data_2GJB # _entry.id 2GJB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 2GJB pdb_00002gjb 10.2210/pdb2gjb/pdb NDB DD0079 ? ? RCSB RCSB037188 ? ? WWPDB D_1000037188 ? ? # 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 2007-04-10 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 2024-04-03 # _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' Advisory 4 4 'Structure model' 'Refinement description' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' 8 5 'Structure model' 'Structure summary' 9 6 '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 4 'Structure model' pdbx_unobs_or_zero_occ_atoms 2 4 'Structure model' software 3 5 'Structure model' chem_comp 4 5 'Structure model' chem_comp_atom 5 5 'Structure model' chem_comp_bond 6 5 'Structure model' database_2 7 5 'Structure model' diffrn_source 8 5 'Structure model' struct_conn 9 5 'Structure model' struct_site 10 6 'Structure model' pdbx_initial_refinement_model # 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' '_software.classification' 2 4 'Structure model' '_software.name' 3 5 'Structure model' '_chem_comp.pdbx_synonyms' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 7 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 5 'Structure model' '_struct_conn.ptnr1_symmetry' 15 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 19 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 20 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 21 5 'Structure model' '_struct_conn.ptnr2_symmetry' 22 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 23 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 24 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2GJB _pdbx_database_status.recvd_initial_deposition_date 2006-03-30 _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.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2GB9 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gan, Y.' 1 'Cardin, C.J.' 2 'Denny, W.A.' 3 # _citation.id primary _citation.title 'Crosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with oligonucleotide d(CGTACG)' _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 'Gan, Y.' 1 ? primary 'Cardin, C.J.' 2 ? primary 'Denny, W.A.' 3 ? # 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(*CP*GP*TP*AP*CP*GP*)-3'" 1809.217 1 ? ? ? ? 2 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 3 non-polymer syn "N-ACRIDIN-9-YL-N'-[3-(ACRIDIN-9-YLAMINO)PROPYL]PROPANE-1,3-DIAMINE" 485.622 1 ? ? ? ? 4 water nat water 18.015 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'POTASSIUM ION' K 3 "N-ACRIDIN-9-YL-N'-[3-(ACRIDIN-9-YLAMINO)PROPYL]PROPANE-1,3-DIAMINE" BMO 4 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 DG n 1 3 DT n 1 4 DA n 1 5 DC n 1 6 DG n # 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 BMO non-polymer . "N-ACRIDIN-9-YL-N'-[3-(ACRIDIN-9-YLAMINO)PROPYL]PROPANE-1,3-DIAMINE" '1,3-PROPANEDIAMINE; N-9-ACRIDINYL-N -[3-(9-ACRIDINYLAMINO)PROPYL]' 'C32 H31 N5' 485.622 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 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 # 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 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . 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 B 2 K 1 7 1 K K A . C 3 BMO 1 8 1 BMO MOX A . D 4 HOH 1 9 1 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0005 ? 