data_1JJ8 # _entry.id 1JJ8 # _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 1JJ8 NDB PD0229 RCSB RCSB013835 WWPDB D_1000013835 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1HCR ;Native wild-type Hin recombinase DNA-binding domain bound to underivatized hixL half-site. ; unspecified PDB 1IJW 'FORM1 BR18 DERIVATIVE' unspecified PDB 1JJ6 'FORM1 I5 DERIVATIVE' unspecified PDB 1JKO 'FORM1 A10G MUTANT' unspecified PDB 1JKP 'FORM1 T11G MUTANT' unspecified PDB 1JKQ 'FORM1 G9T MUTANT' unspecified PDB 1JKR 'FORM1 T11C MUTANT' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1JJ8 _pdbx_database_status.recvd_initial_deposition_date 2001-07-03 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_mr ? _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 'Chiu, T.K.' 1 'Sohn, C.' 2 'Johnson, R.C.' 3 'Dickerson, R.E.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Testing water-mediated DNA recognition by the Hin recombinase.' 'EMBO J.' 21 801 814 2002 EMJODG UK 0261-4189 0897 ? 11847127 10.1093/emboj/21.4.801 1 'How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase.' Thesis ? 145 241 2001 ? ? ? ? ? ? ? 2 'Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions.' Science 263 348 355 1994 SCIEAS US 0036-8075 0038 ? 8278807 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Chiu, T.K.' 1 primary 'Sohn, C.' 2 primary 'Dickerson, R.E.' 3 primary 'Johnson, R.C.' 4 1 'Chiu, T.K.' 5 2 'Feng, J.A.' 6 2 'Johnson, R.C.' 7 2 'Dickerson, R.E.' 8 # _cell.entry_id 1JJ8 _cell.length_a 66.328 _cell.length_b 68.693 _cell.length_c 62.136 _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 1JJ8 _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 syn "5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3'" 4436.707 1 ? ? ? ? 2 polymer syn "5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'" 4231.806 1 ? ? ? ? 3 polymer syn 'DNA-INVERTASE HIN' 6047.051 1 ? ? 'RESIDUES 139 TO 190' ? 4 water nat water 18.015 12 ? ? ? ? # _entity_name_com.entity_id 3 _entity_name_com.name 'Hin Recombinase' # 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 polydeoxyribonucleotide no yes '(DT)(DG)(5IU)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DA)(DA)(DG)(DA)' TGUTTTTGATAAGA A ? 2 polydeoxyribonucleotide no no '(DA)(DT)(DC)(DT)(DT)(DA)(DT)(DC)(DA)(DA)(DA)(DA)(DA)(DC)' ATCTTATCAAAAAC B ? 3 'polypeptide(L)' no no GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN C ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DG n 1 3 5IU n 1 4 DT n 1 5 DT n 1 6 DT n 1 7 DT n 1 8 DG n 1 9 DA n 1 10 DT n 1 11 DA n 1 12 DA n 1 13 DG n 1 14 DA n 2 1 DA n 2 2 DT n 2 3 DC n 2 4 DT n 2 5 DT n 2 6 DA n 2 7 DT n 2 8 DC n 2 9 DA n 2 10 DA n 2 11 DA n 2 12 DA n 2 13 DA n 2 14 DC n 3 1 GLY n 3 2 ARG n 3 3 PRO n 3 4 ARG n 3 5 ALA n 3 6 ILE n 3 7 ASN n 3 8 LYS n 3 9 HIS n 3 10 GLU n 3 11 GLN n 3 12 GLU n 3 13 GLN n 3 14 ILE n 3 15 SER n 3 16 ARG n 3 17 LEU n 3 18 LEU n 3 19 GLU n 3 20 LYS n 3 21 GLY n 3 22 HIS n 3 23 PRO n 3 24 ARG n 3 25 GLN n 3 26 GLN n 3 27 LEU n 3 28 ALA n 3 29 ILE n 3 30 ILE n 3 31 PHE n 3 32 GLY n 3 33 ILE n 3 34 GLY n 3 35 VAL n 3 36 SER n 3 37 THR n 3 38 LEU n 3 39 TYR n 3 40 ARG n 3 41 TYR n 3 42 PHE n 3 43 PRO n 3 44 ALA n 3 45 SER n 3 46 SER n 3 47 ILE n 3 48 LYS n 3 49 LYS n 3 50 ARG n 3 51 MET n 3 52 ASN n # _pdbx_entity_src_syn.entity_id 3 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'SYNTHETIC PEPTIDE' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 UNP HIN_SALTY 3 GRPRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASSIKKRMN 139 P03013 ? 