data_4GQD # _entry.id 4GQD # _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 4GQD pdb_00004gqd 10.2210/pdb4gqd/pdb NDB NA2014 ? ? RCSB RCSB074506 ? ? WWPDB D_1000074506 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2ORG . unspecified PDB 2ORF . unspecified PDB 3TOK . unspecified PDB 2ORH . unspecified PDB 4GRE . unspecified PDB 4GS2 . unspecified PDB 4GSG . unspecified PDB 4GSI . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4GQD _pdbx_database_status.recvd_initial_deposition_date 2012-08-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.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 'Carter, M.' 1 'Ho, P.S.' 2 # _citation.id primary _citation.title 'Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.' _citation.journal_abbrev Biochemistry _citation.journal_volume 52 _citation.page_first 4891 _citation.page_last 4903 _citation.year 2013 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23789744 _citation.pdbx_database_id_DOI 10.1021/bi400590h # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Carter, M.' 1 ? primary 'Voth, A.R.' 2 ? primary 'Scholfield, M.R.' 3 ? primary 'Rummel, B.' 4 ? primary 'Sowers, L.C.' 5 ? primary 'Ho, P.S.' 6 ? # _cell.entry_id 4GQD _cell.length_a 65.692 _cell.length_b 23.565 _cell.length_c 37.286 _cell.angle_alpha 90.00 _cell.angle_beta 110.92 _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 4GQD _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _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*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3') ; 3081.423 2 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3') ; 3029.994 2 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 3 ? ? ? ? 4 water nat water 18.015 93 ? ? ? ? # 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 '(DC)(DC)(DG)(DG)(DT)(DA)(UCL)(DC)(DG)(DG)' CCGGTAUCGG A,D ? 2 polydeoxyribonucleotide no no '(DC)(DC)(DG)(DA)(DT)(DA)(DC)(DC)(DG)(DG)' CCGATACCGG B,C ? # 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 DC n 1 3 DG n 1 4 DG n 1 5 DT n 1 6 DA n 1 7 UCL n 1 8 DC n 1 9 DG n 1 10 DG n 2 1 DC n 2 2 DC n 2 3 DG n 2 4 DA n 2 5 DT n 2 6 DA n 2 7 DC n 2 8 DC n 2 9 DG n 2 10 DG n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'synthetically engineered DNA sequence' 2 1 sample ? ? ? ? ? 'synthetically engineered DNA sequence' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 4GQD 4GQD 1 ? CCGGTAUCGG ? 2 PDB 4GQD 4GQD 2 ? CCGATACCGG ? # 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 4GQD A 1 ? 10 ? 4GQD 1 ? 10 ? 1 10 2 1 4GQD D 1 ? 10 ? 4GQD 31 ? 40 ? 31 40 3 2 4GQD B 1 ? 10 ? 4GQD 11 ? 20 ? 11 20 4 2 4GQD C 1 ? 10 ? 4GQD 21 ? 30 ? 21 30 # 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 UCL 'DNA linking' n ;5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C9 H12 Cl N2 O8 P' 342.627 # _exptl.entry_id 4GQD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;0.7mM DNA, 25mM sodium cacodylate pH 7.0 buffer, 10-25mM calcium chloride, and 0.8-1.2mM spermine, equilibrated against a reservoir of 30-40% aqueous MPD., VAPOR DIFFUSION, SITTING DROP, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 