1 MAR345 'data collection' . ? 2 MOSFLM 'data reduction' . ? 3 MOLREP phasing . ? 4 # _cell.entry_id 2GJB _cell.length_a 25.750 _cell.length_b 25.750 _cell.length_c 78.994 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 2GJB _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2GJB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.00 _exptl_crystal.density_percent_sol 38.53 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;The crystals grow in ten days from sitting drops containing 2mM DNA, 12mM spermine, 80mM strontium chloride, 20mM magnesium chloride, 10%MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 spermine ? ? ? 1 2 1 'strontium chloride' ? ? ? 1 3 1 'magnesium chloride' ? ? ? 1 4 1 MPD ? ? ? 1 5 1 H2O ? ? ? 1 6 2 'strontium chloride' ? ? ? 1 7 2 'magnesium chloride' ? ? ? 1 8 2 MPD ? ? ? # _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 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X12' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X12 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 2GJB _reflns.observed_criterion_sigma_I 2 _reflns.observed_criterion_sigma_F 2 _reflns.d_resolution_low 22.3 _reflns.d_resolution_high 1.9 _reflns.number_obs 1472 _reflns.number_all ? _reflns.percent_possible_obs 99.3 _reflns.pdbx_Rmerge_I_obs 0.038 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 49.4 _reflns.B_iso_Wilson_estimate 57.431 _reflns.pdbx_redundancy 20.1 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.9 _reflns_shell.d_res_low 2 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.312 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 9 _reflns_shell.pdbx_redundancy 15.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 204 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2GJB _refine.ls_number_reflns_obs 890 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.00 _refine.ls_d_res_high 2.20 _refine.ls_percent_reflns_obs 99.36 _refine.ls_R_factor_obs 0.27223 _refine.ls_R_factor_all 0.358 _refine.ls_R_factor_R_work 0.27002 _refine.ls_R_factor_R_free 0.30508 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 45 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.943 _refine.correlation_coeff_Fo_to_Fc_free 0.960 _refine.B_iso_mean 37.613 _refine.aniso_B[1][1] 2.09 _refine.aniso_B[2][2] 2.09 _refine.aniso_B[3][3] -3.14 _refine.aniso_B[1][2] 1.05 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _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 'NDB ENTRY DD0018' _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 0.398 _refine.pdbx_overall_ESU_R_Free 0.272 _refine.overall_SU_ML 0.150 _refine.overall_SU_B 5.648 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _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_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 120 _refine_hist.pdbx_number_atoms_ligand 20 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 141 _refine_hist.d_res_high 2.20 _refine_hist.d_res_low 8.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.022 0.021 ? 155 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.391 2.996 ? 233 'X-RAY DIFFRACTION' ? r_chiral_restr 0.165 0.200 ? 23 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.017 0.020 ? 77 'X-RAY DIFFRACTION' ? r_nbd_refined 0.274 0.200 ? 27 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.371 0.200 ? 