2 PDB 1JJ8 1 ? ? 1JJ8 ? 3 PDB 1JJ8 2 ? ? 1JJ8 ? # 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 1JJ8 C 1 ? 52 ? P03013 139 ? 190 ? 139 190 2 2 1JJ8 A 1 ? 14 ? 1JJ8 2 ? 15 ? 2 15 3 3 1JJ8 B 1 ? 14 ? 1JJ8 16 ? 29 ? 16 29 # 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 5IU 'DNA linking' n "5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 I N2 O8 P' 434.078 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 1JJ8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.423 _exptl_crystal.density_percent_sol 47.27 _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 ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.60 _exptl_crystal_grow.pdbx_details ;0.08 MM DNA, 0.04 MM HIN, 25 MM NA ACETATE (PH 4.6), 25 MM MGCL2, 8 MM NACL, 6.3% V/V PEG400, AND 1.25 MM NA CACODYLATE. RESERVOIR SOLUTION CONTAINS 100 MM NA ACETATE (PH 4.6), 100 MM MGCL2, AND 25% PEG400. CONCENTRATION OF PEG400 IN RESERVOIR SOLUTION WAS INCREASED IN 5% INCREMENTS TO 35%. CONDITIONS FOR NATIVE ARE THE SAME EXCEPT THE CONCENTRATION OF MGCL2 IS 5 TIMES SMALLER., pH 4.60, VAPOR DIFFUSION, HANGING DROP ; _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 DNA ? ? ? 1 2 1 HIN ? ? ? 1 3 1 'sodium acetate' ? ? ? 1 4 1 MgCl2 ? ? ? 1 5 1 NaCl ? ? ? 1 6 1 'PEG 400' ? ? ? 1 7 1 'sodium cacodylate' ? ? ? 1 8 2 'sodium acetate' ? ? ? 1 9 2 MgCl2 ? ? ? 1 10 2 'PEG 400' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type RIGAKU _diffrn_detector.pdbx_collection_date 1995-09-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.543 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.543 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1JJ8 _reflns.observed_criterion_sigma_I 1.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 25.0 _reflns.d_resolution_high 2.75 _reflns.number_obs 3765 _reflns.number_all ? _reflns.percent_possible_obs 96.49 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.081 _reflns.pdbx_netI_over_sigmaI 19.6 _reflns.B_iso_Wilson_estimate 44.00 _reflns.pdbx_redundancy 15.000 _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.d_res_high 2.75 _reflns_shell.d_res_low 2.87 _reflns_shell.percent_possible_all 91.64 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.267 _reflns_shell.meanI_over_sigI_obs 4.5 _reflns_shell.pdbx_redundancy 4.2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.entry_id 1JJ8 _refine.ls_number_reflns_obs 3765 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 25.00 _refine.ls_d_res_high 2.75 _refine.ls_percent_reflns_obs 96.49 _refine.ls_R_factor_obs 0.2134 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2134 _refine.ls_R_factor_R_free 0.2771 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.46 _refine.ls_number_reflns_R_free 369 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 45.00 _refine.aniso_B[1][1] 9.450 _refine.aniso_B[2][2] -5.107 _refine.aniso_B[3][3] -4.343 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details ? _refine.solvent_model_param_ksol 0.28 _refine.solvent_model_param_bsol 18.88 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'SIRAS PHASES' _refine.pdbx_method_to_determine_struct SIRAS _refine.pdbx_isotropic_thermal_model ANISOTROPIC_FIXED_ISOTROPIC _refine.pdbx_stereochemistry_target_values MLF _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF 10000.00 _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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_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_analyze.entry_id 1JJ8 _refine_analyze.Luzzati_coordinate_error_obs 0.36 _refine_analyze.Luzzati_sigma_a_obs 0.53 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.46 _refine_analyze.Luzzati_sigma_a_free 0.60 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 375 _refine_hist.pdbx_number_atoms_nucleic_acid 552 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 12 _refine_hist.number_atoms_total 939 _refine_hist.d_res_high 2.75 _refine_hist.d_res_low 25.00 # 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 c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.30 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 19.41 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.45 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.49 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 2.45 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 2.32 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 3.63 2.05 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 8 _refine_ls_shell.d_res_high 2.75 _refine_ls_shell.d_res_low 2.87 _refine_ls_shell.number_reflns_R_work 394 _refine_ls_shell.R_factor_R_work 0.3529 _refine_ls_shell.percent_reflns_obs 91.64 _refine_ls_shell.R_factor_R_free 0.5136 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free 9.39 _refine_ls_shell.number_reflns_R_free 45 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 DNA-RNA_REP.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 3 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' # _struct.entry_id 1JJ8 _struct.title 'Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations' _struct.pdbx_descriptor 'HIN RECOMBINASE/DNA Complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1JJ8 _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN/DNA' _struct_keywords.text 'WATER-MEDIATED RECOGNITION, PROTEIN-DNA COMPLEX, HIN RECOMBINASE, I4 FORM 2, DNA BINDING 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 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 ASN C 7 ? GLU C 19 ? ASN C 145 GLU C 157 1 ? 13 HELX_P HELX_P2 2 PRO C 23 ? GLY C 32 ? PRO C 161 GLY C 170 1 ? 10 HELX_P HELX_P3 3 GLY C 34 ? PHE C 42 ? GLY C 172 PHE C 180 1 ? 9 HELX_P HELX_P4 4 PRO C 43 ? ILE C 47 ? PRO C 181 ILE C 185 5 ? 5 # _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 DG 2 "O3'" ? ? ? 1_555 A 5IU 3 P ? ? A DG 3 A 5IU 4 1_555 ? ? ? ? ? ? ? 1.616 ? covale2 covale ? ? A 5IU 3 "O3'" ? ? ? 1_555 A DT 4 P ? ? A 5IU 4 A DT 5 1_555 ? ? ? ? ? ? ? 1.809 ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 14 N3 ? ? A DG 3 B DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 14 O2 ? ? A DG 3 B DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 14 N4 ? ? A DG 3 B DC 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A 5IU 3 N3 ? ? ? 