? ? ? ? ? ? 1.323 ? metalc1 metalc ? ? B ILE 35 O ? ? ? 1_555 E CA . CA ? ? B ILE 483 B CA 501 1_555 ? ? ? ? ? ? ? 2.245 ? metalc2 metalc ? ? A ASP 42 OD1 ? ? ? 1_555 C CA . CA ? ? A ASP 490 A CA 501 1_555 ? ? ? ? ? ? ? 2.309 ? metalc3 metalc ? ? E CA . CA ? ? ? 1_555 G HOH . O ? ? B CA 501 B HOH 604 1_555 ? ? ? ? ? ? ? 2.372 ? metalc4 metalc ? ? B ASP 39 OD2 ? ? ? 1_555 E CA . CA ? ? B ASP 487 B CA 501 1_555 ? ? ? ? ? ? ? 2.373 ? metalc5 metalc ? ? A ASP 39 O ? ? ? 1_555 C CA . CA ? ? A ASP 487 A CA 501 1_555 ? ? ? ? ? ? ? 2.387 ? metalc6 metalc ? ? A ASP 39 OD1 ? ? ? 1_555 C CA . CA ? ? A ASP 487 A CA 501 1_555 ? ? ? ? ? ? ? 2.405 ? metalc7 metalc ? ? B ASP 38 OD1 ? ? ? 1_555 E CA . CA ? ? B ASP 486 B CA 501 1_555 ? ? ? ? ? ? ? 2.427 ? metalc8 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 502 A HOH 605 1_555 ? ? ? ? ? ? ? 2.504 ? metalc9 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 502 A HOH 639 1_555 ? ? ? ? ? ? ? 2.527 ? metalc10 metalc ? ? A ASP 11 OD1 ? ? ? 1_555 D CA . CA ? ? A ASP 459 A CA 502 1_555 ? ? ? ? ? ? ? 2.551 ? metalc11 metalc ? ? A ASP 11 OD2 ? ? ? 1_555 D CA . CA ? ? A ASP 459 A CA 502 1_555 ? ? ? ? ? ? ? 2.584 ? metalc12 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 502 A HOH 601 1_555 ? ? ? ? ? ? ? 2.597 ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # 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 ? ? ? ? 5 'BINDING SITE FOR RESIDUE CA A 501' AC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE CA A 502' AC3 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE CA B 501' # 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 5 ASP A 13 ? ASP A 461 . ? 5_554 ? 2 AC1 5 ASP A 39 ? ASP A 487 . ? 1_555 ? 3 AC1 5 ASP A 42 ? ASP A 490 . ? 1_555 ? 4 AC1 5 HOH F . ? HOH A 632 . ? 5_554 ? 5 AC1 5 HOH F . ? HOH A 634 . ? 5_554 ? 6 AC2 6 ASP A 11 ? ASP A 459 . ? 1_555 ? 7 AC2 6 ASP A 38 ? ASP A 486 . ? 6_555 ? 8 AC2 6 GLU A 41 ? GLU A 489 . ? 6_555 ? 9 AC2 6 HOH F . ? HOH A 601 . ? 1_555 ? 10 AC2 6 HOH F . ? HOH A 605 . ? 1_555 ? 11 AC2 6 HOH F . ? HOH A 639 . ? 1_555 ? 12 AC3 6 LEU A 40 ? LEU A 488 . ? 6_555 ? 13 AC3 6 ASP A 42 ? ASP A 490 . ? 6_555 ? 14 AC3 6 ILE B 35 ? ILE B 483 . ? 1_555 ? 15 AC3 6 ASP B 38 ? ASP B 486 . ? 1_555 ? 16 AC3 6 ASP B 39 ? ASP B 487 . ? 1_555 ? 17 AC3 6 HOH G . ? HOH B 604 . ? 