data_4HIF # _entry.id 4HIF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4HIF pdb_00004hif 10.2210/pdb4hif/pdb NDB NA2073 ? ? RCSB RCSB075505 ? ? WWPDB D_1000075505 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1ICK . unspecified PDB 211D . unspecified PDB 3P4J . unspecified PDB 1D39 . unspecified PDB 4HID . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4HIF _pdbx_database_status.recvd_initial_deposition_date 2012-10-11 _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 _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Drozdzal, P.' 1 'Gilski, M.' 2 'Kierzek, R.' 3 'Lomozik, L.' 4 'Jaskolski, M.' 5 # 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 'Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.' 'Acta Crystallogr.,Sect.D' 69 1180 1190 2013 ABCRE6 DK 0907-4449 0766 ? 23695262 10.1107/S0907444913007798 1 'High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A' 'Nucleic Acids Res.' 39 6238 6248 2011 NARHAD UK 0305-1048 0389 ? ? ? 2 'Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy' 'Acta Crystallogr.,Sect.D' 57 990 995 2001 ABCRE6 DK 0907-4449 0766 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Drozdzal, P.' 1 ? primary 'Gilski, M.' 2 ? primary 'Kierzek, R.' 3 ? primary 'Lomozik, L.' 4 ? primary 'Jaskolski, M.' 5 ? 1 'Brzezinski, K.' 6 ? 1 'Brzuszkiewicz, A.' 7 ? 1 'Dauter, M.' 8 ? 1 'Kubicki, M.' 9 ? 1 'Jaskolski, M.' 10 ? 1 'Dauter, Z.' 11 ? 2 'Dauter, Z.' 12 ? 2 'Adamiak, D.A.' 13 ? # _cell.entry_id 4HIF _cell.length_a 17.791 _cell.length_b 30.907 _cell.length_c 44.196 _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 4HIF _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*CP*GP*CP*G)-3') ; 1810.205 2 ? ? ? ? 2 non-polymer syn 'ZINC ION' 65.409 2 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 4 non-polymer syn 'SPERMINE (FULLY PROTONATED FORM)' 206.372 1 ? ? ? ? 5 water nat water 18.015 75 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 DG n # _pdbx_entity_src_syn.entity_id 1 _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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details 'Synthetic construct' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4HIF _struct_ref.pdbx_db_accession 4HIF _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4HIF A 1 ? 6 ? 4HIF 1 ? 6 ? 1 6 2 1 4HIF B 1 ? 6 ? 4HIF 7 ? 12 ? 7 12 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 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 HOH non-polymer . WATER ? 'H2 O' 18.015 SPK non-polymer . 'SPERMINE (FULLY PROTONATED FORM)' ? 'C10 H30 N4 4' 206.372 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # _exptl.entry_id 4HIF _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.53 _exptl_crystal.density_percent_sol 19.80 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;A 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/V WITH 10% MPD, 12 MM SPERMINE TETRA-HCL,12 MM NACL, 80 MM KCL AND EQUILIBRATED AGAINST 35% MPD, PH 6. VAPOR DIFFUSION, HANGING DROP METHOD, TEMPERATURE 292K. FOR ZN2+ SOAKING A CRYSTAL WAS PLACED IN 0.002 ML OF THE RESERVOIR SOLUTION MIXED WITH 0.002 ML OF 5 MM ZNCL2 FOR ONE WEEK. ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'MAR555 FLAT PANEL' _diffrn_detector.pdbx_collection_date 2010-12-02 _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 'SI 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8174 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X11' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X11 _diffrn_source.pdbx_wavelength 0.8174 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4HIF _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 17.976 _reflns.d_resolution_high 0.849 _reflns.number_obs 36512 _reflns.number_all ? _reflns.percent_possible_obs 87.9 _reflns.pdbx_Rmerge_I_obs 0.03600 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 20.0200 _reflns.B_iso_Wilson_estimate 8.109 _reflns.pdbx_redundancy 3.020 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 0.85 _reflns_shell.d_res_low 0.90 _reflns_shell.percent_possible_all 63.8 _reflns_shell.Rmerge_I_obs 0.22200 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.110 _reflns_shell.pdbx_redundancy 1.77 _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 ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4HIF _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 36512 _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 17.976 _refine.ls_d_res_high 0.85 _refine.ls_percent_reflns_obs 87.9 _refine.ls_R_factor_obs 0.092 _refine.ls_R_factor_all 0.092 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.113 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 2.75 _refine.ls_number_reflns_R_free 1004 _refine.ls_number_parameters 3228 _refine.ls_number_restraints 709 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'MOEWS & KRETSINGER, J.MOL.BIOL.(1975) 91, 201' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ;THE REFINEMENT WAS CARRIED OUT AGAINST SEPARATE BIJVOET PAIRS. ANISOTROPIC ADPS. ANISOTROPIC REFINEMENT REDUCED FREE R-FACTOR FROM 0.1562 TO 0.1235. HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. THE FINAL REFINEMENT WAS CALCULATED USING WEIGHTED FULL MATRIX LEAST-SQUARES PROCEDURE. ; _refine.pdbx_starting_model 1I0T _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'CLOWNEY, GELBIN & PARKINSON' _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 ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _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_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 4HIF _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 6 _refine_analyze.occupancy_sum_hydrogen 144.60 _refine_analyze.occupancy_sum_non_hydrogen 313.39 # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 240 _refine_hist.pdbx_number_atoms_ligand 17 _refine_hist.number_atoms_solvent 75 _refine_hist.number_atoms_total 332 _refine_hist.d_res_high 0.85 _refine_hist.d_res_low 17.976 # 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 s_bond_d 0.027 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.059 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.123 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.025 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.033 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.076 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 4HIF _pdbx_refine.R_factor_all_no_cutoff 0.092 _pdbx_refine.R_factor_obs_no_cutoff 0.092 _pdbx_refine.free_R_factor_no_cutoff 0.113 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 2.75 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1004 _pdbx_refine.R_factor_all_4sig_cutoff 0.083 _pdbx_refine.R_factor_obs_4sig_cutoff 