85 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.322 0.200 ? 36 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.216 0.200 ? 5 'X-RAY DIFFRACTION' ? r_scbond_it 3.483 3.000 ? 173 'X-RAY DIFFRACTION' ? r_scangle_it 5.224 4.500 ? 233 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.200 _refine_ls_shell.d_res_low 2.253 _refine_ls_shell.number_reflns_R_work 58 _refine_ls_shell.R_factor_R_work 0.367 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.583 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 4 _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' # _database_PDB_matrix.entry_id 2GJB _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 2GJB _struct.title 'Crosslinking of DNA duplexes: X-ray crystal structure of an unsubstituted bisacridine with the oligonucleotide d(CGTACG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2GJB _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA duplex, bis-intercalator, 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 3 ? D N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2GJB _struct_ref.pdbx_db_accession 2GJB _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2GJB _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2GJB _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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' 10_555 -y,-x,-z+1/6 0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 13.1656666667 # _struct_biol.id 1 _struct_biol.details ;The second part of the biological assembly is generated by the two fold axis ; _struct_biol.pdbx_parent_biol_id ? # 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 none ? C BMO . N17 ? ? ? 1_555 C BMO . C19 ? ? A BMO 8 A BMO 8 11_655 ? ? ? ? ? ? ? 1.607 ? ? metalc1 metalc ? ? A DT 3 O4 ? ? ? 10_555 B K . K ? ? A DT 3 A K 7 1_555 ? ? ? ? ? ? ? 2.867 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 6 N1 ? ? A DC 1 A DG 6 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 6 O6 ? ? A DC 1 A DG 6 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 6 N2 ? ? A DC 1 A DG 6 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 2 A DC 5 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 2 A DC 5 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 2 A DC 5 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 3 A DA 4 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 3 A DA 4 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 3 N3 ? ? A DA 4 A DT 3 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 3 O4 ? ? A DA 4 A DT 3 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 2 N1 ? ? A DC 5 A DG 2 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 2 O6 ? ? A DC 5 A DG 2 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 2 N2 ? ? A DC 5 A DG 2 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 6 A DC 1 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 6 A DC 1 10_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 6 A DC 1 10_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 K 7 ? 1 'BINDING SITE FOR RESIDUE K A 7' AC2 Software A BMO 8 ? 5 'BINDING SITE FOR RESIDUE BMO A 8' 1 ? ? ? ? ? ? ? # 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 1 DT A 3 ? DT A 3 . ? 10_555 ? 2 AC2 5 DC A 1 ? DC A 1 . ? 1_555 ? 3 AC2 5 DC A 1 ? DC A 1 . ? 11_655 ? 4 AC2 5 DG A 2 ? DG A 2 . ? 1_555 ? 5 AC2 5 DC A 5 ? DC A 5 . ? 10_555 ? 6 AC2 5 DG A 6 ? DG A 6 . ? 