1_555 ? # _database_PDB_matrix.entry_id 4J3H _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 4J3H _atom_sites.fract_transf_matrix[1][1] 0.024201 _atom_sites.fract_transf_matrix[1][2] 0.013973 _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] 0.027945 _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] 0.005040 _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 CA H N O SE # 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 1 449 ? ? ? A . n A 1 2 SER 2 450 ? ? ? A . n A 1 3 HIS 3 451 ? ? ? A . n A 1 4 MSE 4 452 ? ? ? A . n A 1 5 GLU 5 453 453 GLU GLU A . n A 1 6 GLU 6 454 454 GLU GLU A . n A 1 7 LYS 7 455 455 LYS LYS A . n A 1 8 TYR 8 456 456 TYR TYR A . n A 1 9 TYR 9 457 457 TYR TYR A . n A 1 10 MSE 10 458 458 MSE MSE A . n A 1 11 ASP 11 459 459 ASP ASP A . n A 1 12 ALA 12 460 460 ALA ALA A . n A 1 13 ASP 13 461 461 ASP ASP A . n A 1 14 LEU 14 462 462 LEU LEU A . n A 1 15 LEU 15 463 463 LEU LEU A . n A 1 16 ARG 16 464 464 ARG ARG A . n A 1 17 GLU 17 465 465 GLU GLU A . n A 1 18 ILE 18 466 466 ILE ILE A . n A 1 19 LYS 19 467 467 LYS LYS A . n A 1 20 GLN 20 468 468 GLN GLN A . n A 1 21 HIS 21 469 469 HIS HIS A . n A 1 22 LEU 22 470 470 LEU LEU A . n A 1 23 LYS 23 471 471 LYS LYS A . n A 1 24 GLN 24 472 472 GLN GLN A . n A 1 25 GLN 25 473 473 GLN GLN A . n A 1 26 GLN 26 474 474 GLN GLN A . n A 1 27 GLU 27 475 475 GLU GLU A . n A 1 28 GLY 28 476 476 GLY GLY A . n A 1 29 LEU 29 477 477 LEU LEU A . n A 1 30 SER 30 478 478 SER SER A . n A 1 31 HIS 31 479 479 HIS HIS A . n A 1 32 LEU 32 480 480 LEU LEU A . n A 1 33 MSE 33 481 481 MSE MSE A . n A 1 34 SER 34 482 482 SER SER A . n A 1 35 ILE 35 483 483 ILE ILE A . n A 1 36 ILE 36 484 484 ILE ILE A . n A 1 37 LYS 37 485 485 LYS LYS A . n A 1 38 ASP 38 486 486 ASP ASP A . n A 1 39 ASP 39 487 487 ASP ASP A . n A 1 40 LEU 40 488 488 LEU LEU A . n A 1 41 GLU 41 489 489 GLU GLU A . n A 1 42 ASP 42 490 490 ASP ASP A . n A 1 43 ILE 43 491 491 ILE ILE A . n A 1 44 LYS 44 492 492 LYS LYS A . n A 1 45 LEU 45 493 493 LEU LEU A . n A 1 46 VAL 46 494 494 VAL VAL A . n B 1 1 GLY 1 449 ? ? ? B . n B 1 2 SER 2 450 ? ? ? B . n B 1 3 HIS 3 451 ? ? ? B . n B 1 4 MSE 4 452 ? ? ? B . n B 1 5 GLU 5 453 453 GLU GLU B . n B 1 6 GLU 6 454 454 GLU GLU B . n B 1 7 LYS 7 455 455 LYS LYS B . n B 1 8 TYR 8 456 456 TYR TYR B . n B 1 9 TYR 9 457 457 TYR TYR B . n B 1 10 MSE 10 458 458 MSE MSE B . n B 1 11 ASP 11 459 459 ASP ASP B . n B 1 12 ALA 12 460 460 ALA ALA B . n B 1 13 ASP 13 461 461 ASP ASP B . n B 1 14 LEU 14 462 462 LEU LEU B . n B 1 15 LEU 15 463 463 LEU LEU B . n B 1 16 ARG 16 464 464 ARG ARG B . n B 1 17 GLU 17 465 465 GLU GLU B . n B 1 18 ILE 18 466 466 ILE ILE B . n B 1 19 LYS 19 467 467 LYS LYS B . n B 1 20 GLN 20 468 468 GLN GLN B . n B 1 21 HIS 21 469 469 HIS HIS B . n B 1 22 LEU 22 470 470 LEU LEU B . n B 1 23 LYS 23 471 471 LYS LYS B . n B 1 24 GLN 24 472 472 GLN GLN B . n B 1 25 GLN 25 473 473 GLN GLN B . n B 1 26 GLN 26 474 474 GLN GLN B . n B 1 27 GLU 27 475 475 GLU GLU B . n B 1 28 GLY 28 476 476 GLY GLY B . n B 1 29 LEU 29 477 477 LEU LEU B . n B 1 30 SER 30 478 478 SER SER B . n B 1 31 HIS 31 479 479 HIS HIS B . n B 1 32 LEU 32 480 480 LEU LEU B . n B 1 33 MSE 33 481 481 MSE MSE B . n B 1 34 SER 34 482 482 SER SER B . n B 1 35 ILE 35 483 483 ILE ILE B . n B 1 36 ILE 36 484 484 ILE ILE B . n B 1 37 LYS 37 485 485 LYS LYS B . n B 1 38 ASP 38 486 486 ASP ASP B . n B 1 39 ASP 39 487 487 ASP ASP B . n B 1 40 LEU 40 488 488 LEU LEU B . n B 1 41 GLU 41 489 489 GLU GLU B . n B 1 42 ASP 42 490 490 ASP ASP B . n B 1 43 ILE 43 491 ? ? ? B . n B 1 44 LYS 44 492 ? ? ? B . n B 1 45 LEU 45 493 ? ? ? B . n B 1 46 VAL 46 494 ? ? ? B . 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 C 2 CA 1 501 2 CA CA A . D 2 CA 1 502 3 CA CA A . E 2 CA 1 501 1 CA CA B . F 3 HOH 1 601 3 HOH HOH A . F 3 HOH 2 602 7 HOH HOH A . F 3 HOH 3 603 8 HOH HOH A . F 3 HOH 4 604 10 HOH HOH A . F 3 HOH 5 605 11 HOH HOH A . F 3 HOH 6 606 14 HOH HOH A . F 3 HOH 7 607 15 HOH HOH A . F 3 HOH 8 608 16 HOH HOH A . F 3 HOH 9 609 17 HOH HOH A . F 3 HOH 10 610 18 HOH HOH A . F 3 HOH 11 611 19 HOH HOH A . F 3 HOH 12 612 20 HOH HOH A . F 3 HOH 13 613 21 HOH HOH A . F 3 HOH 14 614 28 HOH HOH A . F 3 HOH 15 615 30 HOH HOH A . F 3 HOH 16 616 31 HOH HOH A . F 3 HOH 17 617 32 HOH HOH A . F 3 HOH 18 618 33 HOH HOH A . F 3 HOH 19 619 35 HOH HOH A . F 3 HOH 20 620 36 HOH HOH A . F 3 HOH 21 621 38 HOH HOH A . F 3 HOH 22 622 40 HOH HOH A . F 3 HOH 23 623 52 HOH HOH A . F 3 HOH 24 624 56 HOH HOH A . F 3 HOH 25 625 59 HOH HOH A . F 3 HOH 26 626 61 HOH HOH A . F 3 HOH 27 627 62 HOH HOH A . F 3 HOH 28 628 65 HOH HOH A . F 3 HOH 29 629 67 HOH HOH A . F 3 HOH 30 630 70 HOH HOH A . F 3 HOH 31 631 75 HOH HOH A . F 3 HOH 32 632 76 HOH HOH A . F 3 HOH 33 633 77 HOH HOH A . F 3 HOH 34 634 78 HOH HOH A . F 3 HOH 35 635 82 HOH HOH A . F 3 HOH 36 636 86 HOH HOH A . F 3 HOH 37 637 93 HOH HOH A . F 3 HOH 38 638 120 HOH HOH A . F 3 HOH 39 639 160 HOH HOH A . F 3 HOH 40 640 161 HOH HOH A . F 3 HOH 41 641 162 HOH HOH A . F 3 HOH 42 642 164 HOH HOH A . F 3 HOH 43 643 171 HOH HOH A . G 3 HOH 1 601 4 HOH HOH B . G 3 HOH 2 602 5 HOH HOH B . G 3 HOH 3 603 6 HOH HOH B . G 3 HOH 4 604 9 HOH HOH B . G 3 HOH 5 605 12 HOH HOH B . G 3 HOH 6 606 13 HOH HOH B . G 3 HOH 7 607 23 HOH HOH B . G 3 HOH 8 608 24 HOH HOH B . G 3 HOH 9 609 26 HOH HOH B . G 3 HOH 10 610 27 HOH HOH B . G 3 HOH 11 611 29 HOH HOH B . G 3 HOH 12 612 34 HOH HOH B . G 3 HOH 13 613 37 HOH HOH B . G 3 HOH 14 614 41 HOH HOH B . G 3 HOH 15 615 42 HOH HOH B . G 3 HOH 16 616 44 HOH HOH B . G 3 HOH 17 617 45 HOH HOH B . G 3 HOH 18 618 57 HOH HOH B . G 3 HOH 19 619 58 HOH HOH B . G 3 HOH 20 620 63 HOH HOH B . G 3 HOH 21 621 68 HOH HOH B . G 3 HOH 22 622 72 HOH HOH B . G 3 HOH 23 623 74 HOH HOH B . G 3 HOH 24 624 83 HOH HOH B . G 3 HOH 25 625 84 HOH HOH B . G 3 HOH 26 626 85 HOH HOH B . G 3 HOH 27 627 89 HOH HOH B . G 3 HOH 28 628 90 HOH HOH B . G 3 HOH 29 629 99 HOH HOH B . G 3 HOH 30 630 123 HOH HOH B . G 3 HOH 31 631 163 HOH HOH B . G 3 HOH 32 632 165 HOH HOH B . G 3 HOH 33 633 166 HOH HOH B . G 3 HOH 34 634 168 HOH HOH B . G 3 HOH 35 635 169 HOH HOH B . G 3 HOH 36 636 170 HOH HOH B . G 3 HOH 37 637 172 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 10 A MSE 458 ? MET SELENOMETHIONINE 2 A MSE 33 A MSE 481 ? MET SELENOMETHIONINE 3 B MSE 10 B MSE 458 ? MET SELENOMETHIONINE 4 B MSE 33 B MSE 481 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # 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)' 6620 ? 1 MORE -104 ? 1 'SSA (A^2)' 11700 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 12_566 x,x-y+1,-z+7/6 0.5000000000 0.8660254038 0.0000000000 -20.6600000000 0.8660254038 -0.5000000000 0.0000000000 35.7841696844 0.0000000000 0.0000000000 -1.0000000000 231.4783333333 # 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 O ? B ILE 35 ? B ILE 483 ? 1_555 CA ? E CA . ? B CA 501 ? 1_555 O ? G HOH . ? B HOH 604 ? 1_555 86.7 ? 2 O ? B ILE 35 ? B ILE 483 ? 1_555 CA ? E CA . ? B CA 501 ? 1_555 OD2 ? B ASP 39 ? B ASP 487 ? 1_555 89.5 ? 3 O ? G HOH . ? B HOH 604 ? 1_555 CA ? E CA . ? B CA 501 ? 1_555 OD2 ? B ASP 39 ? B ASP 487 ? 1_555 163.4 ? 4 O ? B ILE 35 ? B ILE 483 ? 1_555 CA ? E CA . ? B CA 501 ? 1_555 OD1 ? B ASP 38 ? B ASP 486 ? 1_555 96.1 ? 5 O ? G HOH . ? B HOH 604 ? 1_555 CA ? E CA . ? B CA 501 ? 1_555 OD1 ? B ASP 38 ? B ASP 486 ? 1_555 83.2 ? 6 OD2 ? B ASP 39 ? B ASP 487 ? 1_555 CA ? E CA . ? B CA 501 ? 1_555 OD1 ? B ASP 38 ? B ASP 486 ? 1_555 81.1 ? 7 OD1 ? A ASP 42 ? A ASP 490 ? 1_555 CA ? C CA . ? A CA 501 ? 1_555 O ? A ASP 39 ? A ASP 487 ? 1_555 83.5 ? 8 OD1 ? A ASP 42 ? A ASP 490 ? 1_555 CA ? C CA . ? A CA 501 ? 1_555 OD1 ? A ASP 39 ? A ASP 487 ? 1_555 154.1 ? 9 O ? A ASP 39 ? A ASP 487 ? 1_555 CA ? C CA . ? A CA 501 ? 1_555 OD1 ? A ASP 39 ? A ASP 487 ? 1_555 71.7 ? 10 O ? F HOH . ? A HOH 605 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 O ? F HOH . ? A HOH 639 ? 1_555 101.6 ? 11 O ? F HOH . ? A HOH 605 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 OD1 ? A ASP 11 ? A ASP 459 ? 1_555 77.6 ? 12 O ? F HOH . ? A HOH 639 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 OD1 ? A ASP 11 ? A ASP 459 ? 1_555 93.2 ? 13 O ? F HOH . ? A HOH 605 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 OD2 ? A ASP 11 ? A ASP 459 ? 1_555 127.3 ? 14 O ? F HOH . ? A HOH 639 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 OD2 ? A ASP 11 ? A ASP 459 ? 1_555 85.8 ? 