1_555 B DA 13 N1 ? ? A 5IU 4 B DA 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A 5IU 3 O4 ? ? ? 1_555 B DA 13 N6 ? ? A 5IU 4 B DA 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 12 N1 ? ? A DT 5 B DA 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 12 N6 ? ? A DT 5 B DA 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 11 N1 ? ? A DT 6 B DA 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 11 N6 ? ? A DT 6 B DA 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 7 B DA 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 10 N6 ? ? A DT 7 B DA 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 9 N1 ? ? A DT 8 B DA 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 9 N6 ? ? A DT 8 B DA 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DG 8 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 9 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 9 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DG 8 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 9 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 10 B DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 10 B DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 11 B DA 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 11 B DA 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A DA 11 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 12 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A DA 11 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 12 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 13 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 13 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? A DG 13 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 14 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog26 hydrog ? ? A DG 13 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 14 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? A DG 13 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 14 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1JJ8 _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 1JJ8 _atom_sites.fract_transf_matrix[1][1] 0.015077 _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] 0.014557 _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] 0.016094 _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 I N O P # 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 DT 1 2 2 DT T A . n A 1 2 DG 2 3 3 DG G A . n A 1 3 5IU 3 4 4 5IU U A . n A 1 4 DT 4 5 5 DT T A . n A 1 5 DT 5 6 6 DT T A . n A 1 6 DT 6 7 7 DT T A . n A 1 7 DT 7 8 8 DT T A . n A 1 8 DG 8 9 9 DG G A . n A 1 9 DA 9 10 10 DA A A . n A 1 10 DT 10 11 11 DT T A . n A 1 11 DA 11 12 12 DA A A . n A 1 12 DA 12 13 13 DA A A . n A 1 13 DG 13 14 14 DG G A . n A 1 14 DA 14 15 15 DA A A . n B 2 1 DA 1 16 16 DA A B . n B 2 2 DT 2 17 17 DT T B . n B 2 3 DC 3 18 18 DC C B . n B 2 4 DT 4 19 19 DT T B . n B 2 5 DT 5 20 20 DT T B . n B 2 6 DA 6 21 21 DA A B . n B 2 7 DT 7 22 22 DT T B . n B 2 8 DC 8 23 23 DC C B . n B 2 9 DA 9 24 24 DA A B . n B 2 10 DA 10 25 25 DA A B . n B 2 11 DA 11 26 26 DA A B . n B 2 12 DA 12 27 27 DA A B . n B 2 13 DA 13 28 28 DA A B . n B 2 14 DC 14 29 29 DC C B . n C 3 1 GLY 1 139 139 GLY GLY C . n C 3 2 ARG 2 140 140 ARG ARG C . n C 3 3 PRO 3 141 141 PRO PRO C . n C 