data_4NQF # _entry.id 4NQF # _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 4NQF RCSB RCSB083526 WWPDB D_1000083526 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4NQF _pdbx_database_status.recvd_initial_deposition_date 2013-11-25 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _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.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Padavannil, A.' 1 'Jobichen, C.' 2 'Sivaraman, J.' 3 # _citation.id primary _citation.title 'Dimerization of VirD2 Binding Protein Is Essential for Agrobacterium Induced Tumor Formation in Plants' _citation.journal_abbrev 'Plos Pathog.' _citation.journal_volume 10 _citation.page_first e1003948 _citation.page_last e1003948 _citation.year 2014 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1553-7366 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24626239 _citation.pdbx_database_id_DOI 10.1371/journal.ppat.1003948 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Padavannil, A.' 1 primary 'Jobichen, C.' 2 primary 'Qinghua, Y.' 3 primary 'Seetharaman, J.' 4 primary 'Velazquez-campoy, A.' 5 primary 'Yang, L.' 6 primary 'Pan, S.Q.' 7 primary 'Sivaraman, J.' 8 # _cell.entry_id 4NQF _cell.length_a 63.103 _cell.length_b 71.574 _cell.length_c 83.416 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 4NQF _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 Nucleotidyltransferase 18532.447 2 ? 'L168M, L219M, L251M' 'UNP residues 151-308' ? 2 water nat water 18.015 26 ? ? ? ? # _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 ;LSPADALRVAEDHFLRH(MSE)PDARDFADVAKYLVAKGNLHLAAFNLHQAVETAYNCYLLTLTNYSPASHN(MSE)KFL RGLSEGRDRRLIDIWPRDRQRFTTWYNI(MSE)NEAYVKARYSKRFEVSEEALTWLQERTAELHKLVETLCREHIEKLEH AAGQAANSSD ; _entity_poly.pdbx_seq_one_letter_code_can ;LSPADALRVAEDHFLRHMPDARDFADVAKYLVAKGNLHLAAFNLHQAVETAYNCYLLTLTNYSPASHNMKFLRGLSEGRD RRLIDIWPRDRQRFTTWYNIMNEAYVKARYSKRFEVSEEALTWLQERTAELHKLVETLCREHIEKLEHAAGQAANSSD ; _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 LEU n 1 2 SER n 1 3 PRO n 1 4 ALA n 1 5 ASP n 1 6 ALA n 1 7 LEU n 1 8 ARG n 1 9 VAL n 1 10 ALA n 1 11 GLU n 1 12 ASP n 1 13 HIS n 1 14 PHE n 1 15 LEU n 1 16 ARG n 1 17 HIS n 1 18 MSE n 1 19 PRO n 1 20 ASP n 1 21 ALA n 1 22 ARG n 1 23 ASP n 1 24 PHE n 1 25 ALA n 1 26 ASP n 1 27 VAL n 1 28 ALA n 1 29 LYS n 1 30 TYR n 1 31 LEU n 1 32 VAL n 1 33 ALA n 1 34 LYS n 1 35 GLY n 1 36 ASN n 1 37 LEU n 1 38 HIS n 1 39 LEU n 1 40 ALA n 1 41 ALA n 1 42 PHE n 1 43 ASN n 1 44 LEU n 1 45 HIS n 1 46 GLN n 1 47 ALA n 1 48 VAL n 1 49 GLU n 1 50 THR n 1 51 ALA n 1 52 TYR n 1 53 ASN n 1 54 CYS n 1 55 TYR n 1 56 LEU n 1 57 LEU n 1 58 THR n 1 59 LEU n 1 60 THR n 1 61 ASN n 1 62 TYR n 1 63 SER n 1 64 PRO n 1 65 ALA n 1 66 SER n 1 67 HIS n 1 68 ASN n 1 69 MSE n 1 70 LYS n 1 71 PHE n 1 72 LEU n 1 73 ARG n 1 74 GLY n 1 75 LEU n 1 76 SER n 1 77 GLU n 1 78 GLY n 1 79 ARG n 1 80 ASP n 1 81 ARG n 1 82 ARG n 1 83 LEU n 1 84 ILE n 1 85 ASP n 1 86 ILE n 1 87 TRP n 1 88 PRO n 1 89 ARG n 1 90 ASP n 1 91 ARG n 1 92 GLN n 1 93 ARG n 1 94 PHE n 1 95 THR n 1 96 THR n 1 97 TRP n 1 98 TYR n 1 99 ASN n 1 100 ILE n 1 101 MSE n 1 102 ASN n 1 103 GLU n 1 104 ALA n 1 105 TYR n 1 106 VAL n 1 107 LYS n 1 108 ALA n 1 109 ARG n 1 110 TYR n 1 111 SER n 1 112 LYS n 1 113 ARG n 1 114 PHE n 1 115 GLU n 1 116 VAL n 1 117 SER n 1 118 GLU n 1 119 GLU n 1 120 ALA n 1 121 LEU n 1 122 THR n 1 123 TRP n 1 124 LEU n 1 125 GLN n 1 126 GLU n 1 127 ARG n 1 128 THR n 1 129 ALA n 1 130 GLU n 1 131 LEU n 1 132 HIS n 1 133 LYS n 1 134 LEU n 1 135 VAL n 1 136 GLU n 1 137 THR n 1 138 LEU n 1 139 CYS n 1 140 ARG n 1 141 GLU n 1 142 HIS