data_1NVN # _entry.id 1NVN # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1NVN pdb_00001nvn 10.2210/pdb1nvn/pdb NDB UD0025 ? ? RCSB RCSB018254 ? ? WWPDB D_1000018254 ? ? # 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 2003-02-25 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # 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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' diffrn_source 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.value' 11 4 'Structure model' '_struct_conn.pdbx_dist_value' 12 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NVN _pdbx_database_status.recvd_initial_deposition_date 2003-02-04 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type NDB UD0023 'Holliday junction formed by the sequence TCGGTACCGA in the presence of one calcium ion' unspecified NDB UD0018 'Holliday junction formed by TCGGTACCGA in the presence of Na and Ca ions' unspecified NDB UD0021 'Holliday junction formed by TCGGTACCGA with a spine of Sr ions' unspecified NDB UD0015 'Holliday junction formed by CCGGTACCGG in the more symmetrical form' unspecified NDB UD0019 'Holliday junction formed by CCGGTACmCGG with a methylated base' unspecified NDB UD0008 'Holliday junction formed by CCGGTACCGG in the presence of a Na ion' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cardin, C.J.' 1 'Gale, B.C.' 2 'Thorpe, J.H.' 3 'Teixeira, S.C.M.' 4 'Gan, Y.' 5 'Moraes, M.I.A.A.' 6 'Brogden, A.L.' 7 # _citation.id primary _citation.title 'Structural analysis of two Holliday junctions formed by the sequences TCGGTACCGA and CCGGTACCGG' _citation.journal_abbrev 'To be Published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cardin, C.J.' 1 ? primary 'Gale, B.C.' 2 ? primary 'Thorpe, J.H.' 3 ? primary 'Teixeira, S.C.M.' 4 ? primary 'Gan, Y.' 5 ? primary 'Moraes, M.I.A.A.' 6 ? primary 'Brogden, A.L.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(CpCpGpGpTpApCpCpGpG)-3'" 3045.992 2 ? ? ? ? 2 non-polymer syn 'CALCIUM ION' 40.078 2 ? ? ? ? 3 water nat water 18.015 91 ? ? ? ? # _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)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCGGTACCGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CALCIUM ION' CA 3 water HOH # 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 DC n 1 8 DC n 1 9 DG n 1 10 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 ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized' # 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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 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 # 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 C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DC 1 1 1 DC C B . n B 1 2 DC 2 2 2 DC C B . n B 1 3 DG 3 3 3 DG G B . n B 1 4 DG 4 4 4 DG G B . n B 1 5 DT 5 5 5 DT T B . n B 1 6 DA 6 6 6 DA A B . n B 1 7 DC 7 7 7 DC C B . n B 1 8 DC 8 8 8 DC C B . n B 1 9 DG 9 9 9 DG G B . n B 1 10 DG 10 10 10 DG G 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 CA 1 101 101 CA CA A . D 2 CA 1 102 102 CA CA B . E 3 HOH 1 111 111 HOH HOH A . E 3 HOH 2 112 112 HOH HOH A . E 3 HOH 3 114 114 HOH HOH A . E 3 HOH 4 115 115 HOH HOH A . E 3 HOH 5 116 116 HOH HOH A . E 3 HOH 6 119 119 HOH HOH A . E 3 HOH 7 120 120 HOH HOH A . E 3 HOH 8 121 121 HOH HOH A . E 3 HOH 9 124 124 HOH HOH A . E 3 HOH 10 125 125 HOH HOH A . E 3 HOH 11 126 126 HOH HOH A . E 3 HOH 12 127 127 HOH HOH A . E 3 HOH 13 128 128 HOH HOH A . E 3 HOH 14 129 129 HOH HOH A . E 3 HOH 15 130 130 HOH HOH A . E 3 HOH 16 136 136 HOH HOH A . E 3 HOH 17 139 139 HOH HOH A . E 3 HOH 18 143 143 HOH HOH A . E 3 HOH 19 144 144 HOH HOH A . E 3 HOH 20 145 145 HOH HOH A . E 3 HOH 21 146 146 HOH HOH A . E 3 HOH 22 147 147 HOH HOH A . E 3 HOH 23 148 148 HOH HOH A . E 3 HOH 24 149 149 HOH HOH A . E 3 HOH 25 150 150 HOH HOH A . E 3 HOH 26 154 154 HOH HOH A . E 3 HOH 27 155 155 HOH HOH A . E 3 HOH 28 156 156 HOH HOH A . E 3 HOH 29 159 159 HOH HOH A . E 3 HOH 30 160 160 HOH HOH A . E 3 HOH 31 161 161 HOH