3 4 ARG 4 142 142 ARG ARG C . n C 3 5 ALA 5 143 143 ALA ALA C . n C 3 6 ILE 6 144 144 ILE ILE C . n C 3 7 ASN 7 145 145 ASN ASN C . n C 3 8 LYS 8 146 146 LYS LYS C . n C 3 9 HIS 9 147 147 HIS HIS C . n C 3 10 GLU 10 148 148 GLU GLU C . n C 3 11 GLN 11 149 149 GLN GLN C . n C 3 12 GLU 12 150 150 GLU GLU C . n C 3 13 GLN 13 151 151 GLN GLN C . n C 3 14 ILE 14 152 152 ILE ILE C . n C 3 15 SER 15 153 153 SER SER C . n C 3 16 ARG 16 154 154 ARG ARG C . n C 3 17 LEU 17 155 155 LEU LEU C . n C 3 18 LEU 18 156 156 LEU LEU C . n C 3 19 GLU 19 157 157 GLU GLU C . n C 3 20 LYS 20 158 158 LYS LYS C . n C 3 21 GLY 21 159 159 GLY GLY C . n C 3 22 HIS 22 160 160 HIS HIS C . n C 3 23 PRO 23 161 161 PRO PRO C . n C 3 24 ARG 24 162 162 ARG ARG C . n C 3 25 GLN 25 163 163 GLN GLN C . n C 3 26 GLN 26 164 164 GLN GLN C . n C 3 27 LEU 27 165 165 LEU LEU C . n C 3 28 ALA 28 166 166 ALA ALA C . n C 3 29 ILE 29 167 167 ILE ILE C . n C 3 30 ILE 30 168 168 ILE ILE C . n C 3 31 PHE 31 169 169 PHE PHE C . n C 3 32 GLY 32 170 170 GLY GLY C . n C 3 33 ILE 33 171 171 ILE ILE C . n C 3 34 GLY 34 172 172 GLY GLY C . n C 3 35 VAL 35 173 173 VAL VAL C . n C 3 36 SER 36 174 174 SER SER C . n C 3 37 THR 37 175 175 THR THR C . n C 3 38 LEU 38 176 176 LEU LEU C . n C 3 39 TYR 39 177 177 TYR TYR C . n C 3 40 ARG 40 178 178 ARG ARG C . n C 3 41 TYR 41 179 179 TYR TYR C . n C 3 42 PHE 42 180 180 PHE PHE C . n C 3 43 PRO 43 181 181 PRO PRO C . n C 3 44 ALA 44 182 182 ALA ALA C . n C 3 45 SER 45 183 183 SER SER C . n C 3 46 SER 46 184 184 SER SER C . n C 3 47 ILE 47 185 185 ILE ILE C . n C 3 48 LYS 48 186 186 LYS LYS C . n C 3 49 LYS 49 187 187 LYS LYS C . n C 3 50 ARG 50 188 ? ? ? C . n C 3 51 MET 51 189 ? ? ? C . n C 3 52 ASN 52 190 ? ? ? C . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 5IU _pdbx_struct_mod_residue.label_seq_id 3 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id 5IU _pdbx_struct_mod_residue.auth_seq_id 4 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DU _pdbx_struct_mod_residue.details "5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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,F # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 212 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _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 2002-02-22 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2015-02-04 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' Other # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SOLVE phasing . ? 1 CNS refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 5IU _pdbx_validate_rmsd_bond.auth_seq_id_1 4 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 P _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 DT _pdbx_validate_rmsd_bond.auth_seq_id_2 5 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.809 _pdbx_validate_rmsd_bond.bond_target_value 1.607 _pdbx_validate_rmsd_bond.bond_deviation 0.202 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.012 _pdbx_validate_rmsd_bond.linker_flag Y # 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 "O3'" A 5IU 4 ? ? P A DT 5 ? ? "O5'" A DT 5 ? ? 91.33 104.00 -12.67 1.90 Y 2 1 "O5'" A DT 5 ? ? P A DT 5 ? ? OP2 A DT 5 ? ? 120.27 110.70 9.57 1.20 N 3 1 "O4'" B DA 28 ? ? "C1'" B DA 28 ? ? N9 B DA 28 ? ? 