0.083 _pdbx_refine.free_R_factor_4sig_cutoff 0.104 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 2.73 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 850 _pdbx_refine.number_reflns_obs_4sig_cutoff 31130 # _struct.entry_id 4HIF _struct.title 'Ultrahigh-resolution crystal structure of Z-DNA in complex with Zn2+ ions' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4HIF _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'self-complementary DNA, DNA, Z-DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 4 ? G N N 5 ? H N N 5 ? # _struct_biol.id 1 _struct_biol.details ? # 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 _struct_conn.pdbx_role metalc1 metalc ? ? A DG 6 N7 ? ? ? 1_555 C ZN . ZN ? ? A DG 6 A ZN 101 1_555 ? ? ? ? ? ? ? 2.112 ? ? metalc2 metalc ? ? C ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 101 A HOH 201 1_555 ? ? ? ? ? ? ? 2.117 ? ? metalc3 metalc ? ? C ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 101 A HOH 205 1_555 ? ? ? ? ? ? ? 2.097 ? ? metalc4 metalc ? ? C ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 101 A HOH 210 1_555 ? ? ? ? ? ? ? 2.140 ? ? metalc5 metalc ? ? C ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 101 A HOH 234 1_555 ? ? ? ? ? ? ? 2.110 ? ? metalc6 metalc ? ? C ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 101 A HOH 235 1_555 ? ? ? ? ? ? ? 2.114 ? ? metalc7 metalc ? ? B DG 4 N7 ? ? ? 1_555 D ZN . ZN ? ? B DG 10 B ZN 101 1_555 ? ? ? ? ? ? ? 1.991 ? ? metalc8 metalc ? ? D ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 101 B HOH 233 1_555 ? ? ? ? ? ? ? 1.944 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A ZN 101 ? 6 'BINDING SITE FOR RESIDUE ZN A 101' AC2 Software B ZN 101 ? 4 'BINDING SITE FOR RESIDUE ZN B 101' AC3 Software B CL 102 ? 4 'BINDING SITE FOR RESIDUE CL B 102' AC4 Software B SPK 103 ? 12 'BINDING SITE FOR RESIDUE SPK B 103' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 DG A 6 ? DG A 6 . ? 1_555 ? 2 AC1 6 HOH G . ? HOH A 201 . ? 1_555 ? 3 AC1 6 HOH G . ? HOH A 205 . ? 1_555 ? 4 AC1 6 HOH G . ? HOH A 210 . ? 1_555 ? 5 AC1 6 HOH G . ? HOH A 234 . ? 1_555 ? 6 AC1 6 HOH G . ? HOH A 235 . ? 1_555 ? 7 AC2 4 DG B 4 ? DG B 10 . ? 1_555 ? 8 AC2 4 DG B 6 ? DG B 12 . ? 4_566 ? 9 AC2 4 CL E . ? CL B 102 . ? 1_555 ? 10 AC2 4 HOH H . ? HOH B 233 . ? 1_555 ? 11 AC3 4 DG B 2 ? DG B 8 . ? 1_555 ? 12 AC3 4 DG B 4 ? DG B 10 . ? 1_555 ? 13 AC3 4 DG B 6 ? DG B 12 . ? 4_566 ? 14 AC3 4 ZN D . ? ZN B 101 . ? 1_555 ? 15 AC4 12 DG A 2 ? DG A 2 . ? 2_665 ? 16 AC4 12 DC A 3 ? DC A 3 . ? 2_665 ? 17 AC4 12 DG A 4 ? DG A 4 . ? 3_656 ? 18 AC4 12 DC A 5 ? DC A 5 . ? 3_656 ? 19 AC4 12 DG A 6 ? DG A 6 . ? 3_656 ? 20 AC4 12 HOH G . ? HOH A 219 . ? 3_656 ? 21 AC4 12 HOH G . ? HOH A 229 . ? 2_665 ? 22 AC4 12 HOH G . ? HOH A 231 . ? 2_665 ? 23 AC4 12 DC B 3 ? DC B 9 . ? 1_555 ? 24 AC4 12 HOH H . ? HOH B 214 . ? 1_555 ? 25 AC4 12 HOH H . ? HOH B 237 . ? 1_555 ? 26 AC4 12 HOH H . ? HOH B 238 . ? 