10_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DT 3 ? ? "C3'" A DT 3 ? ? 1.351 1.419 -0.068 0.006 N 2 1 "C1'" A DT 3 ? ? N1 A DT 3 ? ? 1.585 1.488 0.097 0.013 N 3 1 C2 A DC 5 ? ? N3 A DC 5 ? ? 1.305 1.353 -0.048 0.008 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.50 108.30 4.20 0.30 N 2 1 "C3'" A DG 2 ? ? "O3'" A DG 2 ? ? P A DT 3 ? ? 134.49 119.70 14.79 1.20 Y 3 1 "O3'" A DG 2 ? ? P A DT 3 ? ? "O5'" A DT 3 ? ? 86.37 104.00 -17.63 1.90 Y 4 1 "O5'" A DT 3 ? ? "C5'" A DT 3 ? ? "C4'" A DT 3 ? ? 104.22 109.40 -5.18 0.80 N 5 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? "C2'" A DT 3 ? ? 101.02 105.90 -4.88 0.80 N 6 1 N1 A DT 3 ? ? C2 A DT 3 ? ? O2 A DT 3 ? ? 129.30 123.10 6.20 0.80 N 7 1 N3 A DT 3 ? ? C2 A DT 3 ? ? O2 A DT 3 ? ? 118.58 122.30 -3.72 0.60 N 8 1 "O5'" A DA 4 ? ? P A DA 4 ? ? OP2 A DA 4 ? ? 118.22 110.70 7.52 1.20 N 9 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 100.10 108.00 -7.90 0.70 N 10 1 "C1'" A DC 5 ? ? "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? 103.49 110.10 -6.61 1.00 N 11 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? "C2'" A DC 5 ? ? 110.35 106.80 3.55 0.50 N 12 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 111.00 108.30 2.70 0.30 N 13 1 C6 A DC 5 ? ? N1 A DC 5 ? ? C2 A DC 5 ? ? 123.23 120.30 2.93 0.40 N 14 1 N3 A DC 5 ? ? C4 A DC 5 ? ? N4 A DC 5 ? ? 113.38 118.00 -4.62 0.70 N 15 1 "O4'" A DG 6 ? ? "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? 101.13 104.50 -3.37 0.40 N 16 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.60 108.30 2.30 0.30 N 17 1 N3 A DG 6 ? ? C2 A DG 6 ? ? N2 A DG 6 ? ? 115.20 119.90 -4.70 0.70 N 18 1 N1 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 123.60 119.90 3.70 0.60 N 19 1 C5 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 124.12 128.60 -4.48 0.60 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text bis-intercalation # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id BMO _pdbx_struct_special_symmetry.auth_seq_id 8 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id C _pdbx_struct_special_symmetry.label_comp_id BMO _pdbx_struct_special_symmetry.label_seq_id . # 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 BMO N17 N N N 1 BMO C19 C N N 2 BMO C36 C N N 3 BMO C22 C N N 4 BMO N20 N N N 5 BMO C21 C Y N 6 BMO C27 C Y N 7 BMO C26 C Y N 8 BMO C25 C Y N 9 BMO C24 C Y N 10 BMO C23 C Y N 11 BMO C28 C Y N 12 BMO N29 N Y N 13 BMO C31 C Y N 14 BMO C30 C Y N 15 BMO C34 C Y N 16 BMO C35 C Y N 17 BMO C32 C Y N 18 BMO C33 C Y N 19 BMO C1 C N N 20 BMO C2 C N N 21 BMO C3 C N N 22 BMO N1 N N N 23 BMO C4 C Y N 24 BMO C5 C Y N 25 BMO C6 C Y N 26 BMO C7 C Y N 27 BMO C8 C Y N 28 BMO C9 C Y N 29 BMO C10 C Y N 30 BMO N2 N Y N 31 BMO C11 C Y N 32 BMO C12 C Y N 33 BMO C13 C Y N 34 BMO C14 C Y N 35 BMO C15 C Y N 36 BMO C16 C Y N 37 BMO H171 H N N 38 BMO H191 H N N 39 BMO H192 H N N 40 BMO H361 H N N 41 BMO H362 H N N 42 BMO H221 H N N 43 BMO H222 H N N 44 BMO HN20 H N N 45 BMO H26 H N N 46 BMO H25 H N N 47 BMO H24 H N N 48 BMO H23 H N N 49 BMO H34 H N N 50 BMO H35 H N N 51 BMO H32 H N N 52 BMO H33 H N N 53 BMO H11 H N N 54 BMO H12A H N N 55 BMO H21 H N N 56 BMO H22 H N N 57 BMO H31 H N N 58 BMO H32A H N N 59 BMO HN1 H N N 60 BMO H6 H N N 61 BMO H7 H N N 62 BMO H8 H N N 63 BMO H9 H N N 64 BMO H12 H N N 65 BMO H13 H N N 66 BMO H14 H N N 67 BMO H15 H N N 68 DA OP3 O N N 69 DA P P N N 70 DA