data_4GSG # _entry.id 4GSG # _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 4GSG pdb_00004gsg 10.2210/pdb4gsg/pdb NDB NA2017 ? ? RCSB RCSB074578 ? ? WWPDB D_1000074578 ? ? # 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 4GQD . unspecified PDB 4GRE . unspecified PDB 4GS2 . unspecified PDB 4GSI . unspecified # _pdbx_database_status.entry_id 4GSG _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-08-27 _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 'Ho, P.S.' 1 'Carter, M.' 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.length_a 65.578 _cell.length_b 24.355 _cell.length_c 37.243 _cell.angle_alpha 90.000 _cell.angle_beta 110.850 _cell.angle_gamma 90.000 _cell.entry_id 4GSG _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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.space_group_name_H-M 'C 1 2 1' _symmetry.entry_id 4GSG _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 5 _symmetry.cell_setting ? _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*AP*TP*AP*CP*CP*GP*G)-3') ; 3029.994 2 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*CP*GP*GP*TP*AP*(UCL)P*CP*GP*G)-3') ; 3081.423 2 ? ? ? ? 3 water nat water 18.015 159 ? ? ? ? # 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 no '(DC)(DC)(DG)(DA)(DT)(DA)(DC)(DC)(DG)(DG)' CCGATACCGG A,D ? 2 polydeoxyribonucleotide no yes '(DC)(DC)(DG)(DG)(DT)(DA)(UCL)(DC)(DG)(DG)' CCGGTAUCGG 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 DA n 1 5 DT n 1 6 DA n 1 7 DC 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 DG n 2 5 DT n 2 6 DA n 2 7 UCL 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 4GSG 4GSG 1 ? CCGATACCGG ? 2 PDB 4GSG 4GSG 2 ? CCGGTAUCGG ? # 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 4GSG A 1 ? 10 ? 4GSG 1 ? 10 ? 1 10 2 1 4GSG D 1 ? 10 ? 4GSG 31 ? 40 ? 31 40 3 2 4GSG B 1 ? 10 ? 4GSG 11 ? 20 ? 11 20 4 2 4GSG C 1 ? 10 ? 4GSG 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 UCL 'DNA linking' n ;5-CHLORO-2'-DEOXYURIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C9 H12 Cl N2 O8 P' 342.627 # _exptl.crystals_number 1 _exptl.entry_id 4GSG _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews ? _exptl_crystal.density_meas ? _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 'hanging drop' _exptl_crystal_grow.pH 7 _exptl_crystal_grow.temp 298 _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, hanging drop, temperature 298K ; _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 133 _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.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _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_wavelength_list 0.9 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 4.2.2 # _reflns.entry_id 4GSG _reflns.B_iso_Wilson_estimate 6.700 _reflns.observed_criterion_sigma_F 1.4 _reflns.observed_criterion_sigma_I 2 _reflns.d_resolution_high 1.7 _reflns.d_resolution_low 50 _reflns.number_all 6244 _reflns.number_obs 4947 _reflns.percent_possible_obs 79.2 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _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 # _refine.entry_id 4GSG _refine.ls_d_res_high 2.0000 _refine.ls_d_res_low 30.6400 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF 35514.0000 _refine.pdbx_data_cutoff_low_absF 0.0000 _refine.ls_percent_reflns_obs 94.8000 _refine.ls_number_reflns_obs 3667 _refine.ls_number_reflns_all 6244 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'BULK