1_555 ? # _database_PDB_matrix.entry_id 4HIF _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 4HIF _atom_sites.fract_transf_matrix[1][1] 0.056208 _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] 0.032355 _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] 0.022626 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C CL N O P ZN # 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 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n B 1 1 DC 1 7 7 DC DC B . n B 1 2 DG 2 8 8 DG DG B . n B 1 3 DC 3 9 9 DC DC B . n B 1 4 DG 4 10 10 DG DG B . n B 1 5 DC 5 11 11 DC DC B . n B 1 6 DG 6 12 12 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 ZN 1 101 14 ZN ZN A . D 2 ZN 1 101 13 ZN ZN B . E 3 CL 1 102 15 CL CL B . F 4 SPK 1 103 16 SPK SPK B . G 5 HOH 1 201 21 HOH HOH A . G 5 HOH 2 202 24 HOH HOH A . G 5 HOH 3 203 25 HOH HOH A . G 5 HOH 4 204 27 HOH HOH A . G 5 HOH 5 205 28 HOH HOH A . G 5 HOH 6 206 30 HOH HOH A . G 5 HOH 7 207 32 HOH HOH A . G 5 HOH 8 208 33 HOH HOH A . G 5 HOH 9 209 35 HOH HOH A . G 5 HOH 10 210 42 HOH HOH A . G 5 HOH 11 211 44 HOH HOH A . G 5 HOH 12 212 45 HOH HOH A . G 5 HOH 13 213 46 HOH HOH A . G 5 HOH 14 214 47 HOH HOH A . G 5 HOH 15 215 48 HOH HOH A . G 5 HOH 16 216 50 HOH HOH A . G 5 HOH 17 217 52 HOH HOH A . G 5 HOH 18 218 53 HOH HOH A . G 5 HOH 19 219 54 HOH HOH A . G 5 HOH 20 220 59 HOH HOH A . G 5 HOH 21 221 60 HOH HOH A . G 5 HOH 22 222 61 HOH HOH A . G 5 HOH 23 223 68 HOH HOH A . G 5 HOH 24 224 69 HOH HOH A . G 5 HOH 25 225 70 HOH HOH A . G 5 HOH 26 226 71 HOH HOH A . G 5 HOH 27 227 72 HOH HOH A . G 5 HOH 28 228 73 HOH HOH A . G 5 HOH 29 229 74 HOH HOH A . G 5 HOH 30 230 76 HOH HOH A . G 5 HOH 31 231 79 HOH HOH A . G 5 HOH 32 232 80 HOH HOH A . G 5 HOH 33 233 81 HOH HOH A . G 5 HOH 34 234 82 HOH HOH A . G 5 HOH 35 235 83 HOH HOH A . G 5 HOH 36 236 87 HOH HOH A . H 5 HOH 1 201 17 HOH HOH B . H 5 HOH 2 202 18 HOH HOH B . H 5 HOH 3 203 19 HOH HOH B . H 5 HOH 4 204 20 HOH HOH B . H 5 HOH 5 205 22 HOH HOH B . H 5 HOH 6 206 23 HOH HOH B . H 5 HOH 7 207 26 HOH HOH B . H 5 HOH 8 208 29 HOH HOH B . H 5 HOH 9 209 31 HOH HOH B . H 5 HOH 10 210 34 HOH HOH B . H 5 HOH 11 211 36 HOH HOH B . H 5 HOH 12 212 37 HOH HOH B . H 5 HOH 13 213 38 HOH HOH B . H 5 HOH 14 214 39 HOH HOH B . H 5 HOH 15 215 40 HOH HOH B . H 5 HOH 16 216 41 HOH HOH B . H 5 HOH 17 217 43 HOH HOH B . H 5 HOH 18 218 49 HOH HOH B . H 5 HOH 19 219 51 HOH HOH B . H 5 HOH 20 220 55 HOH HOH B . H 5 HOH 21 221 56 HOH HOH B . H 5 HOH 22 222 57 HOH HOH B . H 5 HOH 23 223 58 HOH HOH B . H 5 HOH 24 224 62 HOH HOH B . H 5 HOH 25 225 63 HOH HOH B . H 5 HOH 26 226 64 HOH HOH B . H 5 HOH 27 227 65 HOH HOH B . H 5 HOH 28 228 66 HOH HOH B . H 5 HOH 29 229 67 HOH HOH B . H 5 HOH 30 230 75 HOH HOH B . H 5 HOH 31 231 77 HOH HOH B . H 5 HOH 32 232 78 HOH HOH B . H 5 HOH 33 233 84 HOH HOH B . H 5 HOH 34 234 85 HOH HOH B . H 5 HOH 35 235 86 HOH HOH B . H 5 HOH 36 236 88 HOH HOH B . H 5 HOH 37 237 89 HOH HOH B . H 5 HOH 38 238 90 HOH HOH B . H 5 HOH 39 239 91 HOH HOH B . # _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 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # 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)' 630 ? 1 MORE -5 ? 1 'SSA (A^2)' 2340 ? # _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_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N7 ? A DG 6 ? A DG 6 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 201 ? 1_555 90.2 ? 2 N7 ? A DG 6 ? A DG 6 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 205 ? 1_555 92.9 ? 3 O ? G HOH . ? A HOH 201 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 205 ? 1_555 87.1 ? 4 N7 ? A DG 6 ? A DG 6 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 92.2 ? 5 O ? G HOH . ? A HOH 201 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 177.5 ? 6 O ? G HOH . ? A HOH 205 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 93.3 ? 7 N7 ? A DG 6 ? A DG 6 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 234 ? 1_555 86.2 ? 8 O ? G HOH . ? A HOH 201 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 234 ? 1_555 91.3 ? 9 O ? G HOH . ? A HOH 205 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 234 ? 1_555 178.1 ? 10 O ? G HOH . ? A HOH 210 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 234 ? 1_555 88.4 ? 11 N7 ? A DG 6 ? A DG 6 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 235 ? 1_555 176.3 ? 12 O ? G HOH . ? A HOH 201 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 235 ? 1_555 88.2 ? 13 O ? G HOH . ? A HOH 205 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 235 ? 1_555 90.4 ? 14 O ? G HOH . ? A HOH 210 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 235 ? 1_555 89.3 ? 15 O ? G HOH . ? A HOH 234 ? 1_555 ZN ? C ZN . ? A ZN 101 ? 1_555 O ? G HOH . ? A HOH 235 ? 1_555 90.5 ? 16 N7 ? B DG 4 ? B DG 10 ? 1_555 ZN ? D ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 233 ? 1_555 111.0 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2013-06-05 2 'Structure model' 1 1 2017-09-27 3 'Structure model' 1 2 2023-09-20 # _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_details.details ? # 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' Advisory 2 2 'Structure model' 'Data collection' 3 3 'Structure model' Advisory 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 3 'Structure model' 'Derived calculations' 7 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' diffrn_detector 2 2 'Structure model' pdbx_unobs_or_zero_occ_atoms 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' database_2 6 3 'Structure model' diffrn_source 7 3 'Structure model' pdbx_initial_refinement_model 8 3 'Structure model' pdbx_struct_conn_angle 9 3 'Structure model' pdbx_unobs_or_zero_occ_atoms 10 3 'Structure model' struct_conn 11 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_diffrn_detector.detector' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 16 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 17 3 'Structure model' '_pdbx_struct_conn_angle.value' 18 3 'Structure model' '_struct_conn.pdbx_dist_value' 19 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 20 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 21 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 22 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 23 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 24 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 25 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 26 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 27 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 28 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 29 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 30 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 31 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 32 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 PHASER phasing . ? 2 SHELXL-97 refinement . ? 3 XDS 'data reduction' . ? 