110.16 108.30 1.86 0.30 N # 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 GLU C 157 ? ? -103.47 63.58 2 1 LYS C 158 ? ? -169.06 -1.92 3 1 LYS C 186 ? ? -53.33 -5.15 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DA B 25 ? ? 0.064 'SIDE CHAIN' 2 1 DA B 28 ? ? 0.075 'SIDE CHAIN' # _pdbx_validate_polymer_linkage.id 1 _pdbx_validate_polymer_linkage.PDB_model_num 1 _pdbx_validate_polymer_linkage.auth_atom_id_1 "O3'" _pdbx_validate_polymer_linkage.auth_asym_id_1 A _pdbx_validate_polymer_linkage.auth_comp_id_1 5IU _pdbx_validate_polymer_linkage.auth_seq_id_1 4 _pdbx_validate_polymer_linkage.PDB_ins_code_1 ? _pdbx_validate_polymer_linkage.label_alt_id_1 ? _pdbx_validate_polymer_linkage.auth_atom_id_2 P _pdbx_validate_polymer_linkage.auth_asym_id_2 A _pdbx_validate_polymer_linkage.auth_comp_id_2 DT _pdbx_validate_polymer_linkage.auth_seq_id_2 5 _pdbx_validate_polymer_linkage.PDB_ins_code_2 ? _pdbx_validate_polymer_linkage.label_alt_id_2 ? _pdbx_validate_polymer_linkage.dist 1.81 # 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 DA 15 ? "C4'" ? A DA 14 "C4'" 2 1 Y 1 A DA 15 ? "O4'" ? A DA 14 "O4'" 3 1 Y 1 A DA 15 ? "C3'" ? A DA 14 "C3'" 4 1 Y 1 A DA 15 ? "O3'" ? A DA 14 "O3'" 5 1 Y 1 A DA 15 ? "C2'" ? A DA 14 "C2'" 6 1 Y 1 A DA 15 ? "C1'" ? A DA 14 "C1'" 7 1 Y 1 A DA 15 ? N9 ? A DA 14 N9 8 1 Y 1 A DA 15 ? C8 ? A DA 14 C8 9 1 Y 1 A DA 15 ? N7 ? A DA 14 N7 10 1 Y 1 A DA 15 ? C5 ? A DA 14 C5 11 1 Y 1 A DA 15 ? C6 ? A DA 14 C6 12 1 Y 1 A DA 15 ? N6 ? A DA 14 N6 13 1 Y 1 A DA 15 ? N1 ? A DA 14 N1 14 1 Y 1 A DA 15 ? C2 ? A DA 14 C2 15 1 Y 1 A DA 15 ? N3 ? A DA 14 N3 16 1 Y 1 A DA 15 ? C4 ? A DA 14 C4 17 1 Y 1 C LYS 146 ? CB ? C LYS 8 CB 18 1 Y 1 C LYS 146 ? CG ? C LYS 8 CG 19 1 Y 1 C LYS 146 ? CD ? C LYS 8 CD 20 1 Y 1 C LYS 146 ? CE ? C LYS 8 CE 21 1 Y 1 C LYS 146 ? NZ ? C LYS 8 NZ 22 1 Y 1 C GLU 150 ? CG ? C GLU 12 CG 23 1 Y 1 C GLU 150 ? CD ? C GLU 12 CD 24 1 Y 1 C GLU 150 ? OE1 ? C GLU 12 OE1 25 1 Y 1 C GLU 150 ? OE2 ? C GLU 12 OE2 26 1 Y 1 C ARG 154 ? CD ? C ARG 16 CD 27 1 Y 1 C ARG 154 ? NE ? C ARG 16 NE 28 1 Y 1 C ARG 154 ? CZ ? C ARG 16 CZ 29 1 Y 1 C ARG 154 ? NH1 ? C ARG 16 NH1 30 1 Y 1 C ARG 154 ? NH2 ? C ARG 16 NH2 31 1 Y 1 C LYS 158 ? CG ? C LYS 20 CG 32 1 Y 1 C LYS 158 ? CD ? C LYS 20 CD 33 1 Y 1 C LYS 158 ? CE ? C LYS 20 CE 34 1 Y 1 C LYS 158 ? NZ ? C LYS 20 NZ 35 1 Y 1 C LYS 187 ? CB ? C LYS 49 CB 36 1 Y 1 C LYS 187 ? CG ? C LYS 49 CG 37 1 Y 1 C LYS 187 ? CD ? C LYS 49 CD 38 1 Y 1 C LYS 187 ? CE ? C LYS 49 CE 39 1 Y 1 C LYS 187 ? NZ ? C LYS 49 NZ # 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 C ARG 188 ? C ARG 50 2 1 Y 1 C MET 189 ? C MET 51 3 1 Y 1 C ASN 190 ? C ASN 52 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1JJ8 'double helix' 1JJ8 '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 A DG 2 1_555 B DC 14 1_555 0.297 -0.109 -0.500 -14.683 -9.559 2.557 1 A_DG3:DC29_B A 3 ? B 29 ? 19 1 1 A 5IU 3 1_555 B DA 13 1_555 0.725 0.123 -0.128 -3.727 -0.701 -6.744 2 A_5IU4:DA28_B A 4 ? B 28 ? 20 1 1 A DT 4 1_555 B DA 12 1_555 -0.175 -0.278 -0.010 -7.007 -11.966 1.218 3 A_DT5:DA27_B A 5 ? B 27 ? 20 1 1 A DT 5 1_555 B DA 11 1_555 -0.062 -0.085 -0.130 -2.100 -23.330 0.544 4 A_DT6:DA26_B A 6 ? B 26 ? 20 1 1 A DT 6 1_555 B DA 10 1_555 -0.139 -0.298 -0.057 -11.183 -14.275 -9.120 5 A_DT7:DA25_B A 7 ? B 25 ? 