SOLVENT MODEL USED' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.2710 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.3220 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.8000 _refine.ls_number_reflns_R_free 212 _refine.ls_R_factor_R_free_error 0.0220 _refine.B_iso_mean 14.3574 _refine.solvent_model_param_bsol 74.8641 _refine.solvent_model_param_ksol 0.3500 _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.aniso_B[1][1] 1.8000 _refine.aniso_B[2][2] 3.6400 _refine.aniso_B[3][3] -5.4400 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -0.9400 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT MODEL' _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 2ORG _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 52.010 _refine.B_iso_min 1.120 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.150 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_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 4GSG _refine_analyze.Luzzati_coordinate_error_obs 0.320 _refine_analyze.Luzzati_sigma_a_obs 0.320 _refine_analyze.Luzzati_d_res_low_obs 5.000 _refine_analyze.Luzzati_coordinate_error_free 0.380 _refine_analyze.Luzzati_sigma_a_free 0.270 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_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 0 _refine_hist.number_atoms_solvent 159 _refine_hist.number_atoms_total 967 _refine_hist.d_res_high 2.0000 _refine_hist.d_res_low 30.6400 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id c_bond_d ? 0.001 ? ? ? 'X-RAY DIFFRACTION' c_angle_deg ? 0.400 ? ? ? 'X-RAY DIFFRACTION' c_dihedral_angle_d ? 16.500 ? ? ? 'X-RAY DIFFRACTION' c_improper_angle_d ? 0.880 ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it ? 0.000 1.500 ? ? 'X-RAY DIFFRACTION' c_mcangle_it ? 0.000 2.000 ? ? 'X-RAY DIFFRACTION' c_scbond_it ? 1.770 2.000 ? ? 'X-RAY DIFFRACTION' c_scangle_it ? 2.420 2.500 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.0000 _refine_ls_shell.d_res_low 2.1300 _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.percent_reflns_obs 95.4000 _refine_ls_shell.number_reflns_R_work 572 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.3360 _refine_ls_shell.R_factor_R_free 0.3060 _refine_ls_shell.percent_reflns_R_free 4.7000 _refine_ls_shell.number_reflns_R_free 28 _refine_ls_shell.R_factor_R_free_error 0.0580 _refine_ls_shell.number_reflns_all 600 _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 mcdna-rna_rep.param mcdna-rna.top 'X-RAY DIFFRACTION' 2 ion.param ? 'X-RAY DIFFRACTION' 3 water_rep.param ? 'X-RAY DIFFRACTION' # _struct.entry_id 4GSG _struct.title 'DNA Holliday junction stabilized by chlorine halogen bond. Cl1J construct of related reference.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4GSG _struct_keywords.text 'DNA Holliday junction, halogen bond, DNA' _struct_keywords.pdbx_keywords 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 3 ? # _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 covale1 covale both ? B DA 6 "O3'" A ? ? 1_555 B UCL 7 P A ? B DA 16 B UCL 17 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale2 covale one ? B UCL 7 "O3'" A ? ? 1_555 B DC 8 P A ? B UCL 17 B DC 18 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale3 covale both ? C DA 6 "O3'" B ? ? 1_555 C UCL 7 P B ? C DA 26 C UCL 27 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale4 covale one ? C UCL 7 "O3'" B ? ? 