200 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type NOIR-1 _diffrn_detector.pdbx_collection_date 2009-10-21 _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 'ROSENBAUM-ROCK SI(111) SAGITALLY FOCUSED MONOCHROMATOR' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 4.2.2' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 4.2.2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9 # _reflns.entry_id 4GQD _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 1.4 _reflns.d_resolution_low 30.68 _reflns.d_resolution_high 1.94 _reflns.number_obs 3538 _reflns.number_all 4793 _reflns.percent_possible_obs 73.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 4.6 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.94 _reflns_shell.d_res_low 2.06 _reflns_shell.percent_possible_all 54.2 _reflns_shell.Rmerge_I_obs 0.228 _reflns_shell.pdbx_Rsym_value 0.268 _reflns_shell.meanI_over_sigI_obs 3.25 _reflns_shell.pdbx_redundancy 1.02 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 638 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4GQD _refine.ls_number_reflns_obs 3323 _refine.ls_number_reflns_all 4793 _refine.pdbx_ls_sigma_I 2.0 _refine.pdbx_ls_sigma_F 1.4 _refine.pdbx_data_cutoff_high_absF 28646.87 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.68 _refine.ls_d_res_high 1.94 _refine.ls_percent_reflns_obs 81.0 _refine.ls_R_factor_obs 0.264 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.264 _refine.ls_R_factor_R_free 0.300 _refine.ls_R_factor_R_free_error 0.023 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.2 _refine.ls_number_reflns_R_free 174 _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 17.2 _refine.aniso_B[1][1] 1.08 _refine.aniso_B[2][2] 5.95 _refine.aniso_B[3][3] -7.03 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.07 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.3 _refine.solvent_model_param_bsol 77.8587 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'BULK SOLVENT MODEL USED' _refine.pdbx_starting_model 2ORG _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values CNS _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.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_analyze.entry_id 4GQD _refine_analyze.Luzzati_coordinate_error_obs 0.32 _refine_analyze.Luzzati_sigma_a_obs 0.39 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.35 _refine_analyze.Luzzati_sigma_a_free 0.41 _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_Luzzati_d_res_high_obs ? _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 0 _refine_hist.pdbx_number_atoms_nucleic_acid 808 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 93 _refine_hist.number_atoms_total 904 _refine_hist.d_res_high 1.94 _refine_hist.d_res_low 30.68 # 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 c_bond_d 0.005 ? ? ? ? '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 1.0 ? ? ? ? 'X-RAY DIFFRACTION' c_angle_deg_na ? ? ? ? ? 'X-RAY DIFFRACTION' c_angle_deg_prot ? ? ? ? ? 'X-RAY DIFFRACTION' c_dihedral_angle_d 21.3 ? ? ? ? 'X-RAY DIFFRACTION' c_dihedral_angle_d_na ? ? ? ? ? 'X-RAY DIFFRACTION' c_dihedral_angle_d_prot ? ? ? ? ? 