20 1 1 A DT 7 1_555 B DA 9 1_555 0.217 -0.070 -0.137 -7.404 -17.312 -5.587 6 A_DT8:DA24_B A 8 ? B 24 ? 20 1 1 A DG 8 1_555 B DC 8 1_555 -0.359 -0.354 -0.486 -6.581 -5.072 0.284 7 A_DG9:DC23_B A 9 ? B 23 ? 19 1 1 A DA 9 1_555 B DT 7 1_555 0.118 -0.262 -0.050 5.705 -14.048 -2.913 8 A_DA10:DT22_B A 10 ? B 22 ? 20 1 1 A DT 10 1_555 B DA 6 1_555 0.238 -0.209 -0.067 7.273 -11.070 0.573 9 A_DT11:DA21_B A 11 ? B 21 ? 20 1 1 A DA 11 1_555 B DT 5 1_555 0.097 -0.227 -0.223 -3.703 -15.375 -2.907 10 A_DA12:DT20_B A 12 ? B 20 ? 20 1 1 A DA 12 1_555 B DT 4 1_555 0.018 0.001 0.272 5.019 -12.572 6.340 11 A_DA13:DT19_B A 13 ? B 19 ? 20 1 1 A DG 13 1_555 B DC 3 1_555 0.122 0.271 -0.019 5.209 -19.653 5.982 12 A_DG14:DC18_B A 14 ? B 18 ? 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 A DG 2 1_555 B DC 14 1_555 A 5IU 3 1_555 B DA 13 1_555 -0.626 -1.007 3.123 0.186 -1.379 35.471 -1.458 1.053 3.156 -2.262 -0.306 35.498 1 AA_DG35IU4:DA28DC29_BB A 3 ? B 29 ? A 4 ? B 28 ? 1 A 5IU 3 1_555 B DA 13 1_555 A DT 4 1_555 B DA 12 1_555 -0.258 -0.567 3.231 2.811 1.318 30.124 -1.346 1.051 3.167 2.528 -5.390 30.280 2 AA_5IU4DT5:DA27DA28_BB A 4 ? B 28 ? A 5 ? B 27 ? 1 A DT 4 1_555 B DA 12 1_555 A DT 5 1_555 B DA 11 1_555 -0.054 0.010 3.159 2.762 3.979 34.018 -0.585 0.509 3.126 6.759 -4.692 34.351 3 AA_DT5DT6:DA26DA27_BB A 5 ? B 27 ? A 6 ? B 26 ? 1 A DT 5 1_555 B DA 11 1_555 A DT 6 1_555 B DA 10 1_555 0.177 -0.015 3.515 0.643 -0.701 37.408 0.076 -0.185 3.518 -1.093 -1.002 37.419 4 AA_DT6DT7:DA25DA26_BB A 6 ? B 26 ? A 7 ? B 25 ? 1 A DT 6 1_555 B DA 10 1_555 A DT 7 1_555 B DA 9 1_555 -0.686 -0.484 3.127 -1.362 0.418 34.800 -0.870 0.948 3.145 0.698 2.276 34.828 5 AA_DT7DT8:DA24DA25_BB A 7 ? B 25 ? A 8 ? B 24 ? 1 A DT 7 1_555 B DA 9 1_555 A DG 8 1_555 B DC 8 1_555 0.976 1.173 3.391 2.954 3.613 33.925 1.386 -1.161 3.563 6.156 -5.034 34.235 6 AA_DT8DG9:DC23DA24_BB A 8 ? B 24 ? A 9 ? B 23 ? 1 A DG 8 1_555 B DC 8 1_555 A DA 9 1_555 B DT 7 1_555 -1.116 0.992 3.089 -8.281 0.796 38.284 1.387 0.689 3.270 1.196 12.448 39.144 7 AA_DG9DA10:DT22DC23_BB A 9 ? B 23 ? A 10 ? B 22 ? 1 A DA 9 1_555 B DT 7 1_555 A DT 10 1_555 B DA 6 1_555 0.254 -0.752 3.277 1.619 2.824 29.619 -2.049 -0.159 3.202 5.503 -3.155 29.793 8 AA_DA10DT11:DA21DT22_BB A 10 ? B 22 ? A 11 ? B 21 ? 1 A DT 10 1_555 B DA 6 1_555 A DA 11 1_555 B DT 5 1_555 -0.564 0.763 3.654 -1.928 4.993 39.305 0.463 0.576 3.742 7.382 2.850 39.654 9 AA_DT11DA12:DT20DA21_BB A 11 ? B 21 ? A 12 ? B 20 ? 1 A DA 11 1_555 B DT 5 1_555 A DA 12 1_555 B DT 4 1_555 0.371 -0.062 2.936 -1.957 -2.326 34.754 0.212 -0.884 2.909 -3.885 3.269 34.883 10 AA_DA12DA13:DT19DT20_BB A 12 ? B 20 ? A 13 ? B 19 ? 1 A DA 12 1_555 B DT 4 1_555 A DG 13 1_555 B DC 3 1_555 -0.117 -0.332 3.346 1.887 6.691 33.501 -1.635 0.500 3.210 11.455 -3.231 34.194 11 AA_DA13DG14:DC18DT19_BB A 13 ? B 19 ? A 14 ? B 18 ? # _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 1 205 205 HOH HOH A . D 4 HOH 2 206 206 HOH HOH A . E 4 HOH 1 204 204 HOH HOH B . E 4 HOH 2 207 207 HOH HOH B . E 4 HOH 3 208 208 HOH HOH B . E 4 HOH 4 210 210 HOH HOH B . E 4 HOH 5 211 211 HOH HOH B . E 4 HOH 6 212 212 HOH HOH B . F 4 HOH 1 201 201 HOH HOH C . F 4 HOH 2 202 202 HOH HOH C . F 4 HOH 3 203 203 HOH HOH C . F 4 HOH 4 209 209 HOH HOH C . #