OP1 O N N 71 DA OP2 O N N 72 DA "O5'" O N N 73 DA "C5'" C N N 74 DA "C4'" C N R 75 DA "O4'" O N N 76 DA "C3'" C N S 77 DA "O3'" O N N 78 DA "C2'" C N N 79 DA "C1'" C N R 80 DA N9 N Y N 81 DA C8 C Y N 82 DA N7 N Y N 83 DA C5 C Y N 84 DA C6 C Y N 85 DA N6 N N N 86 DA N1 N Y N 87 DA C2 C Y N 88 DA N3 N Y N 89 DA C4 C Y N 90 DA HOP3 H N N 91 DA HOP2 H N N 92 DA "H5'" H N N 93 DA "H5''" H N N 94 DA "H4'" H N N 95 DA "H3'" H N N 96 DA "HO3'" H N N 97 DA "H2'" H N N 98 DA "H2''" H N N 99 DA "H1'" H N N 100 DA H8 H N N 101 DA H61 H N N 102 DA H62 H N N 103 DA H2 H N N 104 DC OP3 O N N 105 DC P P N N 106 DC OP1 O N N 107 DC OP2 O N N 108 DC "O5'" O N N 109 DC "C5'" C N N 110 DC "C4'" C N R 111 DC "O4'" O N N 112 DC "C3'" C N S 113 DC "O3'" O N N 114 DC "C2'" C N N 115 DC "C1'" C N R 116 DC N1 N N N 117 DC C2 C N N 118 DC O2 O N N 119 DC N3 N N N 120 DC C4 C N N 121 DC N4 N N N 122 DC C5 C N N 123 DC C6 C N N 124 DC HOP3 H N N 125 DC HOP2 H N N 126 DC "H5'" H N N 127 DC "H5''" H N N 128 DC "H4'" H N N 129 DC "H3'" H N N 130 DC "HO3'" H N N 131 DC "H2'" H N N 132 DC "H2''" H N N 133 DC "H1'" H N N 134 DC H41 H N N 135 DC H42 H N N 136 DC H5 H N N 137 DC H6 H N N 138 DG OP3 O N N 139 DG P P N N 140 DG OP1 O N N 141 DG OP2 O N N 142 DG "O5'" O N N 143 DG "C5'" C N N 144 DG "C4'" C N R 145 DG "O4'" O N N 146 DG "C3'" C N S 147 DG "O3'" O N N 148 DG "C2'" C N N 149 DG "C1'" C N R 150 DG N9 N Y N 151 DG C8 C Y N 152 DG N7 N Y N 153 DG C5 C Y N 154 DG C6 C N N 155 DG O6 O N N 156 DG N1 N N N 157 DG C2 C N N 158 DG N2 N N N 159 DG N3 N N N 160 DG C4 C Y N 161 DG HOP3 H N N 162 DG HOP2 H N N 163 DG "H5'" H N N 164 DG "H5''" H N N 165 DG "H4'" H N N 166 DG "H3'" H N N 167 DG "HO3'" H N N 168 DG "H2'" H N N 169 DG "H2''" H N N 170 DG "H1'" H N N 171 DG H8 H N N 172 DG H1 H N N 173 DG H21 H N N 174 DG H22 H N N 175 DT OP3 O N N 176 DT P P N N 177 DT OP1 O N N 178 DT OP2 O N N 179 DT "O5'" O N N 180 DT "C5'" C N N 181 DT "C4'" C N R 182 DT "O4'" O N N 183 DT "C3'" C N S 184 DT "O3'" O N N 185 DT "C2'" C N N 186 DT "C1'" C N R 187 DT N1 N N N 188 DT C2 C N N 189 DT O2 O N N 190 DT N3 N N N 191 DT C4 C N N 192 DT O4 O N N 193 DT C5 C N N 194 DT C7 C N N 195 DT C6 C N N 196 DT HOP3 H N N 197 DT HOP2 H N N 198 DT "H5'" H N N 199 DT "H5''" H N N 200 DT "H4'" H N N 201 DT "H3'" H N N 202 DT "HO3'" H N N 203 DT "H2'" H N N 204 DT "H2''" H N N 205 DT "H1'" H N N 206 DT H3 H N N 207 DT H71 H N N 208 DT H72 H N N 209 DT H73 H N N 210 DT H6 H N N 211 HOH O O N N 212 HOH H1 H N N 213 HOH H2 H N N 214 K K K N N 215 # 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 BMO N17 C19 sing N N 1 BMO N17 C1 sing N N 2 BMO N17 H171 sing N N 3 BMO C19 C36 sing N N 4 BMO C19 H191 sing N N 5 BMO C19 H192 sing N N 6 BMO C36 C22 sing N N 7 BMO C36 H361 sing N N 8 BMO C36 H362 sing N N 9 BMO C22 N20 sing N N 10 BMO C22 H221 sing N N 11 BMO C22 H222 sing N N 12 BMO N20 C21 sing N N 13 BMO N20 HN20 sing N N 14 BMO C21 C27 doub Y N 15 BMO C21 C30 sing Y N 16 BMO C27 C26 sing Y N 17 BMO C27 C28 sing Y N 18 BMO C26 C25 doub Y N 19 BMO C26 H26 sing N N 20 BMO C25 C24 sing Y N 21 BMO C25 H25 sing N N 22 BMO C24 C23 doub Y N 23 BMO C24 H24 sing N N 24 BMO C23 C28 sing Y N 25 BMO C23 H23 sing N N 26 BMO C28 N29 doub Y N 27 BMO N29 C31 sing Y N 28 BMO C31 C30 sing Y N 29 BMO C31 C33 doub Y N 30 BMO C30 C34 doub Y N 31 BMO C34 C35 sing Y N 32 BMO C34 H34 sing N