1_555 C DC 8 P B ? C UCL 27 C DC 28 1_555 ? ? ? ? ? ? ? 1.606 ? ? 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 N3 A ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N2 A ? ? 1_555 B DC 8 O2 A ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 O6 A ? ? 1_555 B DC 8 N4 A ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N1 A ? ? 1_555 B UCL 7 N3 A ? A DA 4 B UCL 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N6 A ? ? 1_555 B UCL 7 O4 A ? A DA 4 B UCL 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 5 O4 A ? ? 1_555 B DA 6 N6 A ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog11 hydrog ? ? A DA 6 N1 A ? ? 1_555 B DT 5 N3 A ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 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 ? ? hydrog ? ? # _database_PDB_matrix.entry_id 4GSG _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 4GSG _atom_sites.fract_transf_matrix[1][1] 0.015249 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005807 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.041059 _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] 0.028731 _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 # 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 DA 4 4 4 DA DA 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 DC 7 7 7 DC DC 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 DG 4 14 14 DG DG 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 UCL 7 17 17 UCL UCL 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 DG 4 24 24 DG DG 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 UCL 7 27 27 UCL UCL 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 DA 4 34 34 DA DA 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 DC 7 37 37 DC DC 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 HOH 1 101 55 HOH HOH A . E 3 HOH 2 102 78 HOH HOH A . E 3 HOH 3 103 90 HOH HOH A . E 3 HOH 4 104 92 HOH HOH A . E 3 HOH 5 105 93 HOH HOH A . E 3 HOH 6 106 98 HOH HOH A . E 3 HOH 7 107 109 HOH HOH A . E 3 HOH 8 108 113 HOH HOH A . E 3 HOH 9 109 117 HOH HOH A . E 3 HOH 10 110 134 HOH HOH A . E 3 HOH 11 111 141 HOH HOH A . E 3 HOH 12 112 146 HOH HOH A . E 3 HOH 13 113 148 HOH HOH A . E 3 HOH 14 114 166 HOH HOH A . E 3 HOH 15 115 170 HOH HOH A . E 3 HOH 16 116 171 HOH HOH A . E 3 HOH 17 117 172 HOH HOH A . E 3 HOH 18 118 182 HOH HOH A . E 3 HOH 19 119 183 HOH HOH A . E 3 HOH 20 120 184 HOH HOH A . E 3 HOH 21 121 185 HOH HOH A . E 3 HOH 22 122 186 HOH HOH A . E 3 HOH 23 123 192 HOH HOH A . E 3 HOH 24 124 194 HOH HOH A . E 3 HOH 25 125 195 HOH HOH A . E 3 HOH 26 126 196 HOH HOH A . E 3 HOH 27 127 198 HOH HOH A . F 3 HOH 1 101 41 HOH HOH B . F 3 HOH 2 102 61 HOH HOH B . F 3 HOH 3 103 63 HOH HOH B . F 3 HOH 4 104 68 HOH HOH B . F 3 HOH 5 105 70 HOH HOH B . F 3 HOH 6 106 72 HOH HOH B . F 3 HOH 7 107 79 HOH HOH B . F 3 HOH 8 108 88 HOH HOH B . F 3 HOH 9 109 102 HOH HOH B . F 3 HOH 10 110 111 HOH HOH B . F 3 HOH 11 111 114 HOH HOH B . F 3 HOH 12 112 127 HOH HOH B . F 3 HOH 13 113 132 HOH HOH B . F 3 HOH 14 114 136 HOH HOH B . F 3 HOH 15 115 137 HOH HOH B . F 3 HOH 16 116 138 HOH HOH B . F 3 HOH 17 117 139 HOH HOH B . F 3 HOH 18 118 143 HOH HOH B . F 3 HOH 19 119 145 HOH HOH B . F 3 HOH 20 120 151 HOH HOH B . F 3 HOH 21 121 157 HOH HOH B . F 3 HOH 22 122 160 HOH HOH B . F 3 HOH 23 123 162 HOH HOH B . F 3 HOH 24 124 163 HOH HOH B . F 3 HOH 25 125 174 HOH HOH B . F 3 HOH 26 126 175 HOH HOH B . F 3 HOH 27 127 177 HOH HOH B . F 3 HOH 28 