n 1 143 ILE n 1 144 GLU n 1 145 LYS n 1 146 LEU n 1 147 GLU n 1 148 HIS n 1 149 ALA n 1 150 ALA n 1 151 GLY n 1 152 GLN n 1 153 ALA n 1 154 ALA n 1 155 ASN n 1 156 SER n 1 157 SER n 1 158 ASP 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 Atu4856 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'C58 / ATCC 33970' _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 'Agrobacterium fabrum' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 176299 _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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q7CW19_AGRT5 _struct_ref.pdbx_db_accession Q7CW19 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;LSPADALRVAEDHFLRHLPDARDFADVAKYLVAKGNLHLAAFNLHQAVETAYNCYLLTLTNYSPASHNLKFLRGLSEGRD RRLIDIWPRDRQRFTTWYNILNEAYVKARYSKRFEVSEEALTWLQERTAELHKLVETLCREHIEKLEHAAGQAANSSD ; _struct_ref.pdbx_align_begin 151 _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 4NQF A 1 ? 158 ? Q7CW19 151 ? 308 ? 151 308 2 1 4NQF B 1 ? 158 ? Q7CW19 151 ? 308 ? 151 308 # 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 4NQF MSE A 18 ? UNP Q7CW19 LEU 168 'ENGINEERED MUTATION' 168 1 1 4NQF MSE A 69 ? UNP Q7CW19 LEU 219 'ENGINEERED MUTATION' 219 2 1 4NQF MSE A 101 ? UNP Q7CW19 LEU 251 'ENGINEERED MUTATION' 251 3 2 4NQF MSE B 18 ? UNP Q7CW19 LEU 168 'ENGINEERED MUTATION' 168 4 2 4NQF MSE B 69 ? UNP Q7CW19 LEU 219 'ENGINEERED MUTATION' 219 5 2 4NQF MSE B 101 ? UNP Q7CW19 LEU 251 'ENGINEERED MUTATION' 251 6 # 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 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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 4NQF _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.54 _exptl_crystal.density_percent_sol 51.60 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details '8% Polyethylene glycol 3350, 100mM Imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _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 315' _diffrn_detector.pdbx_collection_date 2011-05-19 _diffrn_detector.details Mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9798 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X6A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X6A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9798 # _reflns.entry_id 4NQF _reflns.observed_criterion_sigma_I 1 _reflns.observed_criterion_sigma_F 1 _reflns.d_resolution_low 36.04 _reflns.d_resolution_high 2.7 _reflns.number_obs 10678 _reflns.number_all 10678 _reflns.percent_possible_obs 99.04 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.05 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.5 _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 2.7 _reflns_shell.d_res_low 36.04 _reflns_shell.percent_possible_all 99 _reflns_shell.Rmerge_I_obs 0.05 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 7.5 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4NQF _refine.ls_number_reflns_obs 9671 _refine.ls_number_reflns_all 9671 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 36.04 _refine.ls_d_res_high 2.70 _refine.ls_percent_reflns_obs 99.04 _refine.ls_R_factor_obs 0.22395 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21760 _refine.ls_R_factor_R_free 0.28005 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 1075 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.936 _refine.correlation_coeff_Fo_to_Fc_free 0.907 _refine.B_iso_mean 66.507 _refine.aniso_B[1][1] 0.86 _refine.aniso_B[2][2] 2.00 _refine.aniso_B[3][3] -2.85 _refine.aniso_B[1][2] 0.00 _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' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _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 ? _refine.pdbx_overall_ESU_R_Free 0.396 _refine.overall_SU_ML 0.261 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 12.632 _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 2427 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 26 _refine_hist.number_atoms_total 2453 _refine_hist.d_res_high 2.70 _refine_hist.d_res_low 36.04 # 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 r_bond_refined_d 0.011 0.019 ? 