15 OD1 ? A ASP 11 ? A ASP 459 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 OD2 ? A ASP 11 ? A ASP 459 ? 1_555 49.8 ? 16 O ? F HOH . ? A HOH 605 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 O ? F HOH . ? A HOH 601 ? 1_555 65.7 ? 17 O ? F HOH . ? A HOH 639 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 O ? F HOH . ? A HOH 601 ? 1_555 91.6 ? 18 OD1 ? A ASP 11 ? A ASP 459 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 O ? F HOH . ? A HOH 601 ? 1_555 143.2 ? 19 OD2 ? A ASP 11 ? A ASP 459 ? 1_555 CA ? D CA . ? A CA 502 ? 1_555 O ? F HOH . ? A HOH 601 ? 1_555 167.0 ? # 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 2013-04-10 2 'Structure model' 1 1 2013-04-17 # _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 ? # 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' 'Structure summary' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 0.0690 39.4392 130.3270 0.1622 0.1258 0.1708 0.0019 0.0329 0.0221 0.8671 0.3838 0.7172 -0.0887 -0.1913 0.5542 0.0597 -0.0657 -0.0345 -0.1545 0.0215 0.3942 -0.1204 -0.0901 -0.0032 'X-RAY DIFFRACTION' 2 ? refined 13.0815 29.4968 121.5124 0.1587 0.1884 0.2415 -0.0233 0.0894 -0.0834 5.7128 5.5150 6.7713 -3.1529 -5.4379 2.7350 -0.4254 -0.3378 -0.5689 0.3440 0.4785 -0.7921 0.3932 0.7101 0.0175 'X-RAY DIFFRACTION' 3 ? refined 22.2747 24.2793 107.6354 0.1839 0.2143 0.2327 -0.0193 0.0614 -0.0834 6.5139 2.9006 7.6088 -1.7496 -4.3370 1.7805 -0.0790 -0.6599 0.4184 0.2035 0.3797 -0.1677 -0.2475 0.5067 -0.2241 'X-RAY DIFFRACTION' 4 ? refined 33.0357 26.3222 98.7180 0.1908 0.1108 0.3459 -0.0087 0.0867 -0.0792 7.1495 5.2560 1.3165 5.9241 0.9846 0.2020 0.2548 -0.3824 0.8196 0.4255 -0.2077 0.1046 -0.3379 -0.2601 0.0739 'X-RAY DIFFRACTION' 5 ? refined 17.2699 15.6654 97.7067 0.2098 0.1933 0.1601 0.0345 -0.0325 -0.0361 3.4322 4.0221 1.3007 2.7062 0.2986 1.7432 0.0120 0.1356 -0.2777 -0.6164 0.0052 0.3239 -0.0138 0.0579 0.0375 'X-RAY DIFFRACTION' 6 ? refined 13.9262 16.9324 113.1248 0.1476 0.1891 0.0999 0.0393 -0.0063 0.0205 7.1275 4.5267 5.7591 -3.2376 -4.7194 3.4432 -0.3411 -0.8104 -0.4043 0.4464 0.2750 0.0313 0.5688 0.5623 0.0342 'X-RAY DIFFRACTION' 7 ? refined 2.2700 24.9233 121.5887 0.1315 0.1951 0.0790 -0.0025 0.0077 -0.0190 3.0781 1.5680 8.2547 0.5703 -4.2075 0.9900 -0.0570 0.1921 0.0074 -0.0759 0.1269 -0.0044 -0.1613 -0.3777 -0.0257 'X-RAY DIFFRACTION' 8 ? refined -8.2364 32.3900 126.1671 0.2389 0.3426 0.3383 0.0263 -0.0325 0.0350 9.4295 4.0966 4.3298 -5.0228 -6.3713 3.4820 0.2221 0.8718 -0.1382 -0.6010 -0.0363 1.3166 -0.3746 -1.2332 -0.1990 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? ;chain 'A' and resseq 453:466 ; 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? ;chain 'A' and resseq 