'X-RAY DIFFRACTION' c_improper_angle_d 1.38 ? ? ? ? 'X-RAY DIFFRACTION' c_improper_angle_d_na ? ? ? ? ? 'X-RAY DIFFRACTION' c_improper_angle_d_prot ? ? ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it 0.00 1.50 ? ? ? 'X-RAY DIFFRACTION' c_mcangle_it 0.00 2.00 ? ? ? 'X-RAY DIFFRACTION' c_scbond_it 1.54 2.00 ? ? ? 'X-RAY DIFFRACTION' c_scangle_it 2.16 2.50 ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.94 _refine_ls_shell.d_res_low 2.06 _refine_ls_shell.number_reflns_R_work 351 _refine_ls_shell.R_factor_R_work 0.379 _refine_ls_shell.percent_reflns_obs 54.2 _refine_ls_shell.R_factor_R_free 0.492 _refine_ls_shell.R_factor_R_free_error 0.127 _refine_ls_shell.percent_reflns_R_free 4.1 _refine_ls_shell.number_reflns_R_free 15 _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 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 voth_topolo voth_topolo 'X-RAY DIFFRACTION' 2 ion.param ? 'X-RAY DIFFRACTION' 3 water_rep.param ? 'X-RAY DIFFRACTION' # _struct_ncs_dom.id 1 _struct_ncs_dom.details ? _struct_ncs_dom.pdbx_ens_id 1 # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _struct.entry_id 4GQD _struct.title 'DNA Holliday junction stabilized by chlorine halogen bond.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4GQD _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA Holliday junction, halogen bond, 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 2 ? C N N 2 ? D N N 1 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 4 ? I N N 4 ? J N N 4 ? K N N 4 ? # _struct_biol.id 1 _struct_biol.details ;The biological assembly of this structure is the four stranded DNA Holliday junction. DNA Holliday junctions are generated from the two stranded asymmetric subunit through the two-fold symmetry operator at the center of the four-stranded junction. ; # 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 covale1 covale both ? A DA 6 "O3'" A ? ? 1_555 A UCL 7 P A ? A DA 6 A UCL 7 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale2 covale one ? A UCL 7 "O3'" A ? ? 1_555 A DC 8 P A ? A UCL 7 A DC 8 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale3 covale both ? D DA 6 "O3'" B ? ? 1_555 D UCL 7 P B ? D DA 36 D UCL 37 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale4 covale one ? D UCL 7 "O3'" B ? ? 1_555 D DC 8 P B ? D UCL 37 D DC 38 1_555 ? ? ? ? ? ? ? 1.603 ? ? metalc1 metalc ? ? B DC 2 O2 A ? ? 1_555 F NA . NA ? ? B DC 12 B NA 101 1_555 ? ? ? ? ? ? ? 3.143 ? ? metalc2 metalc ? ? B DG 9 OP1 A ? ? 1_555 G NA . NA ? ? B DG 19 B NA 102 1_555 ? ? ? ? ? ? ? 2.569 ? ? metalc3 metalc ? ? F NA . NA ? ? ? 1_555 I HOH . O ? ? B NA 101 B HOH 210 1_555 ? ? ? ? ? ? ? 2.770 ? ? metalc4 metalc ? ? F NA . NA ? ? ? 1_555 D DC 2 O2 B ? B NA 101 D DC 32 1_555 ? ? ? ? ? ? ? 3.099 ? ? metalc5 metalc ? ? F NA . NA ? ? ? 1_555 K HOH . O ? ? B NA 101 D HOH 128 1_555 ? ? ? ? ? ? ? 2.787 ? ? metalc6 metalc ? ? G NA . NA ? ? ? 1_555 D DG 9 OP1 B ? B NA 102 D DG 39 1_555 ? ? ? ? ? ? ? 2.678 ? ? metalc7 metalc ? ? G NA . NA ? ? ? 1_555 K HOH . O ? ? B NA 102 D HOH 123 1_555 ? ? ? ? ? ? ? 2.147 ? ? hydrog1 hydrog ? ? A DC 1 O2 A ? ? 