2486 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.004 0.020 ? 2337 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.372 1.940 ? 3370 ? 'X-RAY DIFFRACTION' r_angle_other_deg 1.001 3.000 ? 5329 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 6.803 5.000 ? 294 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 37.650 22.556 ? 133 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 18.629 15.000 ? 395 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 15.126 15.000 ? 26 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.077 0.200 ? 364 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.007 0.020 ? 2822 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.004 0.020 ? 642 ? 'X-RAY DIFFRACTION' r_mcbond_it 5.053 6.407 ? 1182 ? 'X-RAY DIFFRACTION' r_mcbond_other 5.047 6.404 ? 1181 ? 'X-RAY DIFFRACTION' r_mcangle_it 7.594 9.596 ? 1474 ? 'X-RAY DIFFRACTION' r_mcangle_other 7.592 9.600 ? 1475 ? 'X-RAY DIFFRACTION' r_scbond_it 5.092 6.838 ? 1304 ? 'X-RAY DIFFRACTION' r_scbond_other 5.091 6.841 ? 1305 ? 'X-RAY DIFFRACTION' r_scangle_other 7.977 10.069 ? 1897 ? 'X-RAY DIFFRACTION' r_long_range_B_refined 10.553 51.256 ? 2922 ? 'X-RAY DIFFRACTION' r_long_range_B_other 10.553 51.260 ? 2918 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.pdbx_refine_id _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso 1 A 8220 0.11 0.05 'interatomic distance' 1 1 'X-RAY DIFFRACTION' ? ? ? 2 B 8220 0.11 0.05 'interatomic distance' 1 2 '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 2.700 _refine_ls_shell.d_res_low 2.770 _refine_ls_shell.number_reflns_R_work 692 _refine_ls_shell.R_factor_R_work 0.270 _refine_ls_shell.percent_reflns_obs 99.10 _refine_ls_shell.R_factor_R_free 0.369 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 77 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # loop_ _struct_ncs_dom.id _struct_ncs_dom.details _struct_ncs_dom.pdbx_ens_id 1 A 1 2 B 1 # loop_ _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.selection_details 1 A 151 A 294 0 0 ? ? ? ? ? ? ? ? 1 ? 2 B 151 B 294 0 0 ? ? ? ? ? ? ? ? 1 ? # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _struct.entry_id 4NQF _struct.title 'Crystal structure of HEPN domain protein' _struct.pdbx_descriptor Nucleotidyltransferase _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NQF _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text 'HEPN domain, Nucleotidyltransferase activity, TRANSFERASE' # 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 ? # _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 SER A 2 ? GLY A 35 ? SER A 152 GLY A 185 1 ? 34 HELX_P HELX_P2 2 ASN A 36 ? ASN A 61 ? ASN A 186 ASN A 211 1 ? 26 HELX_P HELX_P3 3 ASN A 68 ? ASP A 80 ? ASN A 218 ASP A 230 1 ? 13 HELX_P HELX_P4 4 ARG A 81 ? ASP A 85 ? ARG A 231 ASP A 235 5 ? 5 HELX_P HELX_P5 5 GLN A 92 ? LYS A 107 ? GLN A 242 LYS A 257 1 ? 16 HELX_P HELX_P6 6 SER A 117 ? HIS A 142 ? SER A 267 HIS A 292 1 ? 26 HELX_P HELX_P7 7 SER B 2 ? LYS B 34 ? SER B 152 LYS B 184 1 ? 33 HELX_P HELX_P8 8 ASN B 36 ? ASN B 61 ? ASN B 186 ASN B 211 1 ? 26 HELX_P HELX_P9 9 ASN B 68 ? ASP B 80 ? ASN B 218 ASP B 230 1 ? 