data_3FMY # _entry.id 3FMY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3FMY RCSB RCSB050788 WWPDB D_1000050788 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3FMY _pdbx_database_status.recvd_initial_deposition_date 2008-12-22 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Page, R.' 1 'Brown, B.L.' 2 'Arruda, J.M.' 3 'Peti, W.' 4 # _citation.id primary _citation.title ;Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties ; _citation.journal_abbrev 'Plos Pathog.' _citation.journal_volume 5 _citation.page_first e1000706 _citation.page_last e1000706 _citation.year 2009 _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 20041169 _citation.pdbx_database_id_DOI 10.1371/journal.ppat.1000706 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Brown, B.L.' 1 primary 'Grigoriu, S.' 2 primary 'Kim, Y.' 3 primary 'Arruda, J.M.' 4 primary 'Davenport, A.' 5 primary 'Wood, T.K.' 6 primary 'Peti, W.' 7 primary 'Page, R.' 8 # _cell.entry_id 3FMY _cell.length_a 39.573 _cell.length_b 39.573 _cell.length_c 78.306 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 3FMY _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _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 'HTH-type transcriptional regulator MQSA (ygiT/b3021)' 8125.364 1 ? ? 'C-terminus (UNP residues 62 to 131)' ? 2 water nat water 18.015 80 ? ? ? ? # _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 'GHMASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNA(MEQ)PHPSTIKLLRVLDKHPELLNEIR' _entity_poly.pdbx_seq_one_letter_code_can GHMASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR _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 HIS n 1 3 MET n 1 4 ALA n 1 5 SER n 1 6 VAL n 1 7 ASN n 1 8 ALA n 1 9 GLU n 1 10 THR n 1 11 VAL n 1 12 ALA n 1 13 PRO n 1 14 GLU n 1 15 PHE n 1 16 ILE n 1 17 VAL n 1 18 LYS n 1 19 VAL n 1 20 ARG n 1 21 LYS n 1 22 LYS n 1 23 LEU n 1 24 SER n 1 25 LEU n 1 26 THR n 1 27 GLN n 1 28 LYS n 1 29 GLU n 1 30 ALA n 1 31 SER n 1 32 GLU n 1 33 ILE n 1 34 PHE n 1 35 GLY n 1 36 GLY n 1 37 GLY n 1 38 VAL n 1 39 ASN n 1 40 ALA n 1 41 PHE n 1 42 SER n 1 43 ARG n 1 44 TYR n 1 45 GLU n 1 46 LYS n 1 47 GLY n 1 48 ASN n 1 49 ALA n 1 50 MEQ n 1 51 PRO n 1 52 HIS n 1 53 PRO n 1 54 SER n 1 55 THR n 1 56 ILE n 1 57 LYS n 1 58 LEU n 1 59 LEU n 1 60 ARG n 1 61 VAL n 1 62 LEU n 1 63 ASP n 1 64 LYS n 1 65 HIS n 1 66 PRO n 1 67 GLU n 1 68 LEU n 1 69 LEU n 1 70 ASN n 1 71 GLU n 1 72 ILE n 1 73 ARG 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 'b3021, JW2989, ygiT' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain K12 _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 'Escherichia coli K-12' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 83333 _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 '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 RP1B _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code YGIT_ECOLI _struct_ref.pdbx_db_accession Q46864 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIKLLRVLDKHPELLNEIR _struct_ref.pdbx_align_begin 62 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3FMY _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 73 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q46864 _struct_ref_seq.db_align_beg 62 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 131 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 62 _struct_ref_seq.pdbx_auth_seq_align_end 131 # 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 3FMY GLY A 1 ? UNP Q46864 ? ? 