467:478 ; 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? ;chain 'A' and resseq 479:489 ; 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? ;chain 'A' and resseq 490:494 ; 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? ;chain 'B' and resseq 453:459 ; 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? ;chain 'B' and resseq 460:472 ; 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? ;chain 'B' and resseq 473:482 ; 'X-RAY DIFFRACTION' 8 8 ? ? ? ? ? ? ? ? ? ;chain 'B' and resseq 483:490 ; # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 PHENIX 'model building' . ? 2 PHENIX refinement '(phenix.refine: 1.7.2_869)' ? 3 XDS 'data reduction' . ? 4 XSCALE 'data scaling' . ? 5 PHENIX phasing . ? 6 # 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 B HOH 623 ? ? O B HOH 633 ? ? 2.08 2 1 OE1 B GLN 473 ? A O B HOH 601 ? ? 2.15 3 1 O B HOH 635 ? ? O B HOH 636 ? ? 2.17 4 1 OD2 A ASP 487 ? ? O A HOH 612 ? ? 2.19 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 OE1 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 GLN _pdbx_validate_symm_contact.auth_seq_id_1 473 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 A _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 601 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 12_566 _pdbx_validate_symm_contact.dist 2.07 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id GLU _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 454 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -140.76 _pdbx_validate_torsion.psi -20.41 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 0 A GLU 453 ? CB ? A GLU 5 CB 2 1 Y 0 A GLU 453 ? CG ? A GLU 5 CG 3 1 Y 0 A GLU 453 ? CD ? A GLU 5 CD 4 1 Y 0 A GLU 453 ? OE1 ? A GLU 5 OE1 5 1 Y 0 A GLU 453 ? OE2 ? A GLU 5 OE2 6 1 Y 0 A GLU 454 ? CD ? A GLU 6 CD 7 1 Y 0 A GLU 454 ? OE1 ? A GLU 6 OE1 8 1 Y 0 A GLU 454 ? OE2 ? A GLU 6 OE2 9 1 Y 0 B GLU 453 ? CB ? B GLU 5 CB 10 1 Y 0 B GLU 453 ? CG ? B GLU 5 CG 11 1 Y 0 B GLU 453 ? CD ? B GLU 5 CD 12 1 Y 0 B GLU 453 ? OE1 ? B GLU 5 OE1 13 1 Y 0 B GLU 453 ? OE2 ? B GLU 5 OE2 14 1 Y 0 B ASP 490 ? CB ? B ASP 42 CB 15 1 Y 0 B ASP 490 ? CG ? B ASP 42 CG 16 1 Y 0 B ASP 490 ? OD1 ? B ASP 42 OD1 17 1 Y 0 B ASP 490 ? OD2 ? B ASP 42 OD2 # 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 449 ? A GLY 1 2 1 Y 1 A SER 450 ? A SER 2 3 1 Y 1 A HIS 451 ? A HIS 3 4 1 Y 1 A MSE 452 ? A MSE 4 5 1 Y 1 B GLY 449 ? B GLY 1 6 1 Y 1 B SER 450 ? B SER 2 7 1 Y 1 B HIS 451 ? B HIS 3 8 1 Y 1 B MSE 452 ? B MSE 4 9 1 Y 1 B ILE 491 ? B ILE 43 10 1 Y 1 B LYS 492 ? B LYS 44 11 1 Y 1 B LEU 493 ? B LEU 45 12 1 Y 1 B VAL 494 ? B VAL 46 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 water HOH #