13 HELX_P HELX_P10 10 ARG B 81 ? TRP B 87 ? ARG B 231 TRP B 237 5 ? 7 HELX_P HELX_P11 11 GLN B 92 ? LYS B 107 ? GLN B 242 LYS B 257 1 ? 16 HELX_P HELX_P12 12 SER B 117 ? HIS B 142 ? SER B 267 HIS B 292 1 ? 26 # _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 HIS 17 C ? ? ? 1_555 A MSE 18 N ? ? A HIS 167 A MSE 168 1_555 ? ? ? ? ? ? ? 1.314 ? covale2 covale ? ? A MSE 18 C ? ? ? 1_555 A PRO 19 N ? ? A MSE 168 A PRO 169 1_555 ? ? ? ? ? ? ? 1.338 ? covale3 covale ? ? A ASN 68 C ? ? ? 1_555 A MSE 69 N ? ? A ASN 218 A MSE 219 1_555 ? ? ? ? ? ? ? 1.332 ? covale4 covale ? ? A ILE 100 C ? ? ? 1_555 A MSE 101 N ? ? A ILE 250 A MSE 251 1_555 ? ? ? ? ? ? ? 1.322 ? covale5 covale ? ? A MSE 101 C ? ? ? 1_555 A ASN 102 N ? ? A MSE 251 A ASN 252 1_555 ? ? ? ? ? ? ? 1.321 ? covale6 covale ? ? B HIS 17 C ? ? ? 1_555 B MSE 18 N ? ? B HIS 167 B MSE 168 1_555 ? ? ? ? ? ? ? 1.313 ? covale7 covale ? ? B MSE 18 C ? ? ? 1_555 B PRO 19 N ? ? B MSE 168 B PRO 169 1_555 ? ? ? ? ? ? ? 1.329 ? covale8 covale ? ? B ASN 68 C ? ? ? 1_555 B MSE 69 N ? ? B ASN 218 B MSE 219 1_555 ? ? ? ? ? ? ? 1.328 ? covale9 covale ? ? B ILE 100 C ? ? ? 1_555 B MSE 101 N ? ? B ILE 250 B MSE 251 1_555 ? ? ? ? ? ? ? 1.321 ? covale10 covale ? ? B MSE 101 C ? ? ? 1_555 B ASN 102 N ? ? B MSE 251 B ASN 252 1_555 ? ? ? ? ? ? ? 1.328 ? covale11 covale ? ? A MSE 69 C ? ? ? 1_555 A LYS 70 N ? ? A MSE 219 A LYS 220 1_555 ? ? ? ? ? ? ? 1.336 ? covale12 covale ? ? B MSE 69 C ? ? ? 1_555 B LYS 70 N ? ? B MSE 219 B LYS 220 1_555 ? ? ? ? ? ? ? 1.338 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 4NQF _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 4NQF _atom_sites.fract_transf_matrix[1][1] 0.015847 _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] 0.013972 _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] 0.011988 _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 S 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 LEU 1 151 151 LEU LEU A . n A 1 2 SER 2 152 152 SER SER A . n A 1 3 PRO 3 153 153 PRO PRO A . n A 1 4 ALA 4 154 154 ALA ALA A . n A 1 5 ASP 5 155 155 ASP ASP A . n A 1 6 ALA 6 156 156 ALA ALA A . n A 1 7 LEU 7 157 157 LEU LEU A . n A 1 8 ARG 8 158 158 ARG ARG A . n A 1 9 VAL 9 159 159 VAL VAL A . n A 1 10 ALA 10 160 160 ALA ALA A . n A 1 11 GLU 11 161 161 GLU GLU A . n A 1 12 ASP 12 162 162 ASP ASP A . n A 1 13 HIS 13 163 163 HIS HIS A . n A 1 14 PHE 14 164 164 PHE PHE A . n A 1 15 LEU 15 165 165 LEU LEU A . n A 1 16 ARG 16 166 166 ARG ARG A . n A 1 17 HIS 17 167 167 HIS HIS A . n A 1 18 MSE 18 168 168 MSE MSE A . n A 1 19 PRO 19 169 169 PRO PRO A . n A 1 20 ASP 20 170 170 ASP ASP A . n A 1 21 ALA 21 171 171 ALA ALA A . n A 1 22 ARG 22 172 172 ARG ARG A . n A 1 23 ASP 23 173 173 ASP ASP A . n A 1 24 PHE 24 174 174 PHE PHE A . n A 1 25 ALA 25 175 175 ALA ALA A . n A 1 26 ASP 26 176 176 ASP ASP A . n A 1 27 VAL 27 177 177 VAL VAL A . n A 1 28 ALA 28 178 178 ALA ALA A . n A 1 29 LYS 29 179 179 LYS LYS A . n A 1 30 TYR 30 180 180 TYR TYR A . n A 1 31 LEU 31 181 181 LEU LEU A . n A 1 32 VAL 32 182 182 VAL VAL A . n A 1 33 ALA 33 183 183 ALA ALA A . n A 1 34 LYS 34 184 184 LYS LYS A . n A 1 35 GLY 35 185 185 GLY GLY A . n A 1 36 ASN 36 186 186 ASN ASN A . n A 1 37 LEU 37 187 187 LEU LEU A . n A 1 38 HIS 38 188 188 HIS HIS A . n A 1 39 LEU 39 189 189 LEU LEU A . n A 1 40 ALA 40 190 190 ALA ALA A . n A 1 41 ALA 41 191 191 ALA ALA A . n A 1 42 PHE 42 192 192 PHE PHE A . n A 1 43 ASN 43 193 193 ASN ASN A . n A 1 44 LEU 44 194 194 LEU LEU A . n A 1 45 HIS 45 195 195 HIS HIS A . n A 1 46 GLN 46 196 196 GLN GLN A . n A 1 