'EXPRESSION TAG' -2 1 1 3FMY HIS A 2 ? UNP Q46864 ? ? 'EXPRESSION TAG' -1 2 1 3FMY MET A 3 ? UNP Q46864 ? ? 'EXPRESSION TAG' 0 3 # 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 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 MEQ 'L-peptide linking' n N5-METHYLGLUTAMINE ? 'C6 H12 N2 O3' 160.171 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3FMY _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # loop_ _exptl_crystal.id _exptl_crystal.density_meas _exptl_crystal.density_Matthews _exptl_crystal.density_percent_sol _exptl_crystal.description _exptl_crystal.F_000 _exptl_crystal.preparation 1 ? 2.18 43.51 ? ? ? 2 ? ? ? ? ? ? # loop_ _exptl_crystal_grow.crystal_id _exptl_crystal_grow.method _exptl_crystal_grow.temp _exptl_crystal_grow.temp_details _exptl_crystal_grow.pH _exptl_crystal_grow.pdbx_pH_range _exptl_crystal_grow.pdbx_details 1 'VAPOR DIFFUSION, SITTING DROP' 277 ? 8.5 ? '20% PEG 300, 5% PEG 8000, 10% glycerol, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K' 2 'VAPOR DIFFUSION, SITTING DROP' 277 ? 7.5 ? '40% PEG 300, 0.1M Hepes, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K' # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 210' 2008-07-18 'Toroidal focusing mirror' 2 CCD 'ADSC QUANTUM 210' 2008-09-28 'Toroidal focusing mirror' # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'Si (111) channel cut monochromator' 'SINGLE WAVELENGTH' x-ray 2 1 M 'Si (111) channel cut monochromator' MAD x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.0 1.0 2 0.9322 1.0 3 0.9794 1.0 4 0.9788 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'NSLS BEAMLINE X6A' NSLS X6A ? 1.0 2 SYNCHROTRON 'NSLS BEAMLINE X6A' NSLS X6A ? '0.9322, 0.9794, 0.9788' # _reflns.entry_id 3FMY _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50.0 _reflns.d_resolution_high 1.40 _reflns.number_obs 14556 _reflns.number_all 14613 _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.032 _reflns.pdbx_netI_over_sigmaI 31.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.7 _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_diffrn_id 1,2 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.40 _reflns_shell.d_res_low 1.42 _reflns_shell.percent_possible_all 99.2 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.232 _reflns_shell.meanI_over_sigI_obs 6.19 _reflns_shell.pdbx_redundancy 4.5 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3FMY _refine.ls_number_reflns_obs 13813 _refine.ls_number_reflns_all 14529 _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 20.77 _refine.ls_d_res_high 1.40 _refine.ls_percent_reflns_obs 99.71 _refine.ls_R_factor_obs 0.15654 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.15532 _refine.ls_R_factor_R_free 0.18151 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.9 _refine.ls_number_reflns_R_free 716 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.968 _refine.correlation_coeff_Fo_to_Fc_free 0.963 _refine.B_iso_mean 12.155 _refine.aniso_B[1][1] 0.02 _refine.aniso_B[2][2] 0.02 _refine.aniso_B[3][3] -0.03 _refine.aniso_B[1][2] 0.01 _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 MAD _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 0.063 _refine.pdbx_overall_ESU_R_Free 0.056 _refine.overall_SU_ML 0.029 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.525 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _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_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 571 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 80 _refine_hist.number_atoms_total 651 _refine_hist.d_res_high 1.40 _refine_hist.d_res_low 20.77 # 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 0.011 0.022 ? 590 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 424 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.413 2.007 ? 809 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.935 3.000 ? 1056 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 4.893 5.000 ? 84 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 25.507 24.400 ? 25 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 12.363 15.000 ? 119 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 8.215 15.000 ? 4 'X-RAY DIFFRACTION' ? r_chiral_restr 0.085 0.200 ? 93 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 658 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 110 'X-RAY DIFFRACTION' ? r_nbd_refined 0.245 0.200 ? 118 'X-RAY DIFFRACTION' ? r_nbd_other 0.190 0.200 ? 432 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.191 0.200 ? 292 'X-RAY DIFFRACTION' ? r_nbtor_other 0.089 0.200 ? 294 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.174 0.200 ? 49 '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 0.241 0.200 ? 8 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.277 0.200 ? 22 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.163 0.200 ? 16 '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 2.228 3.000 ? 371 'X-RAY DIFFRACTION' ? r_mcbond_other 1.295 3.000 ? 140 'X-RAY DIFFRACTION' ? r_mcangle_it 2.970 5.000 ? 596 'X-RAY DIFFRACTION' ? r_scbond_it 4.157 8.000 ? 239 'X-RAY DIFFRACTION' ? r_scangle_it 5.560 11.000 ? 203 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 2.211 3.000 ? 1077 'X-RAY DIFFRACTION' ? r_sphericity_free 5.727 3.000 ? 80 'X-RAY DIFFRACTION' ? r_sphericity_bonded 3.252 3.000 ? 995 '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 1.400 _refine_ls_shell.d_res_low 1.436 _refine_ls_shell.number_reflns_R_work 993 _refine_ls_shell.R_factor_R_work 0.143 _refine_ls_shell.percent_reflns_obs 99.53 _refine_ls_shell.R_factor_R_free 0.197 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 58 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 3FMY _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? # _struct.entry_id 3FMY _struct.title 'Structure of the C-terminal domain of the E. coli protein MQSA (YgiT/b3021)' _struct.pdbx_descriptor 'Uncharacterized HTH-type transcriptional regulator ygiT' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3FMY _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN' _struct_keywords.text 'helix-turn-helix, DNA-binding, Transcription, Transcription regulation, DNA BINDING 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 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 ALA A 12 ? LEU A 23 ? ALA A 70 LEU A 81 1 ? 12 HELX_P HELX_P2 2 THR A 26 ? GLY A 35 ? THR A 84 GLY A 93 1 ? 10 HELX_P HELX_P3 3 ASN A 39 ? LYS A 46 ? ASN A 97 LYS A 104 1 ? 8 HELX_P HELX_P4 4 HIS A 52 ? HIS A 65 ? HIS A 110 HIS A 123 1 ? 14 HELX_P HELX_P5 5 LEU A 68 ? ARG A 73 ? LEU A 126 ARG A 131 1 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A ALA 49 C ? ? ? 1_555 A MEQ 50 N ? ? A ALA 107 A MEQ 108 1_555 ? ? ? ? ? ? ? 1.325 ? covale2 covale ? ? A MEQ 50 C ? ? ? 1_555 A PRO 51 N ? ? A MEQ 108 A PRO 109 1_555 ? ? ? ? ? ? ? 1.350 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 3FMY _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 3FMY _atom_sites.fract_transf_matrix[1][1] 0.025270 _atom_sites.fract_transf_matrix[1][2] 0.014589 _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] 0.029179 _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] 0.012770 _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 # 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 -2 ? ? ? A . n A 1 2 HIS 2 -1 ? ? ? A . n A 1 3 MET 3 0 ? ? ? A . n A 1 4 ALA 4 62 ? ? ? A . n A 1 5 SER 5 63 ? ? ? A . n A 1 6 VAL 6 64 ? ? ? A . n A 1 7 ASN 7 65 ? ? ? A . n A 1 8 ALA 8 66 66 ALA ALA A . n A 1 9 GLU 9 67 67 GLU GLU A . n A 1 10 THR 10 68 68 THR THR A . n A 1 11 VAL 11 69 69 VAL VAL A . n A 1 12 ALA 12 70 70 ALA ALA A . n A 1 13 PRO 13 71 71 PRO PRO A . n A 1 14 GLU 14 72 72 GLU GLU A . n A 1 15 PHE 15 73 73 PHE PHE A . n A 1 16 ILE 16 74 74 ILE ILE A . n A 1 17 VAL 17 75 75 VAL VAL A . n A 1 18 LYS 18 76 76 LYS LYS A . n A 1 19 VAL 19 77 77 VAL VAL A . n A 1 20 ARG 20 78 78 ARG ARG A . n A 1 21 LYS 21 79 79 LYS LYS A . n A 1 22 LYS 22 80 80 LYS LYS A . n A 1 23 LEU 23 81 81 LEU LEU A . n A 1 24 SER 24 82 82 SER SER A . n A 1 25 LEU 25 83 83 LEU LEU A . n A 1 26 THR 26 84 84 THR THR A . n A 1 27 GLN 27 85 85 GLN GLN A . n A 1 28 LYS 28 86 86 LYS LYS A . n A 1 29 GLU 29 87 87 GLU GLU A . n A 1 30 ALA 30 88 88 ALA ALA A . n A 1 31 SER 31 89 89 SER SER A . n A 1 32 GLU 32 90 90 GLU GLU A . n A 1 33 ILE 33 91 91 ILE ILE A . n A 1 34 PHE 34 92 92 PHE PHE A . n A 1 35 GLY 35 93 93 GLY GLY A . n A 1 36 GLY 36 94 94 GLY GLY A . n A 1 37 GLY 37 95 95 GLY GLY A . n A 1 38 VAL 38 96 96 VAL VAL A . n A 1 39 ASN 39 97 97 ASN ASN A . n A 1 40 ALA 40 98 98 ALA ALA A . n A 1 41 PHE 41 99 99 PHE PHE A . n A 1 42 SER 42 100 100 SER SER A . n A 1 43 ARG 43 101 101 ARG ARG A . n A 1 44 TYR 44 102 102 TYR TYR A . n A 1 45 GLU 45 103 103 GLU GLU A . n A 1 46 LYS 46 104 104 LYS LYS A . n A 1 47 GLY 47 105 105 GLY GLY A . n A 1 48 ASN 48 106 106 ASN ASN A . n A 1 49 ALA 49 107 107 ALA ALA A . n A 1 50 MEQ 50 108 108 MEQ MEQ A . n A 1 51 PRO 51 109 109 PRO PRO A . n A 1 52 HIS 52 110 110 HIS HIS A . n A 1 53 PRO 53 111 111 PRO PRO A . n A 1 54 SER 54 112 112 SER SER A . n A 1 55 THR 55 113 113 THR THR A . n A 1 56 ILE 56 114 114 ILE ILE A . n A 1 57 LYS 57 115 115 LYS LYS A . n A 1 58 LEU 58 116 116 LEU LEU A . n A 1 59 LEU 59 117 117 LEU LEU A . n A 1 60 ARG 60 118 118 ARG ARG A . n A 1 61 VAL 61 119 119 VAL VAL A . n A 1 62 LEU 62 120 120 LEU LEU A . n A 1 63 ASP 63 121 121 ASP ASP A . n A 1 64 LYS 64 122 122 LYS LYS A . n A 1 65 HIS 65 123 123 HIS HIS A . n A 1 66 PRO 66 124 124 PRO PRO A . n A 1 67 GLU 67 125 125 GLU GLU A . n A 1 68 LEU 68 126 126 LEU LEU A . n A 1 69 LEU 69 127 127 LEU LEU A . n A 1 70 ASN 70 128 128 ASN ASN A . n A 1 71 GLU 71 129 129 GLU GLU A . n A 1 72 ILE 72 130 130 ILE ILE A . n A 1 73 ARG 73 131 131 ARG ARG A . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id MEQ _pdbx_struct_mod_residue.label_seq_id 50 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MEQ _pdbx_struct_mod_residue.auth_seq_id 108 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id GLN _pdbx_struct_mod_residue.details N5-METHYLGLUTAMINE # _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 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # 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)' 1600 ? 1 MORE -6 ? 1 'SSA (A^2)' 6760 ? # 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_555 y,x,-z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 160 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2010-01-12 2 'Structure model' 1 1 2011-07-13 # _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 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SOLVE phasing . ? 2 REFMAC refinement 5.2.0019 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OD2 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 ASP _pdbx_validate_close_contact.auth_seq_id_1 121 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 163 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.18 # 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 -2 ? A GLY 1 2 1 Y 1 A HIS -1 ? A HIS 2 3 1 Y 1 A MET 0 ? A MET 3 4 1 Y 1 A ALA 62 ? A ALA 4 5 1 Y 1 A SER 63 ? A SER 5 6 1 Y 1 A VAL 64 ? A VAL 6 7 1 Y 1 A ASN 65 ? A ASN 7 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # 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 HOH 1 1 1 HOH HOH A . B 2 HOH 2 2 2 HOH HOH A . B 2 HOH 3 3 3 HOH HOH A . B 2 HOH 4 4 4 HOH HOH A . B 2 HOH 5 5 5 HOH HOH A . B 2 HOH 6 7 7 HOH HOH A . B 2 HOH 7 8 8 HOH HOH A . B 2 HOH 8 9 9 HOH HOH A . B 2 HOH 9 10 10 HOH HOH A . B 2 HOH 10 11 11 HOH HOH A . B 2 HOH 11 12 12 HOH HOH A . B 2 HOH 12 13 13 HOH HOH A . B 2 HOH 13 14 14 HOH HOH A . B 2 HOH 14 16 16 HOH HOH A . B 2 HOH 15 17 17 HOH HOH A . B 2 HOH 16 18 18 HOH HOH A . B 2 HOH 17 19 19 HOH HOH A . B 2 HOH 18 20 20 HOH HOH A . B 2 HOH 19 21 21 HOH HOH A . B 2 HOH 20 24 24 HOH HOH A . B 2 HOH 21 26 26 HOH HOH A . B 2 HOH 22 27 27 HOH HOH A . B 2 HOH 23 28 28 HOH HOH A . B 2 HOH 24 29 29 HOH HOH A . B 2 HOH 25 30 30 HOH HOH A . B 2 HOH 26 34 34 HOH HOH A . B 2 HOH 27 35 35 HOH HOH A . B 2 HOH 28 36 36 HOH HOH A . B 2 HOH 29 38 38 HOH HOH A . B 2 HOH 30 41 41 HOH HOH A . B 2 HOH 31 42 42 HOH HOH A . B 2 HOH 32 43 43 HOH HOH A . B 2 HOH 33 44 44 HOH HOH A . B 2 HOH 34 47 47 HOH HOH A . B 2 HOH 35 50 50 HOH HOH A . B 2 HOH 36 51 51 HOH HOH A . B 2 HOH 37 53 53 HOH HOH A . B 2 HOH 38 55 55 HOH HOH A . B 2 HOH 39 132 59 HOH HOH A . B 2 HOH 40 133 60 HOH HOH A . B 2 HOH 41 134 62 HOH HOH A . B 2 HOH 42 135 63 HOH HOH A . B 2 HOH 43 136 64 HOH HOH A . B 2 HOH 44 137 65 HOH HOH A . B 2 HOH 45 138 66 HOH HOH A . B 2 HOH 46 139 67 HOH HOH A . B 2 HOH 47 140 69 HOH HOH A . B 2 HOH 48 141 70 HOH HOH A . B 2 HOH 49 142 71 HOH HOH A . B 2 HOH 50 143 72 HOH HOH A . B 2 HOH 51 144 73 HOH HOH A . B 2 HOH 52 145 74 HOH HOH A . B 2 HOH 53 146 75 HOH HOH A . B 2 HOH 54 147 76 HOH HOH A . B 2 HOH 55 148 77 HOH HOH A . B 2 HOH 56 149 78 HOH HOH A . B 2 HOH 57 150 79 HOH HOH A . B 2 HOH 58 151 80 HOH HOH A . B 2 HOH 59 152 81 HOH HOH A . B 2 HOH 60 153 82 HOH HOH A . B 2 HOH 61 154 83 HOH HOH A . B 2 HOH 62 155 84 HOH HOH A . B 2 HOH 63 156 85 HOH HOH A . B 2 HOH 64 157 86 HOH HOH A . B 2 HOH 65 158 87 HOH HOH A . B 2 HOH 66 159 88 HOH HOH A . B 2 HOH 67 160 89 HOH HOH A . B 2 HOH 68 161 90 HOH HOH A . B 2 HOH 69 162 91 HOH HOH A . B 2 HOH 70 163 92 HOH HOH A . B 2 HOH 71 164 93 HOH HOH A . B 2 HOH 72 165 94 HOH HOH A . B 2 HOH 73 166 95 HOH HOH A . B 2 HOH 74 167 96 HOH HOH A . B 2 HOH 75 168 97 HOH HOH A . B 2 HOH 76 169 98 HOH HOH A . B 2 HOH 77 170 99 HOH HOH A . B 2 HOH 78 171 100 HOH HOH A . B 2 HOH 79 172 101 HOH HOH A . B 2 HOH 80 173 102 HOH HOH A . #