1_555 B DG 10 N2 A ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog2 hydrog ? ? A DC 2 N3 A ? ? 1_555 B DG 9 N1 A ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N4 A ? ? 1_555 B DG 9 O6 A ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 O2 A ? ? 1_555 B DG 9 N2 A ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N1 A ? ? 1_555 B DC 8 O2 A ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog6 hydrog ? ? A DG 4 N1 A ? ? 1_555 B DC 7 N3 A ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 N2 A ? ? 1_555 B DC 7 O2 A ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 O6 A ? ? 1_555 B DC 7 N4 A ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 6 N1 A ? ? 1_555 B DT 5 N3 A ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N6 A ? ? 1_555 B DT 5 O4 A ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 NA 101 ? 5 'BINDING SITE FOR RESIDUE NA A 101' AC2 Software B NA 101 ? 6 'BINDING SITE FOR RESIDUE NA B 101' AC3 Software B NA 102 ? 3 'BINDING SITE FOR RESIDUE NA B 102' # 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 5 DG A 3 ? DG A 3 . ? 2_656 ? 2 AC1 5 DG A 4 ? DG A 4 . ? 2_656 ? 3 AC1 5 DG C 3 ? DG C 23 . ? 2_656 ? 4 AC1 5 DA C 4 ? DA C 24 . ? 2_656 ? 5 AC1 5 HOH J . ? HOH C 110 . ? 2_656 ? 6 AC2 6 DC B 2 ? DC B 12 . ? 1_555 ? 7 AC2 6 DG B 3 ? DG B 13 . ? 1_555 ? 8 AC2 6 HOH I . ? HOH B 210 . ? 1_555 ? 9 AC2 6 DC D 2 ? DC D 32 . ? 1_555 ? 10 AC2 6 DG D 3 ? DG D 33 . ? 1_555 ? 11 AC2 6 HOH K . ? HOH D 128 . ? 1_555 ? 12 AC3 3 DG B 9 ? DG B 19 . ? 1_555 ? 13 AC3 3 DG D 9 ? DG D 39 . ? 1_555 ? 14 AC3 3 HOH K . ? HOH D 123 . ? 1_555 ? # _database_PDB_matrix.entry_id 4GQD _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 4GQD _atom_sites.fract_transf_matrix[1][1] 0.015223 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005819 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.042436 _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] 0.028713 _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 CL N NA 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 DC 1 1 1 DC DC A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 UCL 7 7 7 UCL UCL A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DG 10 10 10 DG DG A . n B 2 1 DC 1 11 11 DC DC B . n B 2 2 DC 2 12 12 DC DC B . n B 2 3 DG 3 13 13 DG DG B . n B 2 4 DA 4 14 14 DA DA B . n B 2 5 DT 5 15 15 DT DT B . n B 2 6 DA 6 16 16 DA DA B . n B 2 7 DC 7 17 17 DC DC B . n B 2 8 DC 8 18 18 DC DC B . n B 2 9 DG 9 19 19 DG DG B . n B 2 10 DG 10 20 20 DG DG B . n C 2 1 DC 1 21 21 DC DC C . n C 2 2 DC 2 22 22 DC DC C . n C 2 3 DG 3 23 23 DG DG C . n C 2 4 DA 4 24 24 DA DA C . n C 2 5 DT 5 25 25 DT DT C . n C 2 6 DA 6 26 26 DA DA C . n C 2 7 DC 7 27 27 DC DC C . n C 2 8 DC 8 28 28 DC DC C . n C 2 9 DG 9 29 29 DG DG C . n C 2 10 DG 10 30 30 DG DG C . n D 1 1 DC 1 31 31 DC DC D . n D 1 2 DC 2 32 32 DC DC D . n D 1 3 DG 3 33 33 DG DG D . n D 1 4 DG 4 34 34 DG DG D . n D 1 5 DT 5 35 35 DT DT D . n D 1 6 DA 6 36 36 DA DA D . n D 1 7 UCL 7 37 37 UCL UCL D . n D 1 8 DC 8 38 38 DC DC D . n D 1 9 DG 9 39 39 DG DG D . n D 1 10 DG 10 40 40 DG DG D . 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 E 3 NA 1 101 272 NA NA A . F 3 NA 1 101 265 NA NA B . G 3 NA 1 102 269 NA NA B . H 4 HOH 1 201 80 HOH HOH A . H 4 HOH 2 202 127 HOH HOH A . H 4 HOH 3 203 141 HOH HOH A . H 4 HOH 4 204 150 HOH HOH A . H 4 HOH 5 205 259 HOH HOH A . H 4 HOH 6 206 274 HOH HOH A . H 4 HOH 7 207 297 HOH HOH A . H 4 HOH 8 208 304 HOH HOH A . H 4 HOH 9 209 315 HOH HOH A . H 4 HOH 10 210 319 HOH HOH A . H 4 HOH 11 211 328 HOH HOH A . H 4 HOH 12 212 343 HOH HOH A . H 4 HOH 13 213 349 HOH HOH A . H 4 HOH 14 214 423 HOH HOH A . H 4 HOH 15 215 425 HOH HOH A . I 4 HOH 1 201 49 HOH HOH B . I 4 HOH 2 202 79 HOH HOH B . I 4 HOH 3 203 81 HOH HOH B . I 4 HOH 4 204 88 HOH HOH B . I 4 HOH 5 205 111 HOH HOH B . I 4 HOH 6 206 118 HOH HOH B . I 4 HOH 7 207 125 HOH HOH B . I 4 HOH 8 208 144 HOH HOH B . I 4 HOH 9 209 145 HOH HOH B . I 4 HOH 10 210 252 HOH HOH B . I 4 HOH 11 211 264 HOH HOH B . I 4 HOH 12 212 278 HOH HOH B . I 4 HOH 13 213 290 HOH HOH B . I 4 HOH 14 214 308 HOH HOH B . I 4 HOH 15 215 351 HOH HOH B . I 4 HOH 16 216 401 HOH HOH B . I 4 HOH 17 217 402 HOH HOH B . I 4 HOH 18 218 405 HOH HOH B . I 4 HOH 19 219 406 HOH HOH B . I 4 HOH 20 220 407 HOH HOH B . I 4 HOH 21 221 410 HOH HOH B . I 4 HOH 22 222 411 HOH HOH B . I 4 HOH 23 223 412 HOH HOH B . I 4 HOH 24 224 414 HOH HOH B . I 4 HOH 25 225 426 HOH HOH B . I 4 HOH 26 226 122 HOH HOH B . J 4 HOH 1 101 244 HOH HOH C . J 4 HOH 2 102 251 HOH HOH C . J 4 HOH 3 103 348 HOH HOH C . J 4 HOH 4 104 47 HOH HOH C . J 4 HOH 5 105 67 HOH HOH C . J 4 HOH 6 106 75 HOH HOH C . J 4 HOH 7 107 113 HOH HOH C . J 4 HOH 8 108 246 HOH HOH C . J 4 HOH 9 109 268 HOH HOH C . J 4 HOH 10 110 276 HOH HOH C . J 4 HOH 11 111 285 HOH HOH C . J 4 HOH 12 112 292 HOH HOH C . J 4 HOH 13 113 295 HOH HOH C . J 4 HOH 14 114 305 HOH HOH C . J 4 HOH 15 115 309 HOH HOH C . J 4 HOH 16 116 314 HOH HOH C . J 4 HOH 17 117 324 HOH HOH C . J 4 HOH 18 118 335 HOH HOH C . J 4 HOH 19 119 403 HOH HOH C . J 4 HOH 20 120 404 HOH HOH C . J 4 HOH 21 121 408 HOH HOH C . J 4 HOH 22 122 419 HOH HOH C . J 4 HOH 23 123 422 HOH HOH C . K 4 HOH 1 101 43 HOH HOH D . K 4 HOH 2 102 62 HOH HOH D . K 4 HOH 3 103 86 HOH HOH D . K 4 HOH 4 104 99 HOH HOH D . K 4 HOH 5 105 123 HOH HOH D . K 4 HOH 6 106 130 HOH HOH D . K 4 HOH 7 107 137 HOH HOH D . K 4 HOH 8 108 248 HOH HOH D . K 4 HOH 9 109 250 HOH HOH D . K 4 HOH 10 110 253 HOH HOH D . K 4 HOH 11 111 257 HOH HOH D . K 4 HOH 12 112 258 HOH HOH D . K 4 HOH 13 113 263 HOH HOH D . K 4 HOH 14 114 270 HOH HOH D . K 4 HOH 15 115 271 HOH HOH D . K 4 HOH 16 116 293 HOH HOH D . K 4 HOH 17 117 294 HOH HOH D . K 4 HOH 18 118 298 HOH HOH D . K 4 HOH 19 119 301 HOH HOH D . K 4 HOH 20 120 310 HOH HOH D . K 4 HOH 21 121 334 HOH HOH D . K 4 HOH 22 122 347 HOH HOH D . K 4 HOH 23 123 413 HOH HOH D . K 4 HOH 24 124 409 HOH HOH D . K 4 HOH 25 125 415 HOH HOH D . K 4 HOH 26 126 416 HOH HOH D . K 4 HOH 27 127 417 HOH HOH D . K 4 HOH 28 128 418 HOH HOH D . K 4 HOH 29 129 429 HOH HOH D . # 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 UCL 7 A UCL 7 ? DU ? 2 D UCL 7 D UCL 37 ? DU ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 52.3785088452 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 34.8281028664 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 212 ? H HOH . 2 1 D HOH 113 ? K HOH . # 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 O2 A B DC 2 ? B DC 12 ? 1_555 NA ? F NA . ? B NA 101 ? 1_555 O ? I HOH . ? B HOH 210 ? 1_555 148.4 ? 2 O2 A B DC 2 ? B DC 12 ? 1_555 NA ? F NA . ? B NA 101 ? 1_555 O2 B D DC 2 ? D DC 32 ? 1_555 2.3 ? 3 O ? I HOH . ? B HOH 210 ? 1_555 NA ? F NA . ? B NA 101 ? 1_555 O2 B D DC 2 ? D DC 32 ? 1_555 146.1 ? 4 O2 A B DC 2 ? B DC 12 ? 1_555 NA ? F NA . ? B NA 101 ? 1_555 O ? K HOH . ? D HOH 128 ? 1_555 77.6 ? 5 O ? I HOH . ? B HOH 210 ? 1_555 NA ? F NA . ? B NA 101 ? 1_555 O ? K HOH . ? D HOH 128 ? 1_555 110.2 ? 6 O2 B D DC 2 ? D DC 32 ? 1_555 NA ? F NA . ? B NA 101 ? 1_555 O ? K HOH . ? D HOH 128 ? 1_555 78.6 ? 7 OP1 A B DG 9 ? B DG 19 ? 1_555 NA ? G NA . ? B NA 102 ? 1_555 OP1 B D DG 9 ? D DG 39 ? 1_555 4.6 ? 8 OP1 A B DG 9 ? B DG 19 ? 1_555 NA ? G NA . ? B NA 102 ? 1_555 O ? K HOH . ? D HOH 123 ? 1_555 140.7 ? 9 OP1 B D DG 9 ? D DG 39 ? 1_555 NA ? G NA . ? B NA 102 ? 1_555 O ? K HOH . ? D HOH 123 ? 1_555 136.2 ? # 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 2013-07-31 2 'Structure model' 1 1 2013-12-18 3 'Structure model' 1 2 2023-09-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn 7 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_alt_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 16 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_alt_id' 17 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 18 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 19 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 20 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 21 3 'Structure model' '_pdbx_struct_conn_angle.value' 22 3 'Structure model' '_struct_conn.conn_type_id' 23 3 'Structure model' '_struct_conn.id' 24 3 'Structure model' '_struct_conn.pdbx_dist_value' 25 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 26 3 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 27 3 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 28 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 29 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 30 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 31 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 32 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 33 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 34 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 35 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 36 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 37 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 38 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 39 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 40 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 41 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 42 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 43 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 44 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 CNS refinement . ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 CNS phasing . ? 5 # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 NA NA NA N N 147 UCL O3P O N N 148 UCL P P N N 149 UCL O1P O N N 150 UCL O2P O N N 151 UCL "O5'" O N N 152 UCL "C5'" C N N 153 UCL "C4'" C N R 154 UCL "O4'" O N N 155 UCL "C3'" C N S 156 UCL "O3'" O N N 157 UCL "C2'" C N N 158 UCL "C1'" C N R 159 UCL N1 N N N 160 UCL C2 C N N 161 UCL O2 O N N 162 UCL N3 N N N 163 UCL C4 C N N 164 UCL O4 O N N 165 UCL C5 C N N 166 UCL C6 C N N 167 UCL CL CL N N 168 UCL HO1P H N N 169 UCL HO2P H N N 170 UCL "H5'1" H N N 171 UCL "H5'2" H N N 172 UCL "H4'" H N N 173 UCL "H3'" H N N 174 UCL "HO3'" H N N 175 UCL "H2'1" H N N 176 UCL "H2'2" H N N 177 UCL "H1'" H N N 178 UCL HN3 H N N 179 UCL H6 H N N 180 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 UCL O3P P doub N N 152 UCL P O1P sing N N 153 UCL P O2P sing N N 154 UCL P "O5'" sing N N 155 UCL O1P HO1P sing N N 156 UCL O2P HO2P sing N N 157 UCL "O5'" "C5'" sing N N 158 UCL "C5'" "C4'" sing N N 159 UCL "C5'" "H5'1" sing N N 160 UCL "C5'" "H5'2" sing N N 161 UCL "C4'" "O4'" sing N N 162 UCL "C4'" "C3'" sing N N 163 UCL "C4'" "H4'" sing N N 164 UCL "O4'" "C1'" sing N N 165 UCL "C3'" "O3'" sing N N 166 UCL "C3'" "C2'" sing N N 167 UCL "C3'" "H3'" sing N N 168 UCL "O3'" "HO3'" sing N N 169 UCL "C2'" "C1'" sing N N 170 UCL "C2'" "H2'1" sing N N 171 UCL "C2'" "H2'2" sing N N 172 UCL "C1'" N1 sing N N 173 UCL "C1'" "H1'" sing N N 174 UCL N1 C2 sing N N 175 UCL N1 C6 sing N N 176 UCL C2 O2 doub N N 177 UCL C2 N3 sing N N 178 UCL N3 C4 sing N N 179 UCL N3 HN3 sing N N 180 UCL C4 O4 doub N N 181 UCL C4 C5 sing N N 182 UCL C5 C6 doub N N 183 UCL C5 CL sing N N 184 UCL C6 H6 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4GQD 'double helix' 4GQD '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 DC 1 1_555 B DG 10 1_555 0.636 0.297 0.259 0.569 -17.436 7.168 1 A_DC1:DG20_B A 1 ? B 20 ? ? 1 1 A DC 2 1_555 B DG 9 1_555 0.086 -0.041 0.563 -2.535 -11.963 2.319 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -1.872 0.273 0.121 -15.483 -4.650 5.622 3 A_DG3:DC18_B A 3 ? B 18 ? ? 1 1 A DG 4 1_555 B DC 7 1_555 -0.309 0.190 0.266 -11.281 -19.600 -0.973 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 1 A DA 6 1_555 B DT 5 1_555 -0.454 0.044 -0.075 -5.005 -20.952 2.203 5 A_DA6:DT15_B A 6 ? B 15 ? 20 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 10 1_555 A DC 2 1_555 B DG 9 1_555 0.214 2.419 3.727 4.740 5.093 41.992 2.723 0.273 3.981 7.049 -6.560 42.539 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.164 2.428 3.571 -2.781 0.061 29.459 4.739 -0.964 3.546 0.120 5.454 29.587 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DG 4 1_555 B DC 7 1_555 -1.556 1.405 3.586 -9.111 1.373 45.173 1.661 1.090 3.853 1.765 11.717 46.055 3 AA_DG3DG4:DC17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DG 4 1_555 B DC 7 1_555 A DA 6 1_555 B DT 5 1_555 -0.347 1.713 6.359 3.139 0.792 72.586 1.395 0.493 6.358 0.669 -2.650 72.648 4 AA_DG4DA6:DT15DC17_BB A 4 ? B 17 ? A 6 ? B 15 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'SODIUM ION' NA 4 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 2ORG _pdbx_initial_refinement_model.details ? #