47 ALA 47 197 197 ALA ALA A . n A 1 48 VAL 48 198 198 VAL VAL A . n A 1 49 GLU 49 199 199 GLU GLU A . n A 1 50 THR 50 200 200 THR THR A . n A 1 51 ALA 51 201 201 ALA ALA A . n A 1 52 TYR 52 202 202 TYR TYR A . n A 1 53 ASN 53 203 203 ASN ASN A . n A 1 54 CYS 54 204 204 CYS CYS A . n A 1 55 TYR 55 205 205 TYR TYR A . n A 1 56 LEU 56 206 206 LEU LEU A . n A 1 57 LEU 57 207 207 LEU LEU A . n A 1 58 THR 58 208 208 THR THR A . n A 1 59 LEU 59 209 209 LEU LEU A . n A 1 60 THR 60 210 210 THR THR A . n A 1 61 ASN 61 211 211 ASN ASN A . n A 1 62 TYR 62 212 212 TYR TYR A . n A 1 63 SER 63 213 213 SER SER A . n A 1 64 PRO 64 214 214 PRO PRO A . n A 1 65 ALA 65 215 215 ALA ALA A . n A 1 66 SER 66 216 216 SER SER A . n A 1 67 HIS 67 217 217 HIS HIS A . n A 1 68 ASN 68 218 218 ASN ASN A . n A 1 69 MSE 69 219 219 MSE MSE A . n A 1 70 LYS 70 220 220 LYS ALA A . n A 1 71 PHE 71 221 221 PHE PHE A . n A 1 72 LEU 72 222 222 LEU LEU A . n A 1 73 ARG 73 223 223 ARG ARG A . n A 1 74 GLY 74 224 224 GLY GLY A . n A 1 75 LEU 75 225 225 LEU LEU A . n A 1 76 SER 76 226 226 SER SER A . n A 1 77 GLU 77 227 227 GLU GLU A . n A 1 78 GLY 78 228 228 GLY GLY A . n A 1 79 ARG 79 229 229 ARG ARG A . n A 1 80 ASP 80 230 230 ASP ASP A . n A 1 81 ARG 81 231 231 ARG ALA A . n A 1 82 ARG 82 232 232 ARG ARG A . n A 1 83 LEU 83 233 233 LEU LEU A . n A 1 84 ILE 84 234 234 ILE ILE A . n A 1 85 ASP 85 235 235 ASP ASP A . n A 1 86 ILE 86 236 236 ILE ILE A . n A 1 87 TRP 87 237 237 TRP TRP A . n A 1 88 PRO 88 238 238 PRO PRO A . n A 1 89 ARG 89 239 239 ARG ARG A . n A 1 90 ASP 90 240 240 ASP ASP A . n A 1 91 ARG 91 241 241 ARG ARG A . n A 1 92 GLN 92 242 242 GLN GLN A . n A 1 93 ARG 93 243 243 ARG ARG A . n A 1 94 PHE 94 244 244 PHE PHE A . n A 1 95 THR 95 245 245 THR THR A . n A 1 96 THR 96 246 246 THR THR A . n A 1 97 TRP 97 247 247 TRP TRP A . n A 1 98 TYR 98 248 248 TYR TYR A . n A 1 99 ASN 99 249 249 ASN ASN A . n A 1 100 ILE 100 250 250 ILE ILE A . n A 1 101 MSE 101 251 251 MSE MSE A . n A 1 102 ASN 102 252 252 ASN ASN A . n A 1 103 GLU 103 253 253 GLU GLU A . n A 1 104 ALA 104 254 254 ALA ALA A . n A 1 105 TYR 105 255 255 TYR TYR A . n A 1 106 VAL 106 256 256 VAL VAL A . n A 1 107 LYS 107 257 257 LYS LYS A . n A 1 108 ALA 108 258 258 ALA ALA A . n A 1 109 ARG 109 259 259 ARG ARG A . n A 1 110 TYR 110 260 260 TYR TYR A . n A 1 111 SER 111 261 261 SER SER A . n A 1 112 LYS 112 262 262 LYS LYS A . n A 1 113 ARG 113 263 263 ARG ARG A . n A 1 114 PHE 114 264 264 PHE PHE A . n A 1 115 GLU 115 265 265 GLU GLU A . n A 1 116 VAL 116 266 266 VAL VAL A . n A 1 117 SER 117 267 267 SER SER A . n A 1 118 GLU 118 268 268 GLU GLU A . n A 1 119 GLU 119 269 269 GLU GLU A . n A 1 120 ALA 120 270 270 ALA ALA A . n A 1 121 LEU 121 271 271 LEU LEU A . n A 1 122 THR 122 272 272 THR THR A . n A 1 123 TRP 123 273 273 TRP TRP A . n A 1 124 LEU 124 274 274 LEU LEU A . n A 1 125 GLN 125 275 275 GLN GLN A . n A 1 126 GLU 126 276 276 GLU GLU A . n A 1 127 ARG 127 277 277 ARG ARG A . n A 1 128 THR 128 278 278 THR THR A . n A 1 129 ALA 129 279 279 ALA ALA A . n A 1 130 GLU 130 280 280 GLU GLU A . n A 1 131 LEU 131 281 281 LEU LEU A . n A 1 132 HIS 132 282 282 HIS HIS A . n A 1 133 LYS 133 283 283 LYS LYS A . n A 1 134 LEU 134 284 284 LEU LEU A . n A 1 135 VAL 135 285 285 VAL VAL A . n A 1 136 GLU 136 286 286 GLU GLU A . n A 1 137 THR 137 287 287 THR THR A . n A 1 138 LEU 138 288 288 LEU LEU A . n A 1 139 CYS 139 289 289 CYS CYS A . n A 1 140 ARG 140 290 290 ARG ARG A . n A 1 141 GLU 141 291 291 GLU GLU A . n A 1 142 HIS 142 292 292 HIS HIS A . n A 1 143 ILE 143 293 293 ILE ILE A . n A 1 144 GLU 144 