128 178 HOH HOH B . F 3 HOH 29 129 187 HOH HOH B . F 3 HOH 30 130 189 HOH HOH B . F 3 HOH 31 131 193 HOH HOH B . F 3 HOH 32 132 200 HOH HOH B . F 3 HOH 33 133 201 HOH HOH B . F 3 HOH 34 134 202 HOH HOH B . F 3 HOH 35 135 207 HOH HOH B . F 3 HOH 36 136 208 HOH HOH B . F 3 HOH 37 137 62 HOH HOH B . G 3 HOH 1 101 42 HOH HOH C . G 3 HOH 2 102 43 HOH HOH C . G 3 HOH 3 103 45 HOH HOH C . G 3 HOH 4 104 47 HOH HOH C . G 3 HOH 5 105 49 HOH HOH C . G 3 HOH 6 106 51 HOH HOH C . G 3 HOH 7 107 52 HOH HOH C . G 3 HOH 8 108 57 HOH HOH C . G 3 HOH 9 109 59 HOH HOH C . G 3 HOH 10 110 65 HOH HOH C . G 3 HOH 11 111 66 HOH HOH C . G 3 HOH 12 112 67 HOH HOH C . G 3 HOH 13 113 71 HOH HOH C . G 3 HOH 14 114 73 HOH HOH C . G 3 HOH 15 115 75 HOH HOH C . G 3 HOH 16 116 76 HOH HOH C . G 3 HOH 17 117 80 HOH HOH C . G 3 HOH 18 118 81 HOH HOH C . G 3 HOH 19 119 82 HOH HOH C . G 3 HOH 20 120 86 HOH HOH C . G 3 HOH 21 121 91 HOH HOH C . G 3 HOH 22 122 94 HOH HOH C . G 3 HOH 23 123 95 HOH HOH C . G 3 HOH 24 124 96 HOH HOH C . G 3 HOH 25 125 104 HOH HOH C . G 3 HOH 26 126 107 HOH HOH C . G 3 HOH 27 127 108 HOH HOH C . G 3 HOH 28 128 110 HOH HOH C . G 3 HOH 29 129 115 HOH HOH C . G 3 HOH 30 130 116 HOH HOH C . G 3 HOH 31 131 121 HOH HOH C . G 3 HOH 32 132 123 HOH HOH C . G 3 HOH 33 133 124 HOH HOH C . G 3 HOH 34 134 125 HOH HOH C . G 3 HOH 35 135 128 HOH HOH C . G 3 HOH 36 136 129 HOH HOH C . G 3 HOH 37 137 130 HOH HOH C . G 3 HOH 38 138 133 HOH HOH C . G 3 HOH 39 139 135 HOH HOH C . G 3 HOH 40 140 154 HOH HOH C . G 3 HOH 41 141 158 HOH HOH C . G 3 HOH 42 142 159 HOH HOH C . G 3 HOH 43 143 164 HOH HOH C . G 3 HOH 44 144 165 HOH HOH C . G 3 HOH 45 145 203 HOH HOH C . H 3 HOH 1 101 44 HOH HOH D . H 3 HOH 2 102 48 HOH HOH D . H 3 HOH 3 103 50 HOH HOH D . H 3 HOH 4 104 53 HOH HOH D . H 3 HOH 5 105 54 HOH HOH D . H 3 HOH 6 106 56 HOH HOH D . H 3 HOH 7 107 58 HOH HOH D . H 3 HOH 8 108 64 HOH HOH D . H 3 HOH 9 109 69 HOH HOH D . H 3 HOH 10 110 77 HOH HOH D . H 3 HOH 11 111 83 HOH HOH D . H 3 HOH 12 112 84 HOH HOH D . H 3 HOH 13 113 85 HOH HOH D . H 3 HOH 14 114 87 HOH HOH D . H 3 HOH 15 115 89 HOH HOH D . H 3 HOH 16 116 97 HOH HOH D . H 3 HOH 17 117 99 HOH HOH D . H 3 HOH 18 118 103 HOH HOH D . H 3 HOH 19 119 105 HOH HOH D . H 3 HOH 20 120 106 HOH HOH D . H 3 HOH 21 121 112 HOH HOH D . H 3 HOH 22 122 120 HOH HOH D . H 3 HOH 23 123 122 HOH HOH D . H 3 HOH 24 124 126 HOH HOH D . H 3 HOH 25 125 131 HOH HOH D . H 3 HOH 26 126 140 HOH HOH D . H 3 HOH 27 127 142 HOH HOH D . H 3 HOH 28 128 144 HOH HOH D . H 3 HOH 29 129 147 HOH HOH D . H 3 HOH 30 130 149 HOH HOH D . H 3 HOH 31 131 150 HOH HOH D . H 3 HOH 32 132 152 HOH HOH D . H 3 HOH 33 133 153 HOH HOH D . H 3 HOH 34 134 155 HOH HOH D . H 3 HOH 35 135 156 HOH HOH D . H 3 HOH 36 136 161 HOH HOH D . H 3 HOH 37 137 167 HOH HOH D . H 3 HOH 38 138 168 HOH HOH D . H 3 HOH 39 139 169 HOH HOH D . H 3 HOH 40 140 173 HOH HOH D . H 3 HOH 41 141 176 HOH HOH D . H 3 HOH 42 142 179 HOH HOH D . H 3 HOH 43 143 180 HOH HOH D . H 3 HOH 44 144 181 HOH HOH D . H 3 HOH 45 145 188 HOH HOH D . H 3 HOH 46 146 190 HOH HOH D . H 3 HOH 47 147 191 HOH HOH D . H 3 HOH 48 148 197 HOH HOH D . H 3 HOH 49 149 199 HOH HOH D . H 3 HOH 50 150 206 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 B UCL 7 B UCL 17 ? DU ? 2 C UCL 7 C UCL 27 ? DU ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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 # 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_556 -x,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 -13.2556260022 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 34.8041582040 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id C _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 101 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id G _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 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' struct_conn # 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' '_struct_conn.pdbx_dist_value' 4 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 3 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 6 3 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 7 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 CNS 1.2 ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns-online.org/ Fortran_77 ? 2 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 HKL-2000 . ? ? ? ? 'data collection' ? ? ? 4 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 5 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? 6 EPMR . ? ? ? ? phasing ? ? ? # 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 UCL O3P O N N 147 UCL P P N N 148 UCL O1P O N N 149 UCL O2P O N N 150 UCL "O5'" O N N 151 UCL "C5'" C N N 152 UCL "C4'" C N R 153 UCL "O4'" O N N 154 UCL "C3'" C N S 155 UCL "O3'" O N N 156 UCL "C2'" C N N 157 UCL "C1'" C N R 158 UCL N1 N N N 159 UCL C2 C N N 160 UCL O2 O N N 161 UCL N3 N N N 162 UCL C4 C N N 163 UCL O4 O N N 164 UCL C5 C N N 165 UCL C6 C N N 166 UCL CL CL N N 167 UCL HO1P H N N 168 UCL HO2P H N N 169 UCL "H5'1" H N N 170 UCL "H5'2" H N N 171 UCL "H4'" H N N 172 UCL "H3'" H N N 173 UCL "HO3'" H N N 174 UCL "H2'1" H N N 175 UCL "H2'2" H N N 176 UCL "H1'" H N N 177 UCL HN3 H N N 178 UCL H6 H N N 179 # 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 # _ndb_struct_conf_na.entry_id 4GSG _ndb_struct_conf_na.feature '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 0.739 0.156 0.668 -1.361 -17.869 6.892 1 A_DC1:DG20_B A 1 ? B 20 ? ? 1 1 A DC 2 1_555 B DG 9 1_555 0.852 -0.127 0.581 3.332 -9.385 6.343 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.439 -0.189 0.149 -0.702 -2.472 0.802 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DA 4 1_555 B UCL 7 1_555 -0.453 -0.071 0.445 -0.861 -24.019 -5.275 4 A_DA4:UCL17_B A 4 ? B 17 ? 20 1 1 A DT 5 1_555 B DA 6 1_555 0.677 0.374 0.011 -4.531 -14.536 -5.042 5 A_DT5:DA16_B A 5 ? B 16 ? ? ? 1 A DA 6 1_555 B DT 5 1_555 -0.153 0.105 -0.036 -6.287 -10.057 -1.516 6 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 0.177 2.276 3.527 5.290 -0.064 42.750 3.108 0.323 3.521 -0.088 -7.224 43.061 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 -0.014 2.442 3.487 2.948 -1.284 32.992 4.508 0.545 3.378 -2.254 -5.176 33.144 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 DA 4 1_555 B UCL 7 1_555 -1.223 1.463 3.540 -8.265 -1.933 40.369 2.310 0.748 3.640 -2.765 11.818 41.215 3 AA_DG3DA4:UCL17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DA 4 1_555 B UCL 7 1_555 A DT 5 1_555 B DA 6 1_555 0.088 -0.451 3.391 2.596 1.911 38.460 -0.926 0.198 3.365 2.894 -3.933 38.590 4 AA_DA4DT5:DA16UCL17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DT 5 1_555 B DA 6 1_555 A DA 6 1_555 B DT 5 1_555 0.574 1.153 3.436 3.921 0.218 36.312 1.808 -0.341 3.484 0.349 -6.268 36.517 5 AA_DT5DA6:DT15DA16_BB A 5 ? B 16 ? A 6 ? B 15 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 ? #