N 33 BMO C35 C32 doub Y N 34 BMO C35 H35 sing N N 35 BMO C32 C33 sing Y N 36 BMO C32 H32 sing N N 37 BMO C33 H33 sing N N 38 BMO C1 C2 sing N N 39 BMO C1 H11 sing N N 40 BMO C1 H12A sing N N 41 BMO C2 C3 sing N N 42 BMO C2 H21 sing N N 43 BMO C2 H22 sing N N 44 BMO C3 N1 sing N N 45 BMO C3 H31 sing N N 46 BMO C3 H32A sing N N 47 BMO N1 C4 sing N N 48 BMO N1 HN1 sing N N 49 BMO C4 C5 doub Y N 50 BMO C4 C16 sing Y N 51 BMO C5 C6 sing Y N 52 BMO C5 C10 sing Y N 53 BMO C6 C7 doub Y N 54 BMO C6 H6 sing N N 55 BMO C7 C8 sing Y N 56 BMO C7 H7 sing N N 57 BMO C8 C9 doub Y N 58 BMO C8 H8 sing N N 59 BMO C9 C10 sing Y N 60 BMO C9 H9 sing N N 61 BMO C10 N2 doub Y N 62 BMO N2 C11 sing Y N 63 BMO C11 C12 doub Y N 64 BMO C11 C16 sing Y N 65 BMO C12 C13 sing Y N 66 BMO C12 H12 sing N N 67 BMO C13 C14 doub Y N 68 BMO C13 H13 sing N N 69 BMO C14 C15 sing Y N 70 BMO C14 H14 sing N N 71 BMO C15 C16 doub Y N 72 BMO C15 H15 sing N N 73 DA OP3 P sing N N 74 DA OP3 HOP3 sing N N 75 DA P OP1 doub N N 76 DA P OP2 sing N N 77 DA P "O5'" sing N N 78 DA OP2 HOP2 sing N N 79 DA "O5'" "C5'" sing N N 80 DA "C5'" "C4'" sing N N 81 DA "C5'" "H5'" sing N N 82 DA "C5'" "H5''" sing N N 83 DA "C4'" "O4'" sing N N 84 DA "C4'" "C3'" sing N N 85 DA "C4'" "H4'" sing N N 86 DA "O4'" "C1'" sing N N 87 DA "C3'" "O3'" sing N N 88 DA "C3'" "C2'" sing N N 89 DA "C3'" "H3'" sing N N 90 DA "O3'" "HO3'" sing N N 91 DA "C2'" "C1'" sing N N 92 DA "C2'" "H2'" sing N N 93 DA "C2'" "H2''" sing N N 94 DA "C1'" N9 sing N N 95 DA "C1'" "H1'" sing N N 96 DA N9 C8 sing Y N 97 DA N9 C4 sing Y N 98 DA C8 N7 doub Y N 99 DA C8 H8 sing N N 100 DA N7 C5 sing Y N 101 DA C5 C6 sing Y N 102 DA C5 C4 doub Y N 103 DA C6 N6 sing N N 104 DA C6 N1 doub Y N 105 DA N6 H61 sing N N 106 DA N6 H62 sing N N 107 DA N1 C2 sing Y N 108 DA C2 N3 doub Y N 109 DA C2 H2 sing N N 110 DA N3 C4 sing Y N 111 DC OP3 P sing N N 112 DC OP3 HOP3 sing N N 113 DC P OP1 doub N N 114 DC P OP2 sing N N 115 DC P "O5'" sing N N 116 DC OP2 HOP2 sing N N 117 DC "O5'" "C5'" sing N N 118 DC "C5'" "C4'" sing N N 119 DC "C5'" "H5'" sing N N 120 DC "C5'" "H5''" sing N N 121 DC "C4'" "O4'" sing N N 122 DC "C4'" "C3'" sing N N 123 DC "C4'" "H4'" sing N N 124 DC "O4'" "C1'" sing N N 125 DC "C3'" "O3'" sing N N 126 DC "C3'" "C2'" sing N N 127 DC "C3'" "H3'" sing N N 128 DC "O3'" "HO3'" sing N N 129 DC "C2'" "C1'" sing N N 130 DC "C2'" "H2'" sing N N 131 DC "C2'" "H2''" sing N N 132 DC "C1'" N1 sing N N 133 DC "C1'" "H1'" sing N N 134 DC N1 C2 sing N N 135 DC N1 C6 sing N N 136 DC C2 O2 doub N N 137 DC C2 N3 sing N N 138 DC N3 C4 doub N N 139 DC C4 N4 sing N N 140 DC C4 C5 sing N N 141 DC N4 H41 sing N N 142 DC N4 H42 sing N N 143 DC C5 C6 doub N N 144 DC C5 H5 sing N N 145 DC C6 H6 sing N N 146 DG OP3 P sing N N 147 DG OP3 HOP3 sing N N 148 DG P OP1 doub N N 149 DG P OP2 sing N N 150 DG P "O5'" sing N N 151 DG OP2 HOP2 sing N N 152 DG "O5'" "C5'" sing N N 153 DG "C5'" "C4'" sing N N 154 DG "C5'" "H5'" sing N N 155 DG "C5'" "H5''" sing N N 156 DG "C4'" "O4'" sing N N 157 DG "C4'" "C3'" sing N N 158 DG "C4'" "H4'" sing N N 159 DG "O4'" "C1'" sing N N 160 DG "C3'" "O3'" sing N N 161 DG "C3'" "C2'" sing N N 162 DG "C3'" "H3'" sing N N 163 DG "O3'" "HO3'" sing N N 164 DG "C2'" "C1'" sing N N 165 DG "C2'" "H2'" sing N N 166 DG "C2'" "H2''" sing N N 167 DG "C1'" N9 sing N N 168 DG "C1'" "H1'" sing N N 169 DG N9 C8 sing Y