294 294 GLU GLU A . n A 1 145 LYS 145 295 295 LYS LYS A . n A 1 146 LEU 146 296 ? ? ? A . n A 1 147 GLU 147 297 ? ? ? A . n A 1 148 HIS 148 298 ? ? ? A . n A 1 149 ALA 149 299 ? ? ? A . n A 1 150 ALA 150 300 ? ? ? A . n A 1 151 GLY 151 301 ? ? ? A . n A 1 152 GLN 152 302 ? ? ? A . n A 1 153 ALA 153 303 ? ? ? A . n A 1 154 ALA 154 304 ? ? ? A . n A 1 155 ASN 155 305 ? ? ? A . n A 1 156 SER 156 306 ? ? ? A . n A 1 157 SER 157 307 ? ? ? A . n A 1 158 ASP 158 308 ? ? ? A . n B 1 1 LEU 1 151 151 LEU LEU B . n B 1 2 SER 2 152 152 SER SER B . n B 1 3 PRO 3 153 153 PRO PRO B . n B 1 4 ALA 4 154 154 ALA ALA B . n B 1 5 ASP 5 155 155 ASP ASP B . n B 1 6 ALA 6 156 156 ALA ALA B . n B 1 7 LEU 7 157 157 LEU LEU B . n B 1 8 ARG 8 158 158 ARG ARG B . n B 1 9 VAL 9 159 159 VAL VAL B . n B 1 10 ALA 10 160 160 ALA ALA B . n B 1 11 GLU 11 161 161 GLU GLU B . n B 1 12 ASP 12 162 162 ASP ASP B . n B 1 13 HIS 13 163 163 HIS HIS B . n B 1 14 PHE 14 164 164 PHE PHE B . n B 1 15 LEU 15 165 165 LEU LEU B . n B 1 16 ARG 16 166 166 ARG ARG B . n B 1 17 HIS 17 167 167 HIS HIS B . n B 1 18 MSE 18 168 168 MSE MSE B . n B 1 19 PRO 19 169 169 PRO PRO B . n B 1 20 ASP 20 170 170 ASP ASP B . n B 1 21 ALA 21 171 171 ALA ALA B . n B 1 22 ARG 22 172 172 ARG ARG B . n B 1 23 ASP 23 173 173 ASP ASP B . n B 1 24 PHE 24 174 174 PHE PHE B . n B 1 25 ALA 25 175 175 ALA ALA B . n B 1 26 ASP 26 176 176 ASP ASP B . n B 1 27 VAL 27 177 177 VAL VAL B . n B 1 28 ALA 28 178 178 ALA ALA B . n B 1 29 LYS 29 179 179 LYS LYS B . n B 1 30 TYR 30 180 180 TYR TYR B . n B 1 31 LEU 31 181 181 LEU LEU B . n B 1 32 VAL 32 182 182 VAL VAL B . n B 1 33 ALA 33 183 183 ALA ALA B . n B 1 34 LYS 34 184 184 LYS LYS B . n B 1 35 GLY 35 185 185 GLY GLY B . n B 1 36 ASN 36 186 186 ASN ASN B . n B 1 37 LEU 37 187 187 LEU LEU B . n B 1 38 HIS 38 188 188 HIS HIS B . n B 1 39 LEU 39 189 189 LEU LEU B . n B 1 40 ALA 40 190 190 ALA ALA B . n B 1 41 ALA 41 191 191 ALA ALA B . n B 1 42 PHE 42 192 192 PHE PHE B . n B 1 43 ASN 43 193 193 ASN ASN B . n B 1 44 LEU 44 194 194 LEU LEU B . n B 1 45 HIS 45 195 195 HIS HIS B . n B 1 46 GLN 46 196 196 GLN GLN B . n B 1 47 ALA 47 197 197 ALA ALA B . n B 1 48 VAL 48 198 198 VAL VAL B . n B 1 49 GLU 49 199 199 GLU GLU B . n B 1 50 THR 50 200 200 THR THR B . n B 1 51 ALA 51 201 201 ALA ALA B . n B 1 52 TYR 52 202 202 TYR TYR B . n B 1 53 ASN 53 203 203 ASN ASN B . n B 1 54 CYS 54 204 204 CYS CYS B . n B 1 55 TYR 55 205 205 TYR TYR B . n B 1 56 LEU 56 206 206 LEU LEU B . n B 1 57 LEU 57 207 207 LEU LEU B . n B 1 58 THR 58 208 208 THR THR B . n B 1 59 LEU 59 209 209 LEU LEU B . n B 1 60 THR 60 210 210 THR THR B . n B 1 61 ASN 61 211 211 ASN ASN B . n B 1 62 TYR 62 212 212 TYR TYR B . n B 1 63 SER 63 213 213 SER SER B . n B 1 64 PRO 64 214 214 PRO PRO B . n B 1 65 ALA 65 215 215 ALA ALA B . n B 1 66 SER 66 216 216 SER SER B . n B 1 67 HIS 67 217 217 HIS HIS B . n B 1 68 ASN 68 218 218 ASN ASN B . n B 1 69 MSE 69 219 219 MSE MSE B . n B 1 70 LYS 70 220 220 LYS ALA B . n B 1 71 PHE 71 221 221 PHE PHE B . n B 1 72 LEU 72 222 222 LEU LEU B . n B 1 73 ARG 73 223 223 ARG ARG B . n B 1 74 GLY 74 224 224 GLY GLY B . n B 1 75 LEU 75 225 225 LEU LEU B . n B 1 76 SER 76 226 226 SER SER B . n B 1 77 GLU 77 227 227 GLU GLU B . n B 1 78 GLY 78 228 228 GLY GLY B . n B 1 79 ARG 79 229 229 ARG ARG B . n B 1 80 ASP 80 230 230 ASP ASP B . n B 1 81 ARG 81 231 231 ARG ALA B . n B 1 82 ARG 82 232 232 ARG ARG B . n B 1 83 LEU 83 233 233 LEU LEU B . n B 1 84 ILE 84 234 234 ILE ILE B . n B 1 85 ASP 85 235 235 ASP ASP B . n B 1 86 ILE 86 236 236 ILE ILE B . n B 1 87 TRP 87 237 237 TRP TRP B . n