HOH A . E 3 HOH 32 162 162 HOH HOH A . E 3 HOH 33 163 163 HOH HOH A . E 3 HOH 34 164 164 HOH HOH A . E 3 HOH 35 174 174 HOH HOH A . E 3 HOH 36 176 176 HOH HOH A . E 3 HOH 37 177 177 HOH HOH A . E 3 HOH 38 180 180 HOH HOH A . E 3 HOH 39 181 181 HOH HOH A . E 3 HOH 40 188 188 HOH HOH A . E 3 HOH 41 192 192 HOH HOH A . E 3 HOH 42 193 193 HOH HOH A . F 3 HOH 1 103 103 HOH HOH B . F 3 HOH 2 104 104 HOH HOH B . F 3 HOH 3 105 105 HOH HOH B . F 3 HOH 4 106 106 HOH HOH B . F 3 HOH 5 107 107 HOH HOH B . F 3 HOH 6 108 108 HOH HOH B . F 3 HOH 7 109 109 HOH HOH B . F 3 HOH 8 110 110 HOH HOH B . F 3 HOH 9 113 113 HOH HOH B . F 3 HOH 10 117 117 HOH HOH B . F 3 HOH 11 118 118 HOH HOH B . F 3 HOH 12 122 122 HOH HOH B . F 3 HOH 13 123 123 HOH HOH B . F 3 HOH 14 131 131 HOH HOH B . F 3 HOH 15 132 132 HOH HOH B . F 3 HOH 16 133 133 HOH HOH B . F 3 HOH 17 134 134 HOH HOH B . F 3 HOH 18 135 135 HOH HOH B . F 3 HOH 19 137 137 HOH HOH B . F 3 HOH 20 138 138 HOH HOH B . F 3 HOH 21 140 140 HOH HOH B . F 3 HOH 22 141 141 HOH HOH B . F 3 HOH 23 142 142 HOH HOH B . F 3 HOH 24 151 151 HOH HOH B . F 3 HOH 25 152 152 HOH HOH B . F 3 HOH 26 153 153 HOH HOH B . F 3 HOH 27 157 157 HOH HOH B . F 3 HOH 28 158 158 HOH HOH B . F 3 HOH 29 165 165 HOH HOH B . F 3 HOH 30 166 166 HOH HOH B . F 3 HOH 31 167 167 HOH HOH B . F 3 HOH 32 168 168 HOH HOH B . F 3 HOH 33 169 169 HOH HOH B . F 3 HOH 34 170 170 HOH HOH B . F 3 HOH 35 171 171 HOH HOH B . F 3 HOH 36 172 172 HOH HOH B . F 3 HOH 37 173 173 HOH HOH B . F 3 HOH 38 175 175 HOH HOH B . F 3 HOH 39 178 178 HOH HOH B . F 3 HOH 40 179 179 HOH HOH B . F 3 HOH 41 182 182 HOH HOH B . F 3 HOH 42 183 183 HOH HOH B . F 3 HOH 43 184 184 HOH HOH B . F 3 HOH 44 185 185 HOH HOH B . F 3 HOH 45 186 186 HOH HOH B . F 3 HOH 46 187 187 HOH HOH B . F 3 HOH 47 189 189 HOH HOH B . F 3 HOH 48 190 190 HOH HOH B . F 3 HOH 49 191 191 HOH HOH B . # _software.name REFMAC _software.classification refinement _software.version 5.1.24 _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1NVN _cell.length_a 66.380 _cell.length_b 23.790 _cell.length_c 37.120 _cell.angle_alpha 90.00 _cell.angle_beta 110.13 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NVN _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 # _exptl.entry_id 1NVN _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.16 _exptl_crystal.density_percent_sol 42.97 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details 'MPD, CaCl2, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.811 _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 ? _diffrn_source.pdbx_wavelength_list 0.811 # _reflns.entry_id 1NVN _reflns.observed_criterion_sigma_F 1.0 _reflns.observed_criterion_sigma_I 1.0 _reflns.d_resolution_high 1.8 _reflns.d_resolution_low 34.92 _reflns.number_all 5158 _reflns.number_obs 5158 _reflns.percent_possible_obs 98.3 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.78 _reflns.B_iso_Wilson_estimate 20.904 _reflns.pdbx_redundancy 3.71 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.8 _reflns_shell.d_res_low 2.1 _reflns_shell.percent_possible_all 98.4 _reflns_shell.Rmerge_I_obs 0.2 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 6.06 _reflns_shell.pdbx_redundancy 3.73 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1885 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1NVN _refine.ls_number_reflns_obs 4920 _refine.ls_number_reflns_all 5229 _refine.pdbx_ls_sigma_I 1.0 _refine.pdbx_ls_sigma_F 1.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.92 _refine.ls_d_res_high 1.80 _refine.ls_percent_reflns_obs 98.49 _refine.ls_R_factor_obs 0.20872 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.20629 _refine.ls_R_factor_R_free 0.26361 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 236 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.953 _refine.correlation_coeff_Fo_to_Fc_free 0.899 _refine.B_iso_mean 13.443 _refine.aniso_B[1][1] -0.44 _refine.aniso_B[2][2] 1.55 _refine.aniso_B[3][3] -1.18 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] -0.10 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.331 _refine.pdbx_overall_ESU_R_Free 0.154 _refine.overall_SU_ML 0.104 _refine.overall_SU_B 3.566 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 404 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 91 _refine_hist.number_atoms_total 497 _refine_hist.d_res_high 1.80 _refine_hist.d_res_low 34.92 # 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 r_bond_refined_d 0.008 0.021 ? 