N 170 DG N9 C4 sing Y N 171 DG C8 N7 doub Y N 172 DG C8 H8 sing N N 173 DG N7 C5 sing Y N 174 DG C5 C6 sing N N 175 DG C5 C4 doub Y N 176 DG C6 O6 doub N N 177 DG C6 N1 sing N N 178 DG N1 C2 sing N N 179 DG N1 H1 sing N N 180 DG C2 N2 sing N N 181 DG C2 N3 doub N N 182 DG N2 H21 sing N N 183 DG N2 H22 sing N N 184 DG N3 C4 sing N N 185 DT OP3 P sing N N 186 DT OP3 HOP3 sing N N 187 DT P OP1 doub N N 188 DT P OP2 sing N N 189 DT P "O5'" sing N N 190 DT OP2 HOP2 sing N N 191 DT "O5'" "C5'" sing N N 192 DT "C5'" "C4'" sing N N 193 DT "C5'" "H5'" sing N N 194 DT "C5'" "H5''" sing N N 195 DT "C4'" "O4'" sing N N 196 DT "C4'" "C3'" sing N N 197 DT "C4'" "H4'" sing N N 198 DT "O4'" "C1'" sing N N 199 DT "C3'" "O3'" sing N N 200 DT "C3'" "C2'" sing N N 201 DT "C3'" "H3'" sing N N 202 DT "O3'" "HO3'" sing N N 203 DT "C2'" "C1'" sing N N 204 DT "C2'" "H2'" sing N N 205 DT "C2'" "H2''" sing N N 206 DT "C1'" N1 sing N N 207 DT "C1'" "H1'" sing N N 208 DT N1 C2 sing N N 209 DT N1 C6 sing N N 210 DT C2 O2 doub N N 211 DT C2 N3 sing N N 212 DT N3 C4 sing N N 213 DT N3 H3 sing N N 214 DT C4 O4 doub N N 215 DT C4 C5 sing N N 216 DT C5 C7 sing N N 217 DT C5 C6 doub N N 218 DT C7 H71 sing N N 219 DT C7 H72 sing N N 220 DT C7 H73 sing N N 221 DT C6 H6 sing N N 222 HOH O H1 sing N N 223 HOH O H2 sing N N 224 # _ndb_struct_conf_na.entry_id 2GJB _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 A DG 6 10_555 0.625 -0.539 -0.634 10.301 -3.879 -4.756 1 A_DC1:DG6_A A 1 ? A 6 ? 19 1 1 A DG 2 1_555 A DC 5 10_555 -0.093 -0.068 0.191 -11.221 -6.709 -4.610 2 A_DG2:DC5_A A 2 ? A 5 ? 19 1 1 A DT 3 1_555 A DA 4 10_555 -0.137 -0.079 0.268 -4.447 -3.027 1.204 3 A_DT3:DA4_A A 3 ? A 4 ? 20 1 1 A DA 4 1_555 A DT 3 10_555 0.137 -0.079 0.268 4.447 -3.027 1.204 4 A_DA4:DT3_A A 4 ? A 3 ? 20 1 1 A DC 5 1_555 A DG 2 10_555 0.093 -0.068 0.191 11.221 -6.709 -4.610 5 A_DC5:DG2_A A 5 ? A 2 ? 19 1 1 A DG 6 1_555 A DC 1 10_555 -0.625 -0.539 -0.634 -10.301 -3.879 -4.756 6 A_DG6:DC1_A A 6 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 A DG 6 10_555 A DG 2 1_555 A DC 5 10_555 -0.338 0.819 7.203 -11.225 -2.216 24.244 3.044 -5.728 6.606 -4.939 25.021 26.772 1 AA_DC1DG2:DC5DG6_AA A 1 ? A 6 ? A 2 ? A 5 ? 1 A DG 2 1_555 A DC 5 10_555 A DT 3 1_555 A DA 4 10_555 -0.349 0.195 3.288 -1.744 1.715 32.183 0.044 0.316 3.308 3.088 3.140 32.274 2 AA_DG2DT3:DA4DC5_AA A 2 ? A 5 ? A 3 ? A 4 ? 1 A DT 3 1_555 A DA 4 10_555 A DA 4 1_555 A DT 3 10_555 0.000 0.107 3.122 0.000 4.355 37.268 -0.379 0.000 3.114 6.786 0.000 37.513 3 AA_DT3DA4:DT3DA4_AA A 3 ? A 4 ? A 4 ? A 3 ? 1 A DA 4 1_555 A DT 3 10_555 A DC 5 1_555 A DG 2 10_555 0.349 0.195 3.288 1.744 1.715 32.183 0.044 -0.316 3.308 3.088 -3.140 32.274 4 AA_DA4DC5:DG2DT3_AA A 4 ? A 3 ? A 5 ? A 2 ? 1 A DC 5 1_555 A DG 2 10_555 A DG 6 1_555 A DC 1 10_555 0.338 0.819 7.203 11.225 -2.216 24.244 3.044 5.728 6.606 -4.939 -25.021 26.772 5 AA_DC5DG6:DC1DG2_AA A 5 ? A 2 ? A 6 ? A 1 ? # _pdbx_initial_refinement_model.accession_code 1C9Z _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.details 'NDB ENTRY DD0018' # _atom_sites.entry_id 2GJB _atom_sites.fract_transf_matrix[1][1] 0.038835 _atom_sites.fract_transf_matrix[1][2] 0.022421 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.044842 _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] 0.012659 _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 K N O P # loop_