B 1 88 PRO 88 238 238 PRO PRO B . n B 1 89 ARG 89 239 239 ARG ARG B . n B 1 90 ASP 90 240 240 ASP ASP B . n B 1 91 ARG 91 241 241 ARG ARG B . n B 1 92 GLN 92 242 242 GLN GLN B . n B 1 93 ARG 93 243 243 ARG ARG B . n B 1 94 PHE 94 244 244 PHE PHE B . n B 1 95 THR 95 245 245 THR THR B . n B 1 96 THR 96 246 246 THR THR B . n B 1 97 TRP 97 247 247 TRP TRP B . n B 1 98 TYR 98 248 248 TYR TYR B . n B 1 99 ASN 99 249 249 ASN ASN B . n B 1 100 ILE 100 250 250 ILE ILE B . n B 1 101 MSE 101 251 251 MSE MSE B . n B 1 102 ASN 102 252 252 ASN ASN B . n B 1 103 GLU 103 253 253 GLU GLU B . n B 1 104 ALA 104 254 254 ALA ALA B . n B 1 105 TYR 105 255 255 TYR TYR B . n B 1 106 VAL 106 256 256 VAL VAL B . n B 1 107 LYS 107 257 257 LYS ALA B . n B 1 108 ALA 108 258 258 ALA ALA B . n B 1 109 ARG 109 259 259 ARG ARG B . n B 1 110 TYR 110 260 260 TYR TYR B . n B 1 111 SER 111 261 261 SER SER B . n B 1 112 LYS 112 262 262 LYS LYS B . n B 1 113 ARG 113 263 263 ARG ARG B . n B 1 114 PHE 114 264 264 PHE PHE B . n B 1 115 GLU 115 265 265 GLU GLU B . n B 1 116 VAL 116 266 266 VAL VAL B . n B 1 117 SER 117 267 267 SER SER B . n B 1 118 GLU 118 268 268 GLU GLU B . n B 1 119 GLU 119 269 269 GLU GLU B . n B 1 120 ALA 120 270 270 ALA ALA B . n B 1 121 LEU 121 271 271 LEU LEU B . n B 1 122 THR 122 272 272 THR THR B . n B 1 123 TRP 123 273 273 TRP TRP B . n B 1 124 LEU 124 274 274 LEU LEU B . n B 1 125 GLN 125 275 275 GLN GLN B . n B 1 126 GLU 126 276 276 GLU GLU B . n B 1 127 ARG 127 277 277 ARG ARG B . n B 1 128 THR 128 278 278 THR THR B . n B 1 129 ALA 129 279 279 ALA ALA B . n B 1 130 GLU 130 280 280 GLU GLU B . n B 1 131 LEU 131 281 281 LEU LEU B . n B 1 132 HIS 132 282 282 HIS HIS B . n B 1 133 LYS 133 283 283 LYS LYS B . n B 1 134 LEU 134 284 284 LEU LEU B . n B 1 135 VAL 135 285 285 VAL VAL B . n B 1 136 GLU 136 286 286 GLU GLU B . n B 1 137 THR 137 287 287 THR THR B . n B 1 138 LEU 138 288 288 LEU LEU B . n B 1 139 CYS 139 289 289 CYS CYS B . n B 1 140 ARG 140 290 290 ARG ARG B . n B 1 141 GLU 141 291 291 GLU GLU B . n B 1 142 HIS 142 292 292 HIS HIS B . n B 1 143 ILE 143 293 293 ILE ILE B . n B 1 144 GLU 144 294 294 GLU GLU B . n B 1 145 LYS 145 295 295 LYS LYS B . n B 1 146 LEU 146 296 296 LEU LEU B . n B 1 147 GLU 147 297 297 GLU ALA B . n B 1 148 HIS 148 298 298 HIS HIS B . n B 1 149 ALA 149 299 299 ALA ALA B . n B 1 150 ALA 150 300 300 ALA ALA B . n B 1 151 GLY 151 301 301 GLY GLY B . n B 1 152 GLN 152 302 ? ? ? B . n B 1 153 ALA 153 303 ? ? ? B . n B 1 154 ALA 154 304 ? ? ? B . n B 1 155 ASN 155 305 ? ? ? B . n B 1 156 SER 156 306 ? ? ? B . n B 1 157 SER 157 307 ? ? ? B . n B 1 158 ASP 158 308 ? ? ? 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 HOH 1 401 1 HOH HOH A . C 2 HOH 2 402 2 HOH HOH A . C 2 HOH 3 403 4 HOH HOH A . C 2 HOH 4 404 9 HOH HOH A . C 2 HOH 5 405 13 HOH HOH A . C 2 HOH 6 406 14 HOH HOH A . C 2 HOH 7 407 18 HOH HOH A . C 2 HOH 8 408 19 HOH HOH A . C 2 HOH 9 409 20 HOH HOH A . C 2 HOH 10 410 43 HOH HOH A . C 2 HOH 11 411 55 HOH HOH A . C 2 HOH 12 412 60 HOH HOH A . D 2 HOH 1 401 3 HOH HOH B . D 2 HOH 2 402 5 HOH HOH B . D 2 HOH 3 403 6 HOH HOH B . D 2 HOH 4 404 7 HOH HOH B . D 2 HOH 5 405 8 HOH HOH B . D 2 HOH 6 406 10 HOH HOH B . D 2 HOH 7 407 12 HOH HOH B . D 2 HOH 8 408 15 HOH HOH B . D 2 HOH 9 409 21 HOH HOH B . D 2 HOH 10 410 22 HOH HOH B . D 2 HOH 11 411 30 HOH HOH B . D 2 HOH 12 412 58 HOH HOH B . D 2 HOH 13 413 67 HOH HOH B . D 2 HOH 14 414 16 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 18 A MSE 168 ? MET SELENOMETHIONINE 2 A MSE 69 A MSE 219 ? MET SELENOMETHIONINE 3 A MSE 101 A MSE 251 ? MET SELENOMETHIONINE 4 B MSE 18 B MSE 168 ? MET SELENOMETHIONINE 5 B MSE 69 B MSE 219 ? MET SELENOMETHIONINE 6 B MSE 101 B MSE 251 ? 