452 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 186 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.731 3.000 ? 694 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.501 3.000 ? 472 'X-RAY DIFFRACTION' ? r_chiral_restr 0.053 0.200 ? 60 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.020 ? 210 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.000 0.020 ? 2 'X-RAY DIFFRACTION' ? r_nbd_refined 0.125 0.200 ? 49 'X-RAY DIFFRACTION' ? r_nbd_other 0.193 0.200 ? 202 'X-RAY DIFFRACTION' ? r_nbtor_other 0.094 0.200 ? 102 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.175 0.200 ? 67 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.244 0.200 ? 6 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.107 0.200 ? 20 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.314 0.200 ? 19 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.124 0.200 ? 19 'X-RAY DIFFRACTION' ? r_scbond_it 2.111 3.000 ? 452 'X-RAY DIFFRACTION' ? r_scangle_it 3.269 4.500 ? 694 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.800 _refine_ls_shell.d_res_low 1.847 _refine_ls_shell.number_reflns_R_work 369 _refine_ls_shell.R_factor_R_work 0.253 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.331 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 28 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1NVN _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 # _struct.entry_id 1NVN _struct.title 'Structural Characterisation of the Holliday junction formed by the sequence CCGGTACCGG at 1.8 A' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NVN _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Holliday Junction, Calcium ion, 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 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1NVN _struct_ref.pdbx_db_accession 1NVN _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1NVN A 1 ? 10 ? 1NVN 1 ? 10 ? 1 10 2 1 1NVN B 1 ? 10 ? 1NVN 1 ? 10 ? 1 10 # _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 # 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_655 -x+1,y,-z -1.0000000000 0.0000000000 0.0000000000 66.3800000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # 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 ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 115 1_555 ? ? ? ? ? ? ? 2.183 ? ? metalc2 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 116 1_555 ? ? ? ? ? ? ? 2.614 ? ? metalc3 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 143 1_555 ? ? ? ? ? ? ? 2.106 ? ? metalc4 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 101 A HOH 159 1_555 ? ? ? ? ? ? ? 2.207 ? ? metalc5 metalc ? ? C CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 101 B HOH 142 1_555 ? ? ? ? ? ? ? 2.835 ? ? metalc6 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? B CA 102 B HOH 103 1_555 ? ? ? ? ? ? ? 2.580 ? ? metalc7 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? B CA 102 B HOH 106 1_555 ? ? ? ? ? ? ? 2.518 ? ? metalc8 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? B CA 102 B HOH 107 1_555 ? ? ? ? ? ? ? 2.224 ? ? metalc9 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? B CA 102 B HOH 131 1_555 ? ? ? ? ? ? ? 2.077 ? ? metalc10 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? B CA 102 B HOH 132 1_555 ? ? ? ? ? ? ? 2.423 ? ? metalc11 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? B CA 102 B HOH 141 1_555 ? ? ? ? ? ? ? 2.408 ? ? metalc12 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? B CA 102 B HOH 185 1_555 ? ? ? ? ? ? ? 2.529 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 5 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 5 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 6 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 6 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 O ? E HOH . ? A HOH 115 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 116 ? 1_555 92.1 ? 2 O ? E HOH . ? A HOH 115 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 143 ? 1_555 121.3 ? 3 O ? E HOH . ? A HOH 116 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 143 ? 1_555 85.0 ? 4 O ? E HOH . ? A HOH 115 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 159 ? 1_555 145.3 ? 5 O ? E HOH . ? A HOH 116 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 159 ? 1_555 56.4 ? 6 O ? E HOH . ? A HOH 143 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? E HOH . ? A HOH 159 ? 1_555 74.3 ? 7 O ? E HOH . ? A HOH 115 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? F HOH . ? B HOH 142 ? 1_555 72.3 ? 8 O ? E HOH . ? A HOH 116 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? F HOH . ? B HOH 142 ? 1_555 112.0 ? 9 O ? E HOH . ? A HOH 143 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? F HOH . ? B HOH 142 ? 1_555 158.9 ? 10 O ? E HOH . ? A HOH 159 ? 1_555 CA ? C CA . ? A CA 101 ? 1_555 O ? F HOH . ? B HOH 142 ? 1_555 104.0 ? 11 O ? F HOH . ? B HOH 103 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 106 ? 1_555 72.9 ? 12 O ? F HOH . ? B HOH 103 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 107 ? 1_555 137.1 ? 13 O ? F HOH . ? B HOH 106 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 107 ? 1_555 64.3 ? 14 O ? F HOH . ? B HOH 103 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 107.9 ? 15 O ? F HOH . ? B HOH 106 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 88.2 ? 16 O ? F HOH . ? B HOH 107 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 131 ? 1_555 69.5 ? 17 O ? F HOH . ? B HOH 103 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 132 ? 1_555 82.9 ? 18 O ? F HOH . ? B HOH 106 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 132 ? 1_555 98.5 ? 19 O ? F HOH . ? B HOH 107 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 132 ? 1_555 105.2 ? 20 O ? F HOH . ? B HOH 131 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 132 ? 1_555 168.7 ? 21 O ? F HOH . ? B HOH 103 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 141 ? 1_555 141.4 ? 22 O ? F HOH . ? B HOH 106 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 141 ? 1_555 143.5 ? 23 O ? F HOH . ? B HOH 107 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 141 ? 1_555 81.0 ? 24 O ? F HOH . ? B HOH 131 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 141 ? 1_555 90.0 ? 25 O ? F HOH . ? B HOH 132 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 141 ? 1_555 79.2 ? 26 O ? F HOH . ? B HOH 103 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 185 ? 1_555 81.5 ? 27 O ? F HOH . ? B HOH 106 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 185 ? 1_555 149.0 ? 28 O ? F HOH . ? B HOH 107 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 185 ? 1_555 137.4 ? 29 O ? F HOH . ? B HOH 131 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 185 ? 1_555 83.2 ? 30 O ? F HOH . ? B HOH 132 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 185 ? 1_555 95.4 ? 31 O ? F HOH . ? B HOH 141 ? 1_555 CA ? D CA . ? B CA 102 ? 1_555 O ? F HOH . ? B HOH 185 ? 1_555 66.6 ? # 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 CA 101 ? 5 'BINDING SITE FOR RESIDUE CA A 101' AC2 Software B CA 102 ? 7 'BINDING SITE FOR RESIDUE CA 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 HOH E . ? HOH A 115 . ? 1_555 ? 2 AC1 5 HOH E . ? HOH A 116 . ? 1_555 ? 3 AC1 5 HOH E . ? HOH A 143 . ? 1_555 ? 4 AC1 5 HOH E . ? HOH A 159 . ? 1_555 ? 5 AC1 5 HOH F . ? HOH B 142 . ? 1_555 ? 6 AC2 7 HOH F . ? HOH B 103 . ? 1_555 ? 7 AC2 7 HOH F . ? HOH B 106 . ? 1_555 ? 8 AC2 7 HOH F . ? HOH B 107 . ? 1_555 ? 9 AC2 7 HOH F . ? HOH B 131 . ? 1_555 ? 10 AC2 7 HOH F . ? HOH B 132 . ? 1_555 ? 11 AC2 7 HOH F . ? HOH B 141 . ? 1_555 ? 12 AC2 7 HOH F . ? HOH B 185 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.67 108.30 3.37 0.30 N 2 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 103.27 108.00 -4.73 0.70 N 3 1 "C5'" B DG 3 ? ? "C4'" B DG 3 ? ? "O4'" B DG 3 ? ? 118.22 109.80 8.42 1.10 N 4 1 "O4'" B DG 3 ? ? "C1'" B DG 3 ? ? N9 B DG 3 ? ? 110.13 108.30 1.83 0.30 N 5 1 "O4'" B DA 6 ? ? "C1'" B DA 6 ? ? N9 B DA 6 ? ? 110.49 108.30 2.19 0.30 N 6 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 102.43 108.00 -5.57 0.70 N # 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 126 ? E HOH . 2 1 B HOH 151 ? F HOH . # 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 CA CA CA N N 1 DA OP3 O N N 2 DA P P N N 3 DA OP1 O N N 4 DA OP2 O N N 5 DA "O5'" O N N 6 DA "C5'" C N N 7 DA "C4'" C N R 8 DA "O4'" O N N 9 DA "C3'" C N S 10 DA "O3'" O N N 11 DA "C2'" C N N 12 DA "C1'" C N R 13 DA N9 N Y N 14 DA C8 C Y N 15 DA N7 N Y N 16 DA C5 C Y N 17 DA C6 C Y N 18 DA N6 N N N 19 DA N1 N Y N 20 DA C2 C Y N 21 DA N3 N Y N 22 DA C4 C Y N 23 DA HOP3 H N N 24 DA HOP2 H N N 25 DA "H5'" H N N 26 DA "H5''" H N N 27 DA "H4'" H N N 28 DA "H3'" H N N 29 DA "HO3'" H N N 30 DA "H2'" H N N 31 DA "H2''" H N N 32 DA "H1'" H N N 33 DA H8 H N N 34 DA H61 H N N 35 DA H62 H N N 36 DA H2 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 DT OP3 O N N 109 DT P P N N 110 DT OP1 O N N 111 DT OP2 O N N 112 DT "O5'" O N N 113 DT "C5'" C N N 114 DT "C4'" C N R 115 DT "O4'" O N N 116 DT "C3'" C N S 117 DT "O3'" O N N 118 DT "C2'" C N N 119 DT "C1'" C N R 120 DT N1 N N N 121 DT C2 C N N 122 DT O2 O N N 123 DT N3 N N N 124 DT C4 C N N 125 DT O4 O N N 126 DT C5 C N N 127 DT C7 C N N 128 DT C6 C N N 129 DT HOP3 H N N 130 DT HOP2 H N N 131 DT "H5'" H N N 132 DT "H5''" H N N 133 DT "H4'" H N N 134 DT "H3'" H N N 135 DT "HO3'" H N N 136 DT "H2'" H N N 137 DT "H2''" H N N 138 DT "H1'" H N N 139 DT H3 H N N 140 DT H71 H N N 141 DT H72 H N N 142 DT H73 H N N 143 DT H6 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 # 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 # _ndb_struct_conf_na.entry_id 1NVN _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 0.004 -0.295 0.322 -8.683 -10.858 -3.670 1 A_DC1:DG10_B A 1 ? B 10 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.033 -0.121 0.099 1.879 -3.743 -4.887 2 A_DC2:DG9_B A 2 ? B 9 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.039 -0.253 0.310 5.787 2.706 -4.533 3 A_DG3:DC8_B A 3 ? B 8 ? 19 1 1 A DG 4 1_555 B DC 7 1_555 -0.293 -0.187 0.389 -0.327 -18.122 -1.789 4 A_DG4:DC7_B A 4 ? B 7 ? 19 1 1 A DT 5 1_555 B DA 6 1_555 -0.252 -0.009 0.149 -11.785 -9.012 -2.395 5 A_DT5:DA6_B A 5 ? B 6 ? 20 1 1 A DA 6 1_555 B DT 5 1_555 0.076 -0.042 0.161 7.506 -10.953 -1.327 6 A_DA6:DT5_B A 6 ? B 5 ? 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 0.093 2.039 3.359 6.105 3.607 36.206 2.706 0.729 3.508 5.736 -9.709 36.871 1 AA_DC1DC2:DG9DG10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.258 2.417 3.321 -1.818 -0.628 39.297 3.666 -0.601 3.269 -0.933 2.702 39.342 2 AA_DC2DG3:DC8DG9_BB A 2 ? B 9 ? A 3 ? B 8 ? 1 A DG 3 1_555 B DC 8 1_555 A DG 4 1_555 B DC 7 1_555 -1.096 1.439 3.679 -5.205 3.245 35.542 1.788 0.908 3.907 5.267 8.449 36.050 3 AA_DG3DG4:DC7DC8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A DG 4 1_555 B DC 7 1_555 A DT 5 1_555 B DA 6 1_555 0.595 0.576 3.645 4.004 -4.849 41.278 1.376 -0.366 3.597 -6.830 -5.640 41.734 4 AA_DG4DT5:DA6DC7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A DT 5 1_555 B DA 6 1_555 A DA 6 1_555 B DT 5 1_555 0.099 1.321 2.984 -0.022 5.461 31.762 1.460 -0.183 3.162 9.886 0.041 32.216 5 AA_DT5DA6:DT5DA6_BB A 5 ? B 6 ? A 6 ? B 5 ? # _atom_sites.entry_id 1NVN _atom_sites.fract_transf_matrix[1][1] 0.015065 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005522 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.042034 _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] 0.028692 _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 CA N O P # loop_