4 XDS '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 N7 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DG _pdbx_validate_close_contact.auth_seq_id_1 4 _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_2 232 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.16 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 N7 A DG 2 ? ? C8 A DG 2 ? ? 1.265 1.305 -0.040 0.006 N 2 1 N7 A DG 6 ? ? C8 A DG 6 ? ? 1.341 1.305 0.036 0.006 N 3 1 "C3'" B DG 12 ? B "C2'" B DG 12 ? ? 1.451 1.516 -0.065 0.008 N # 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 "C3'" A DC 1 ? ? "O3'" A DC 1 ? B P A DG 2 ? B 110.53 119.70 -9.17 1.20 Y 2 1 "O3'" A DC 1 ? B P A DG 2 ? B OP1 A DG 2 ? B 126.29 110.50 15.79 1.10 Y 3 1 "O5'" A DG 2 ? B "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 94.26 109.40 -15.14 0.80 N 4 1 "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? "C3'" A DC 3 ? A 110.00 106.00 4.00 0.60 N 5 1 "C5'" A DC 3 ? ? "C4'" A DC 3 ? ? "C3'" A DC 3 ? B 127.33 115.70 11.63 1.20 N 6 1 "C3'" A DC 3 ? B "C2'" A DC 3 ? ? "C1'" A DC 3 ? ? 94.79 102.40 -7.61 0.80 N 7 1 "O5'" A DG 4 ? A "C5'" A DG 4 ? ? "C4'" A DG 4 ? ? 102.12 109.40 -7.28 0.80 N 8 1 "C5'" B DG 12 ? ? "C4'" B DG 12 ? ? "C3'" B DG 12 ? A 134.12 115.70 18.42 1.20 N 9 1 "C4'" B DG 12 ? ? "C3'" B DG 12 ? A "O3'" B DG 12 ? A 125.74 112.30 13.44 2.00 N # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag N _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 0 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id B _pdbx_unobs_or_zero_occ_atoms.auth_comp_id SPK _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 103 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id C8 _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id F _pdbx_unobs_or_zero_occ_atoms.label_comp_id SPK _pdbx_unobs_or_zero_occ_atoms.label_seq_id ? _pdbx_unobs_or_zero_occ_atoms.label_atom_id C8 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal CL CL CL N N 1 DC OP3 O N N 2 DC P P N N 3 DC OP1 O N N 4 DC OP2 O N N 5 DC "O5'" O N N 6 DC "C5'" C N N 7 DC "C4'" C N R 8 DC "O4'" O N N 9 DC "C3'" C N S 10 DC "O3'" O N N 11 DC "C2'" C N N 12 DC "C1'" C N R 13 DC N1 N N N 14 DC C2 C N N 15 DC O2 O N N 16 DC N3 N N N 17 DC C4 C N N 18 DC N4 N N N 19 DC C5 C N N 20 DC C6 C N N 21 DC HOP3 H N N 22 DC HOP2 H N N 23 DC "H5'" H N N 24 DC "H5''" H N N 25 DC "H4'" H N N 26 DC "H3'" H N N 27 DC "HO3'" H N N 28 DC "H2'" H N N 29 DC "H2''" H N N 30 DC "H1'" H N N 31 DC H41 H N N 32 DC H42 H N N 33 DC H5 H N N 34 DC H6 H N N 35 DG OP3 O N N 36 DG P P N N 37 DG OP1 O N N 38 DG OP2 O N N 39 DG "O5'" O N N 40 DG "C5'" C N N 41 DG "C4'" C N R 42 DG "O4'" O N N 43 DG "C3'" C N S 44 DG "O3'" O N N 45 DG "C2'" C N N 46 DG "C1'" C N R 47 DG N9 N Y N 48 DG C8 C Y N 49 DG N7 N Y N 50 DG C5 C Y N 51 DG C6 C N N 52 DG O6 O N N 53 DG N1 N N N 54 DG C2 C N N 55 DG N2 N N N 56 DG N3 N N N 57 DG C4 C Y N 58 DG HOP3 H N N 59 DG HOP2 H N N 60 DG "H5'" H N N 61 DG "H5''" H N N 62 DG "H4'" H N N 63 DG "H3'" H N N 64 DG "HO3'" H N N 65 DG "H2'" H N N 66 DG "H2''" H N N 67 DG "H1'" H N N 68 DG H8 H N N 69 DG H1 H N N 70 DG H21 H N N 71 DG H22 H N N 72 HOH O O N N 73 HOH H1 H N N 74 HOH H2 H N N 75 SPK N1 N N N 76 SPK C2 C N N 77 SPK C3 C N N 78 SPK C4 C N N 79 SPK N5 N N N 80 SPK C6 C N N 81 SPK C7 C N N 82 SPK C8 C N N 83 SPK C9 C N N 84 SPK N10 N N N 85 SPK C11 C N N 86 SPK C12 C N N 87 SPK C13 C N N 88 SPK N14 N N N 89 SPK H1A H N N 90 SPK H1B H N N 91 SPK H1C H N N 92 SPK H2A H N N 93 