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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C 1 2 B,D # 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)' 2410 ? 1 MORE -3 ? 1 'SSA (A^2)' 14840 ? # 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' 4_447 x-1/2,-y-1/2,-z+2 1.0000000000 0.0000000000 0.0000000000 -31.5515000000 0.0000000000 -1.0000000000 0.0000000000 -35.7870000000 0.0000000000 0.0000000000 -1.0000000000 166.8320000000 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2014-03-26 # _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_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 Phenix-AutoSol 'model building' . ? 2 REFMAC refinement 5.8.0049 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 Phenix-AutoSol phasing . ? 6 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 NH2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 ARG _pdbx_validate_symm_contact.auth_seq_id_1 241 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 OD1 _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 ASP _pdbx_validate_symm_contact.auth_seq_id_2 162 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 2_445 _pdbx_validate_symm_contact.dist 2.17 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 SER A 152 ? ? 155.53 117.24 2 1 ALA A 215 ? ? 93.25 -8.38 3 1 ASP A 230 ? ? -163.84 114.49 4 1 LYS A 257 ? ? -81.93 -140.24 5 1 ALA A 258 ? ? 70.48 -48.70 6 1 SER B 152 ? ? 157.92 115.68 7 1 ALA B 215 ? ? 92.59 -8.29 8 1 ASP B 230 ? ? -160.80 112.93 9 1 LYS B 257 ? ? -81.05 -139.27 10 1 ALA B 258 ? ? 70.20 -49.33 11 1 HIS B 298 ? ? -97.48 54.54 12 1 ALA B 300 ? ? -55.75 84.02 # 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 1 A LYS 220 ? CG ? A LYS 70 CG 2 1 Y 1 A LYS 220 ? CD ? A LYS 70 CD 3 1 Y 1 A LYS 220 ? CE ? A LYS 70 CE 4 1 Y 1 A LYS 220 ? NZ ? A LYS 70 NZ 5 1 Y 1 A ARG 231 ? CG ? A ARG 81 CG 6 1 Y 1 A ARG 231 ? CD ? A ARG 81 CD 7 1 Y 1 A ARG 231 ? NE ? A ARG 81 NE 8 1 Y 1 A ARG 231 ? CZ ? A ARG 81 CZ 9 1 Y 1 A ARG 231 ? NH1 ? A ARG 81 NH1 10 1 Y 1 A ARG 231 ? NH2 ? A ARG 81 NH2 11 1 Y 1 B LYS 220 ? CG ? B LYS 70 CG 12 1 Y 1 B LYS 220 ? CD ? B LYS 70 CD 13 1 Y 1 B LYS 220 ? CE ? B LYS 70 CE 14 1 Y 1 B LYS 220 ? NZ ? B LYS 70 NZ 15 1 Y 1 B ARG 231 ? CG ? B ARG 81 CG 16 1 Y 1 B ARG 231 ? CD ? B ARG 81 CD 17 1 Y 1 B ARG 231 ? NE ? B ARG 81 NE 18 1 Y 1 B ARG 231 ? CZ ? B ARG 81 CZ 19 1 Y 1 B ARG 231 ? NH1 ? B ARG 81 NH1 20 1 Y 1 B ARG 231 ? NH2 ? B ARG 81 NH2 21 1 Y 1 B LYS 257 ? CG ? B LYS 107 CG 22 1 Y 1 B LYS 257 ? CD ? B LYS 107 CD 23 1 Y 1 B LYS 257 ? CE ? B LYS 107 CE 24 1 Y 1 B LYS 257 ? NZ ? B LYS 107 NZ 25 1 Y 1 B GLU 297 ? CG ? B GLU 147 CG 26 1 Y 1 B GLU 297 ? CD ? B GLU 147 CD 27 1 Y 1 B GLU 297 ? OE1 ? B GLU 147 OE1 28 1 Y 1 B GLU 297 ? OE2 ? B GLU 147 OE2 # 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 LEU 296 ? A LEU 146 2 1 Y 1 A GLU 297 ? A GLU 147 3 1 Y 1 A HIS 298 ? A HIS 148 4 1 Y 1 A ALA 299 ? A ALA 149 5 1 Y 1 A ALA 300 ? A ALA 150 6 1 Y 1 A GLY 301 ? A GLY 151 7 1 Y 1 A GLN 302 ? A GLN 152 8 1 Y 1 A ALA 303 ? A ALA 153 9 1 Y 1 A ALA 304 ? A ALA 154 10 1 Y 1 A ASN 305 ? A ASN 155 11 1 Y 1 A SER 306 ? A SER 156 12 1 Y 1 A SER 307 ? A SER 157 13 1 Y 1 A ASP 308 ? A ASP 158 14 1 Y 1 B GLN 302 ? B GLN 152 15 1 Y 1 B ALA 303 ? B ALA 153 16 1 Y 1 B ALA 304 ? B ALA 154 17 1 Y 1 B ASN 305 ? B ASN 155 18 1 Y 1 B SER 306 ? B SER 156 19 1 Y 1 B SER 307 ? B SER 157 20 1 Y 1 B ASP 308 ? B ASP 158 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #