data_4ITQ # _entry.id 4ITQ # _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 4ITQ NDB NA2218 RCSB RCSB077197 WWPDB D_1000077197 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4ITQ _pdbx_database_status.recvd_initial_deposition_date 2013-01-18 _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 'Guarne, A.' 1 'Nanji, T.' 2 'Gloyd, M.' 3 'Swiercz, J.P.' 4 'Elliot, M.A.' 5 # _citation.id primary _citation.title 'A novel nucleoid-associated protein specific to the actinobacteria.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 41 _citation.page_first 4171 _citation.page_last 4184 _citation.year 2013 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23427309 _citation.pdbx_database_id_DOI 10.1093/nar/gkt095 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Swiercz, J.P.' 1 primary 'Nanji, T.' 2 primary 'Gloyd, M.' 3 primary 'Guarne, A.' 4 primary 'Elliot, M.A.' 5 # _cell.entry_id 4ITQ _cell.length_a 43.420 _cell.length_b 71.782 _cell.length_c 102.925 _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 4ITQ _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _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 'Putative uncharacterized protein SCO1480' 11717.030 1 ? ? ? ? 2 polymer syn "5'-D(P*CP*CP*GP*CP*GP*CP*GP*C)-3'" 2388.569 1 ? ? ? ? 3 polymer syn "5'-D(P*GP*CP*GP*CP*GP*CP*GP*G)-3'" 2468.617 1 ? ? ? ? 4 water nat water 18.015 6 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name sIHF # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no yes ;(MSE)ALPPLTPEQRAAALEKAAAARRERAEVKNRLKHSGASLHEVIKQGQENDVIGK(MSE)KVSALLESLPGVGKVRA KQI(MSE)ERLGISESRRVRGLGSNQIASLEREFGSTGS ; ;MALPPLTPEQRAAALEKAAAARRERAEVKNRLKHSGASLHEVIKQGQENDVIGKMKVSALLESLPGVGKVRAKQIMERLG ISESRRVRGLGSNQIASLEREFGSTGS ; A ? 2 polydeoxyribonucleotide no no '(DC)(DC)(DG)(DC)(DG)(DC)(DG)(DC)' CCGCGCGC B ? 3 polydeoxyribonucleotide no no '(DG)(DC)(DG)(DC)(DG)(DC)(DG)(DG)' GCGCGCGG C ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MSE n 1 2 ALA n 1 3 LEU n 1 4 PRO n 1 5 PRO n 1 6 LEU n 1 7 THR n 1 8 PRO n 1 9 GLU n 1 10 GLN n 1 11 ARG n 1 12 ALA n 1 13 ALA n 1 14 ALA n 1 15 LEU n 1 16 GLU n 1 17 LYS n 1 18 ALA n 1 19 ALA n 1 20 ALA n 1 21 ALA n 1 22 ARG n 1 23 ARG n 1 24 GLU n 1 25 ARG n 1 26 ALA n 1 27 GLU n 1 28 VAL n 1 29 LYS n 1 30 ASN n 1 31 ARG n 1 32 LEU n 1 33 LYS n 1 34 HIS n 1 35 SER n 1 36 GLY n 1 37 ALA n 1 38 SER n 1 39 LEU n 1 40 HIS n 1 41 GLU n 1 42 VAL n 1 43 ILE n 1 44 LYS n 1 45 GLN n 1 46 GLY n 1 47 GLN n 1 48 GLU n 1 49 ASN n 1 50 ASP n 1 51 VAL n 1 52 ILE n 1 53 GLY n 1 54 LYS n 1 55 MSE n 1 56 LYS n 1 57 VAL n 1 58 SER n 1 59 ALA n 1 60 LEU n 1 61 LEU n 1 62 GLU n 1 63 SER n 1 64 LEU n 1 65 PRO n 1 66 GLY n 1 67 VAL n 1 68 GLY n 1 69 LYS n 1 70 VAL n 1 71 ARG n 1 72 ALA n 1 73 LYS n 1 74 GLN n 1 75 ILE n 1 76 MSE n 1 77 GLU n 1 78 ARG n 1 79 LEU n 1 80 GLY n 1 81 ILE n 1 82 SER n 1 83 GLU n 1 84 SER n 1 85 ARG n 1 86 ARG n 1 87 VAL n 1 88 ARG n 1 89 GLY n 1 90 LEU n 1 91 GLY n 1 92 SER n 1 93 ASN n 1 94 GLN n 1 95 ILE n 1 96 ALA n 1 97 SER n 1 98 LEU n 1 99 GLU n 1 100 ARG n 1 101 GLU n 1 102 PHE n 1 103 GLY n 1 104 SER n 1 105 THR n 1 106 GLY n 1 107 SER n 2 1 DC n 2 2 DC n 2 3 DG n 2 4 DC n 2 5 DG n 2 6 DC n 2 7 DG n 2 8 DC n 3 1 DG n 3 2 DC n 3 3 DG n 3 4 DC n 3 5 DG n 3 6 DC n 3 7 DG n 3 8 DG 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 SCO1480 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'A3(2)' _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details 'protein is MSE-labeled' _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Streptomyces coelicolor' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 100226 _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 'B834(DE3) pRare' _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 pET15b _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP Q9KXR9_STRCO Q9KXR9 1 ;MALPPLTPEQRAAALEKAAAARRERAEVKNRLKHSGASLHEVIKQGQENDVIGKMKVSALLESLPGVGKVRAKQIMERLG ISESRRVRGLGSNQIASLEREFGSTGS ; 1 ? 2 PDB 4ITQ 4ITQ 2 ? ? ? 3 PDB 4ITQ 4ITQ 3 ? ? ? # 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 4ITQ A 1 ? 107 ? Q9KXR9 1 ? 107 ? 1 107 2 2 4ITQ B 1 ? 8 ? 4ITQ 1 ? 8 ? 1 8 3 3 4ITQ C 1 ? 8 ? 4ITQ 1 ? 8 ? 1 8 # 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 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 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 4ITQ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.42 _exptl_crystal.density_percent_sol 49.16 _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 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.6 _exptl_crystal_grow.pdbx_details '19% PEG 3350, 210 mM KSCN, 5% ethylene glycol, 100 mM HEPES pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K' _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 PIXEL _diffrn_detector.type 'PSI PILATUS 6M' _diffrn_detector.pdbx_collection_date 2012-07-31 _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 '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 0.9793 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X25' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X25 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9793 # _reflns.entry_id 4ITQ _reflns.observed_criterion_sigma_I 2 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.6 _reflns.number_obs 5202 _reflns.number_all ? _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.055 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 31.2 _reflns.B_iso_Wilson_estimate 61 _reflns.pdbx_redundancy 6.1 _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _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_ordinal _reflns_shell.pdbx_diffrn_id 2.6 2.64 94.7 .539 ? 1.4 4.6 ? 462 ? ? ? ? 1 1 7.05 50 100 .026 ? 66.4 6.5 ? 480 ? ? ? ? 2 1 5.6 7.05 100 .048 ? 47.5 6.5 ? 491 ? ? ? ? 3 1 4.89 5.6 100 .04 ? 48.1 6.8 ? 475 ? ? ? ? 4 1 4.45 4.89 100 .046 ? 42.1 6.3 ? 483 ? ? ? ? 5 1 4.13 4.45 100 .044 ? 44.9 6.8 ? 471 ? ? ? ? 6 1 3.88 4.13 100 .045 ? 41.7 6.1 ? 488 ? ? ? ? 7 1 3.69 3.88 100 .061 ? 28.6 6.6 ? 469 ? ? ? ? 8 1 3.53 3.69 100 .057 ? 28.5 6.6 ? 477 ? ? ? ? 9 1 3.39 3.53 100 .041 ? 34.7 6.6 ? 476 ? ? ? ? 10 1 3.28 3.39 99.8 .049 ? 25.0 5.8 ? 475 ? ? ? ? 11 1 3.17 3.28 100 .043 ? 22.9 6.2 ? 475 ? ? ? ? 12 1 3.08 3.17 100 .056 ? 14.9 6.4 ? 480 ? ? ? ? 13 1 3.00 3.08 100 .188 ? 6.1 6.2 ? 473 ? ? ? ? 14 1 2.93 3.00 100 .266 ? 4.6 5.7 ? 497 ? ? ? ? 15 1 2.86 2.93 100 .354 ? 3.4 5.9 ? 472 ? ? ? ? 16 1 2.80 2.86 100 .3 ? 3.4 6.0 ? 462 ? ? ? ? 17 1 2.74 2.80 100 .466 ? 2.5 6.1 ? 492 ? ? ? ? 18 1 2.69 2.74 99 .463 ? 2.3 5.8 ? 478 ? ? ? ? 19 1 2.64 2.69 98 .556 ? 1.7 5.1 ? 449 ? ? ? ? 20 1 # _refine.entry_id 4ITQ _refine.ls_number_reflns_obs 4613 _refine.ls_number_reflns_all 4664 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.439 _refine.ls_d_res_high 2.700 _refine.ls_percent_reflns_obs 98.91 _refine.ls_R_factor_obs 0.2672 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2617 _refine.ls_R_factor_R_free 0.3150 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.69 _refine.ls_number_reflns_R_free 447 _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 67.32 _refine.aniso_B[1][1] 29.9819 _refine.aniso_B[2][2] -13.1865 _refine.aniso_B[3][3] -18.3995 _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 0.265 _refine.solvent_model_param_bsol 29.370 _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 ? _refine.pdbx_stereochemistry_target_values MLHL _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 0.56 _refine.pdbx_overall_phase_error 33.06 _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 658 _refine_hist.pdbx_number_atoms_nucleic_acid 328 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 992 _refine_hist.d_res_high 2.700 _refine_hist.d_res_low 29.439 # 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 0.003 ? ? 1042 ? 'X-RAY DIFFRACTION' f_angle_d 0.789 ? ? 1464 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 22.447 ? ? 421 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.038 ? ? 168 ? 'X-RAY DIFFRACTION' f_plane_restr 0.001 ? ? 136 ? '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 . 2.7001 3.0904 1349 0.3679 98.00 0.4179 . . 141 . . 1349 . 'X-RAY DIFFRACTION' . 3.0904 3.8922 1362 0.2428 99.00 0.3276 . . 149 . . 1362 . 'X-RAY DIFFRACTION' . 3.8922 29.4404 1455 0.2501 100.00 0.2903 . . 157 . . 1455 . 'X-RAY DIFFRACTION' # _struct.entry_id 4ITQ _struct.title 'Crystal structure of hypothetical protein SCO1480 bound to DNA' _struct.pdbx_descriptor 'Putative uncharacterized protein SCO1480/DNA complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4ITQ _struct_keywords.pdbx_keywords 'GENE REGULATION, STRUCTURAL PROTEIN/DNA' _struct_keywords.text 'protein-DNA complex, H2TH motif, nucleoid-associated protein, GENE REGULATION, STRUCTURAL PROTEIN-DNA complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 4 ? # _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 14 ? HIS A 34 ? ALA A 14 HIS A 34 1 ? 21 HELX_P HELX_P2 2 SER A 38 ? GLN A 47 ? SER A 38 GLN A 47 1 ? 10 HELX_P HELX_P3 3 ASN A 49 ? LYS A 54 ? ASN A 49 LYS A 54 1 ? 6 HELX_P HELX_P4 4 LYS A 56 ? SER A 63 ? LYS A 56 SER A 63 1 ? 8 HELX_P HELX_P5 5 GLY A 68 ? GLY A 80 ? GLY A 68 GLY A 80 1 ? 13 HELX_P HELX_P6 6 GLY A 91 ? PHE A 102 ? GLY A 91 PHE A 102 1 ? 12 # _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 LYS 54 C ? ? ? 1_555 A MSE 55 N ? ? A LYS 54 A MSE 55 1_555 ? ? ? ? ? ? ? 1.328 ? covale2 covale ? ? A MSE 55 C ? ? ? 1_555 A LYS 56 N ? ? A MSE 55 A LYS 56 1_555 ? ? ? ? ? ? ? 1.329 ? covale3 covale ? ? A ILE 75 C ? ? ? 1_555 A MSE 76 N ? ? A ILE 75 A MSE 76 1_555 ? ? ? ? ? ? ? 1.328 ? covale4 covale ? ? A MSE 76 C ? ? ? 1_555 A GLU 77 N ? ? A MSE 76 A GLU 77 1_555 ? ? ? ? ? ? ? 1.331 ? hydrog1 hydrog ? ? B DC 1 N3 ? ? ? 1_555 C DG 8 N1 ? ? B DC 1 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? B DC 1 N4 ? ? ? 1_555 C DG 8 O6 ? ? B DC 1 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? B DC 1 O2 ? ? ? 1_555 C DG 8 N2 ? ? B DC 1 C DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? B DC 2 N3 ? ? ? 1_555 C DG 7 N1 ? ? B DC 2 C DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? B DC 2 N4 ? ? ? 1_555 C DG 7 O6 ? ? B DC 2 C DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? B DC 2 O2 ? ? ? 1_555 C DG 7 N2 ? ? B DC 2 C DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? B DG 3 N1 ? ? ? 1_555 C DC 6 N3 ? ? B DG 3 C DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? B DG 3 N2 ? ? ? 1_555 C DC 6 O2 ? ? B DG 3 C DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? B DG 3 O6 ? ? ? 1_555 C DC 6 N4 ? ? B DG 3 C DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? B DC 4 N3 ? ? ? 1_555 C DG 5 N1 ? ? B DC 4 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? B DC 4 N4 ? ? ? 1_555 C DG 5 O6 ? ? B DC 4 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? B DC 4 O2 ? ? ? 1_555 C DG 5 N2 ? ? B DC 4 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? B DG 5 N1 ? ? ? 1_555 C DC 4 N3 ? ? B DG 5 C DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? B DG 5 N2 ? ? ? 1_555 C DC 4 O2 ? ? B DG 5 C DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? B DG 5 O6 ? ? ? 1_555 C DC 4 N4 ? ? B DG 5 C DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? B DC 6 N3 ? ? ? 1_555 C DG 3 N1 ? ? B DC 6 C DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? B DC 6 N4 ? ? ? 1_555 C DG 3 O6 ? ? B DC 6 C DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? B DC 6 O2 ? ? ? 1_555 C DG 3 N2 ? ? B DC 6 C DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? B DG 7 N1 ? ? ? 1_555 C DC 2 N3 ? ? B DG 7 C DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? B DG 7 N2 ? ? ? 1_555 C DC 2 O2 ? ? B DG 7 C DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? B DG 7 O6 ? ? ? 1_555 C DC 2 N4 ? ? B DG 7 C DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? B DC 8 N3 ? ? ? 1_555 C DG 1 N1 ? ? B DC 8 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? B DC 8 N4 ? ? ? 1_555 C DG 1 O6 ? ? B DC 8 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? B DC 8 O2 ? ? ? 1_555 C DG 1 N2 ? ? B DC 8 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id PHE _struct_mon_prot_cis.label_seq_id 102 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id PHE _struct_mon_prot_cis.auth_seq_id 102 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 GLY _struct_mon_prot_cis.pdbx_label_seq_id_2 103 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 GLY _struct_mon_prot_cis.pdbx_auth_seq_id_2 103 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -0.84 # _database_PDB_matrix.entry_id 4ITQ _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 4ITQ _atom_sites.fract_transf_matrix[1][1] 0.023031 _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] 0.013931 _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] 0.009716 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P 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 MSE 1 1 ? ? ? A . n A 1 2 ALA 2 2 ? ? ? A . n A 1 3 LEU 3 3 ? ? ? A . n A 1 4 PRO 4 4 ? ? ? A . n A 1 5 PRO 5 5 ? ? ? A . n A 1 6 LEU 6 6 ? ? ? A . n A 1 7 THR 7 7 ? ? ? A . n A 1 8 PRO 8 8 ? ? ? A . n A 1 9 GLU 9 9 ? ? ? A . n A 1 10 GLN 10 10 ? ? ? A . n A 1 11 ARG 11 11 ? ? ? A . n A 1 12 ALA 12 12 ? ? ? A . n A 1 13 ALA 13 13 ? ? ? A . n A 1 14 ALA 14 14 14 ALA ALA A . n A 1 15 LEU 15 15 15 LEU ALA A . n A 1 16 GLU 16 16 16 GLU GLU A . n A 1 17 LYS 17 17 17 LYS ALA A . n A 1 18 ALA 18 18 18 ALA ALA A . n A 1 19 ALA 19 19 19 ALA ALA A . n A 1 20 ALA 20 20 20 ALA ALA A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 ARG 22 22 22 ARG ARG A . n A 1 23 ARG 23 23 23 ARG ALA A . n A 1 24 GLU 24 24 24 GLU GLU A . n A 1 25 ARG 25 25 25 ARG ARG A . n A 1 26 ALA 26 26 26 ALA ALA A . n A 1 27 GLU 27 27 27 GLU GLU A . n A 1 28 VAL 28 28 28 VAL VAL A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 ASN 30 30 30 ASN ALA A . n A 1 31 ARG 31 31 31 ARG ARG A . n A 1 32 LEU 32 32 32 LEU LEU A . n A 1 33 LYS 33 33 33 LYS LYS A . n A 1 34 HIS 34 34 34 HIS HIS A . n A 1 35 SER 35 35 35 SER SER A . n A 1 36 GLY 36 36 36 GLY GLY A . n A 1 37 ALA 37 37 37 ALA ALA A . n A 1 38 SER 38 38 38 SER SER A . n A 1 39 LEU 39 39 39 LEU LEU A . n A 1 40 HIS 40 40 40 HIS ALA A . n A 1 41 GLU 41 41 41 GLU GLU A . n A 1 42 VAL 42 42 42 VAL VAL A . n A 1 43 ILE 43 43 43 ILE ILE A . n A 1 44 LYS 44 44 44 LYS LYS A . n A 1 45 GLN 45 45 45 GLN GLN A . n A 1 46 GLY 46 46 46 GLY GLY A . n A 1 47 GLN 47 47 47 GLN GLN A . n A 1 48 GLU 48 48 48 GLU GLU A . n A 1 49 ASN 49 49 49 ASN ASN A . n A 1 50 ASP 50 50 50 ASP ASP A . n A 1 51 VAL 51 51 51 VAL VAL A . n A 1 52 ILE 52 52 52 ILE ILE A . n A 1 53 GLY 53 53 53 GLY GLY A . n A 1 54 LYS 54 54 54 LYS LYS A . n A 1 55 MSE 55 55 55 MSE MSE A . n A 1 56 LYS 56 56 56 LYS LYS A . n A 1 57 VAL 57 57 57 VAL VAL A . n A 1 58 SER 58 58 58 SER SER A . n A 1 59 ALA 59 59 59 ALA ALA A . n A 1 60 LEU 60 60 60 LEU LEU A . n A 1 61 LEU 61 61 61 LEU LEU A . n A 1 62 GLU 62 62 62 GLU GLU A . n A 1 63 SER 63 63 63 SER SER A . n A 1 64 LEU 64 64 64 LEU LEU A . n A 1 65 PRO 65 65 65 PRO PRO A . n A 1 66 GLY 66 66 66 GLY GLY A . n A 1 67 VAL 67 67 67 VAL VAL A . n A 1 68 GLY 68 68 68 GLY GLY A . n A 1 69 LYS 69 69 69 LYS LYS A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 ARG 71 71 71 ARG ARG A . n A 1 72 ALA 72 72 72 ALA ALA A . n A 1 73 LYS 73 73 73 LYS LYS A . n A 1 74 GLN 74 74 74 GLN GLN A . n A 1 75 ILE 75 75 75 ILE ILE A . n A 1 76 MSE 76 76 76 MSE MSE A . n A 1 77 GLU 77 77 77 GLU GLU A . n A 1 78 ARG 78 78 78 ARG ARG A . n A 1 79 LEU 79 79 79 LEU LEU A . n A 1 80 GLY 80 80 80 GLY GLY A . n A 1 81 ILE 81 81 81 ILE ILE A . n A 1 82 SER 82 82 82 SER SER A . n A 1 83 GLU 83 83 83 GLU GLU A . n A 1 84 SER 84 84 84 SER SER A . n A 1 85 ARG 85 85 85 ARG ARG A . n A 1 86 ARG 86 86 86 ARG ARG A . n A 1 87 VAL 87 87 87 VAL VAL A . n A 1 88 ARG 88 88 88 ARG ARG A . n A 1 89 GLY 89 89 89 GLY GLY A . n A 1 90 LEU 90 90 90 LEU LEU A . n A 1 91 GLY 91 91 91 GLY GLY A . n A 1 92 SER 92 92 92 SER SER A . n A 1 93 ASN 93 93 93 ASN ASN A . n A 1 94 GLN 94 94 94 GLN GLN A . n A 1 95 ILE 95 95 95 ILE ILE A . n A 1 96 ALA 96 96 96 ALA ALA A . n A 1 97 SER 97 97 97 SER SER A . n A 1 98 LEU 98 98 98 LEU LEU A . n A 1 99 GLU 99 99 99 GLU ALA A . n A 1 100 ARG 100 100 100 ARG ALA A . n A 1 101 GLU 101 101 101 GLU GLU A . n A 1 102 PHE 102 102 102 PHE PHE A . n A 1 103 GLY 103 103 103 GLY ALA A . n A 1 104 SER 104 104 ? ? ? A . n A 1 105 THR 105 105 ? ? ? A . n A 1 106 GLY 106 106 ? ? ? A . n A 1 107 SER 107 107 ? ? ? A . n B 2 1 DC 1 1 1 DC DC B . n B 2 2 DC 2 2 2 DC DC B . n B 2 3 DG 3 3 3 DG DG B . n B 2 4 DC 4 4 4 DC DC B . n B 2 5 DG 5 5 5 DG DG B . n B 2 6 DC 6 6 6 DC DC B . n B 2 7 DG 7 7 7 DG DG B . n B 2 8 DC 8 8 8 DC DC B . n C 3 1 DG 1 1 1 DG DG C . n C 3 2 DC 2 2 2 DC DC C . n C 3 3 DG 3 3 3 DG DG C . n C 3 4 DC 4 4 4 DC DC C . n C 3 5 DG 5 5 5 DG DG C . n C 3 6 DC 6 6 6 DC DC C . n C 3 7 DG 7 7 7 DG DG C . n C 3 8 DG 8 8 8 DG DG C . n # 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 55 A MSE 55 ? MET SELENOMETHIONINE 2 A MSE 76 A MSE 76 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 1550 ? 1 MORE -9 ? 1 'SSA (A^2)' 8110 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2013-03-27 2 'Structure model' 1 1 2013-05-22 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Database references' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CBASS 'data collection' . ? 1 AutoSol phasing . ? 2 PHENIX refinement '(phenix.refine: 1.7.3_928)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_entry_details.entry_id 4ITQ _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE ORIGINAL SEQUENCE OF THE DNA DUPLEX INCLUDED IN THE CRYSTALLIZATION DROPS IS: 5' GAGGGAGTGCGTGGGTCTGA 3'/5' CTCAGACCCACGCACTCCCT 3'. THE DUPLEX WAS PARTLY DISORDERED IN THE CRYSTAL STRUCTURE (PROBABLY BECAUSE THE PROTEIN BINDS DNA UNSPECIFICALLY AND COULD BIND ALL ALONG THE DUPLEX). AS A RESULT ONLY 8 BP ARE VISIBLE IN THE ASYMMETRIC UNIT. THE DENSITY COULD NOT BE ASSIGNED TO ANY PARTICULAR SEQUENCE OF THE 19 BP DUPLEX AND HENCE THE ELECTRON DENSITY WAS MODELED BASED ON THE RELATIVE SIZE OF THE NUCLEOTIDE MOIETY (USING GUANOSINE FOR "PURINE-LIKE" DENSITIES AND CYTOSINE FOR "PYRIMIDINE-LIKE" DENSITIES). ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" C DG 1 ? ? "C1'" C DG 1 ? ? N9 C DG 1 ? ? 110.96 108.30 2.66 0.30 N 2 1 "O4'" C DG 3 ? ? "C1'" C DG 3 ? ? N9 C DG 3 ? ? 110.31 108.30 2.01 0.30 N # 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 LEU 15 ? CG ? A LEU 15 CG 2 1 Y 1 A LEU 15 ? CD1 ? A LEU 15 CD1 3 1 Y 1 A LEU 15 ? CD2 ? A LEU 15 CD2 4 1 Y 1 A LYS 17 ? CG ? A LYS 17 CG 5 1 Y 1 A LYS 17 ? CD ? A LYS 17 CD 6 1 Y 1 A LYS 17 ? CE ? A LYS 17 CE 7 1 Y 1 A LYS 17 ? NZ ? A LYS 17 NZ 8 1 Y 1 A ARG 23 ? CG ? A ARG 23 CG 9 1 Y 1 A ARG 23 ? CD ? A ARG 23 CD 10 1 Y 1 A ARG 23 ? NE ? A ARG 23 NE 11 1 Y 1 A ARG 23 ? CZ ? A ARG 23 CZ 12 1 Y 1 A ARG 23 ? NH1 ? A ARG 23 NH1 13 1 Y 1 A ARG 23 ? NH2 ? A ARG 23 NH2 14 1 Y 1 A ASN 30 ? CG ? A ASN 30 CG 15 1 Y 1 A ASN 30 ? OD1 ? A ASN 30 OD1 16 1 Y 1 A ASN 30 ? ND2 ? A ASN 30 ND2 17 1 Y 1 A HIS 40 ? CG ? A HIS 40 CG 18 1 Y 1 A HIS 40 ? ND1 ? A HIS 40 ND1 19 1 Y 1 A HIS 40 ? CD2 ? A HIS 40 CD2 20 1 Y 1 A HIS 40 ? CE1 ? A HIS 40 CE1 21 1 Y 1 A HIS 40 ? NE2 ? A HIS 40 NE2 22 1 Y 1 A GLU 99 ? CG ? A GLU 99 CG 23 1 Y 1 A GLU 99 ? CD ? A GLU 99 CD 24 1 Y 1 A GLU 99 ? OE1 ? A GLU 99 OE1 25 1 Y 1 A GLU 99 ? OE2 ? A GLU 99 OE2 26 1 Y 1 A ARG 100 ? CG ? A ARG 100 CG 27 1 Y 1 A ARG 100 ? CD ? A ARG 100 CD 28 1 Y 1 A ARG 100 ? NE ? A ARG 100 NE 29 1 Y 1 A ARG 100 ? CZ ? A ARG 100 CZ 30 1 Y 1 A ARG 100 ? NH1 ? A ARG 100 NH1 31 1 Y 1 A ARG 100 ? NH2 ? A ARG 100 NH2 # 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 MSE 1 ? A MSE 1 2 1 Y 1 A ALA 2 ? A ALA 2 3 1 Y 1 A LEU 3 ? A LEU 3 4 1 Y 1 A PRO 4 ? A PRO 4 5 1 Y 1 A PRO 5 ? A PRO 5 6 1 Y 1 A LEU 6 ? A LEU 6 7 1 Y 1 A THR 7 ? A THR 7 8 1 Y 1 A PRO 8 ? A PRO 8 9 1 Y 1 A GLU 9 ? A GLU 9 10 1 Y 1 A GLN 10 ? A GLN 10 11 1 Y 1 A ARG 11 ? A ARG 11 12 1 Y 1 A ALA 12 ? A ALA 12 13 1 Y 1 A ALA 13 ? A ALA 13 14 1 Y 1 A SER 104 ? A SER 104 15 1 Y 1 A THR 105 ? A THR 105 16 1 Y 1 A GLY 106 ? A GLY 106 17 1 Y 1 A SER 107 ? A SER 107 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4ITQ 'double helix' 4ITQ 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 B DC 1 1_555 C DG 8 1_555 0.123 -0.120 -0.040 4.634 -12.668 -0.068 1 B_DC1:DG8_C B 1 ? C 8 ? 19 1 1 B DC 2 1_555 C DG 7 1_555 -0.578 -0.111 -0.268 4.842 -13.015 0.525 2 B_DC2:DG7_C B 2 ? C 7 ? 19 1 1 B DG 3 1_555 C DC 6 1_555 0.638 -0.092 0.494 -3.246 -9.807 7.007 3 B_DG3:DC6_C B 3 ? C 6 ? 19 1 1 B DC 4 1_555 C DG 5 1_555 -0.420 -0.091 0.049 3.424 -4.873 -1.758 4 B_DC4:DG5_C B 4 ? C 5 ? 19 1 1 B DG 5 1_555 C DC 4 1_555 -0.535 -0.228 0.060 6.979 -18.565 1.440 5 B_DG5:DC4_C B 5 ? C 4 ? 19 1 1 B DC 6 1_555 C DG 3 1_555 -0.437 -0.129 0.197 -2.884 -9.684 5.756 6 B_DC6:DG3_C B 6 ? C 3 ? 19 1 1 B DG 7 1_555 C DC 2 1_555 1.117 0.044 0.413 0.905 -6.253 6.443 7 B_DG7:DC2_C B 7 ? C 2 ? 19 1 1 B DC 8 1_555 C DG 1 1_555 0.314 -0.167 0.323 -7.459 -8.746 -1.531 8 B_DC8:DG1_C B 8 ? C 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 B DC 1 1_555 C DG 8 1_555 B DC 2 1_555 C DG 7 1_555 -0.071 -0.268 3.228 3.317 1.491 28.912 -0.853 0.854 3.183 2.972 -6.611 29.135 1 BB_DC1DC2:DG7DG8_CC B 1 ? C 8 ? B 2 ? C 7 ? 1 B DC 2 1_555 C DG 7 1_555 B DG 3 1_555 C DC 6 1_555 0.445 0.554 3.515 -3.771 6.667 42.041 0.037 -1.021 3.508 9.201 5.205 42.702 2 BB_DC2DG3:DC6DG7_CC B 2 ? C 7 ? B 3 ? C 6 ? 1 B DG 3 1_555 C DC 6 1_555 B DC 4 1_555 C DG 5 1_555 -0.127 -0.716 3.155 2.098 2.110 25.547 -2.174 0.849 3.067 4.752 -4.725 25.717 3 BB_DG3DC4:DG5DC6_CC B 3 ? C 6 ? B 4 ? C 5 ? 1 B DC 4 1_555 C DG 5 1_555 B DG 5 1_555 C DC 4 1_555 0.621 -0.210 3.133 -1.062 11.459 35.462 -1.773 -1.106 2.910 18.229 1.689 37.226 4 BB_DC4DG5:DC4DG5_CC B 4 ? C 5 ? B 5 ? C 4 ? 1 B DG 5 1_555 C DC 4 1_555 B DC 6 1_555 C DG 3 1_555 -0.375 -0.720 3.455 -2.216 -0.497 31.074 -1.240 0.250 3.484 -0.927 4.129 31.155 5 BB_DG5DC6:DG3DC4_CC B 5 ? C 4 ? B 6 ? C 3 ? 1 B DC 6 1_555 C DG 3 1_555 B DG 7 1_555 C DC 2 1_555 -0.578 0.588 3.396 -1.183 5.649 42.731 0.215 0.664 3.457 7.711 1.615 43.101 6 BB_DC6DG7:DC2DG3_CC B 6 ? C 3 ? B 7 ? C 2 ? 1 B DG 7 1_555 C DC 2 1_555 B DC 8 1_555 C DG 1 1_555 0.299 -0.826 3.451 3.207 2.774 27.725 -2.392 0.175 3.366 5.746 -6.642 28.041 7 BB_DG7DC8:DG1DC2_CC B 7 ? C 2 ? B 8 ? C 1 ? # _pdbx_entity_nonpoly.entity_id 4 _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 D 4 HOH 1 201 2 HOH HOH A . D 4 HOH 2 202 3 HOH HOH A . D 4 HOH 3 203 4 HOH HOH A . D 4 HOH 4 204 5 HOH HOH A . D 4 HOH 5 205 7 HOH HOH A . E 4 HOH 1 101 6 HOH HOH C . #