SPK H2B H N N 94 SPK H3A H N N 95 SPK H3B H N N 96 SPK H4A H N N 97 SPK H4B H N N 98 SPK H5A H N N 99 SPK H5B H N N 100 SPK H6A H N N 101 SPK H6B H N N 102 SPK H7A H N N 103 SPK H7B H N N 104 SPK H8A H N N 105 SPK H8B H N N 106 SPK H9A H N N 107 SPK H9B H N N 108 SPK H101 H N N 109 SPK H102 H N N 110 SPK H111 H N N 111 SPK H112 H N N 112 SPK H121 H N N 113 SPK H122 H N N 114 SPK H131 H N N 115 SPK H132 H N N 116 SPK H141 H N N 117 SPK H142 H N N 118 SPK H143 H N N 119 ZN ZN ZN N N 120 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 SPK N1 C2 sing N N 77 SPK N1 H1A sing N N 78 SPK N1 H1B sing N N 79 SPK N1 H1C sing N N 80 SPK C2 C3 sing N N 81 SPK C2 H2A sing N N 82 SPK C2 H2B sing N N 83 SPK C3 C4 sing N N 84 SPK C3 H3A sing N N 85 SPK C3 H3B sing N N 86 SPK C4 N5 sing N N 87 SPK C4 H4A sing N N 88 SPK C4 H4B sing N N 89 SPK N5 C6 sing N N 90 SPK N5 H5A sing N N 91 SPK N5 H5B sing N N 92 SPK C6 C7 sing N N 93 SPK C6 H6A sing N N 94 SPK C6 H6B sing N N 95 SPK C7 C8 sing N N 96 SPK C7 H7A sing N N 97 SPK C7 H7B sing N N 98 SPK C8 C9 sing N N 99 SPK C8 H8A sing N N 100 SPK C8 H8B sing N N 101 SPK C9 N10 sing N N 102 SPK C9 H9A sing N N 103 SPK C9 H9B sing N N 104 SPK N10 C11 sing N N 105 SPK N10 H101 sing N N 106 SPK N10 H102 sing N N 107 SPK C11 C12 sing N N 108 SPK C11 H111 sing N N 109 SPK C11 H112 sing N N 110 SPK C12 C13 sing N N 111 SPK C12 H121 sing N N 112 SPK C12 H122 sing N N 113 SPK C13 N14 sing N N 114 SPK C13 H131 sing N N 115 SPK C13 H132 sing N N 116 SPK N14 H141 sing N N 117 SPK N14 H142 sing N N 118 SPK N14 H143 sing N N 119 # _ndb_struct_conf_na.entry_id 4HIF _ndb_struct_conf_na.feature 'z-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 DC 1 1_555 B DG 6 1_555 -0.306 -0.151 0.049 1.014 4.461 0.616 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 0.319 -0.112 0.007 -2.983 -4.493 1.804 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 -0.225 -0.137 -0.074 10.879 -7.718 1.299 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.268 -0.113 0.068 -9.983 -4.674 1.505 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B DG 2 1_555 -0.142 -0.123 0.018 2.410 0.399 2.510 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.188 -0.179 0.067 -1.486 5.948 2.242 6 A_DG6:DC7_B A 6 ? B 7 ? 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 DC 1 1_555 B DG 6 1_555 A DG 2 1_555 B DC 5 1_555 -0.422 5.629 3.555 -2.672 -1.257 -12.298 -23.850 -5.538 3.926 5.759 -12.241 -12.646 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 -0.176 -1.070 3.241 -0.628 -2.719 -50.333 1.446 -0.251 3.181 3.194 -0.738 -50.405 2 AA_DG2DC3:DG10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B DG 4 1_555 A DG 4 1_555 B DC 3 1_555 -0.133 5.329 4.029 0.101 -5.434 -2.678 11.885 -0.104 6.563 63.773 1.186 -6.058 3 AA_DC3DG4:DC9DG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 3 1_555 A DC 5 1_555 B DG 2 1_555 0.045 -0.863 3.204 0.749 -2.362 -52.314 1.129 0.099 3.164 2.678 0.849 -52.369 4 AA_DG4DC5:DG8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 0.009 5.320 3.555 2.276 -0.478 -9.639 -29.758 4.936 3.710 2.792 13.290 -9.914 5 AA_DC5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ZINC ION' ZN 3 'CHLORIDE ION' CL 4 'SPERMINE (FULLY PROTONATED FORM)' SPK 5 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1I0T _pdbx_initial_refinement_model.details ? #