data_1P1Y # _entry.id 1P1Y # _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 1P1Y pdb_00001p1y 10.2210/pdb1p1y/pdb NDB UD0031 ? ? RCSB RCSB018912 ? ? WWPDB D_1000018912 ? ? # 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 2004-06-01 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-02 5 'Structure model' 1 4 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' 'Non-polymer description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 '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 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_struct_conn_angle 5 5 'Structure model' struct_conn 6 5 'Structure model' struct_conn_type 7 5 '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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.value' 6 5 'Structure model' '_struct_conn.conn_type_id' 7 5 'Structure model' '_struct_conn.id' 8 5 'Structure model' '_struct_conn.pdbx_dist_value' 9 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 10 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 11 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 12 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 13 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 14 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 15 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 16 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 17 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 18 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 19 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 20 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 21 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 22 5 'Structure model' '_struct_conn_type.id' 23 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 24 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 25 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1P1Y _pdbx_database_status.recvd_initial_deposition_date 2003-04-14 _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.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Paukstelis, P.J.' 1 'Nowakowski, J.' 2 'Birktoft, J.J.' 3 'Seeman, N.C.' 4 # _citation.id primary _citation.title 'Crystal structure of a continuous three-dimensional DNA lattice.' _citation.journal_abbrev Chem.Biol. _citation.journal_volume 11 _citation.page_first 1119 _citation.page_last 1126 _citation.year 2004 _citation.journal_id_ASTM CBOLE2 _citation.country UK _citation.journal_id_ISSN 1074-5521 _citation.journal_id_CSD 2050 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15324813 _citation.pdbx_database_id_DOI 10.1016/j.chembiol.2004.05.021 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Paukstelis, P.J.' 1 ? primary 'Nowakowski, J.' 2 ? primary 'Birktoft, J.J.' 3 ? primary 'Seeman, N.C.' 4 ? # 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(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3'" 4249.451 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 23 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DG)(DA)(CBR)(DA)(DG)(DA)(BRU)(DG)(DG)(DG)(DA)(DG)' _entity_poly.pdbx_seq_one_letter_code_can GGACAGAUGGGAG _entity_poly.pdbx_strand_id X _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DG n 1 3 DA n 1 4 CBR n 1 5 DA n 1 6 DG n 1 7 DA n 1 8 BRU n 1 9 DG n 1 10 DG n 1 11 DG n 1 12 DA n 1 13 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 BRU 'DNA linking' n "5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O8 P' 387.078 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 DG 1 1 1 DG G X . n A 1 2 DG 2 2 2 DG G X . n A 1 3 DA 3 3 3 DA A X . n A 1 4 CBR 4 4 4 CBR CBR X . n A 1 5 DA 5 5 5 DA A X . n A 1 6 DG 6 6 6 DG G X . n A 1 7 DA 7 7 7 DA A X . n A 1 8 BRU 8 8 8 BRU BRU X . n A 1 9 DG 9 9 9 DG G X . n A 1 10 DG 10 10 10 DG G X . n A 1 11 DG 11 11 11 DG G X . n A 1 12 DA 12 12 12 DA A X . n A 1 13 DG 13 13 13 DG G X . 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 MG 1 51 51 MG MO4 X . C 3 HOH 1 52 1 HOH HOH X . C 3 HOH 2 53 2 HOH HOH X . C 3 HOH 3 54 3 HOH HOH X . C 3 HOH 4 55 4 HOH HOH X . C 3 HOH 5 56 5 HOH HOH X . C 3 HOH 6 57 6 HOH HOH X . C 3 HOH 7 58 7 HOH HOH X . C 3 HOH 8 59 8 HOH HOH X . C 3 HOH 9 60 9 HOH HOH X . C 3 HOH 10 61 11 HOH HOH X . C 3 HOH 11 62 13 HOH HOH X . C 3 HOH 12 63 14 HOH HOH X . C 3 HOH 13 64 15 HOH HOH X . C 3 HOH 14 65 20 HOH HOH X . C 3 HOH 15 66 22 HOH HOH X . C 3 HOH 16 67 23 HOH HOH X . C 3 HOH 17 68 25 HOH HOH X . C 3 HOH 18 69 26 HOH HOH X . C 3 HOH 19 70 27 HOH HOH X . C 3 HOH 20 71 51 HOH MO4 X . C 3 HOH 21 72 51 HOH MO4 X . C 3 HOH 22 73 51 HOH MO4 X . C 3 HOH 23 74 51 HOH MO4 X . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 X DG 13 ? "C5'" ? A DG 13 "C5'" 2 1 Y 1 X DG 13 ? "C4'" ? A DG 13 "C4'" 3 1 Y 1 X DG 13 ? "O4'" ? A DG 13 "O4'" 4 1 Y 1 X DG 13 ? "C3'" ? A DG 13 "C3'" 5 1 Y 1 X DG 13 ? "O3'" ? A DG 13 "O3'" 6 1 Y 1 X DG 13 ? "C2'" ? A DG 13 "C2'" 7 1 Y 1 X DG 13 ? "C1'" ? A DG 13 "C1'" 8 1 Y 1 X DG 13 ? N9 ? A DG 13 N9 9 1 Y 1 X DG 13 ? C8 ? A DG 13 C8 10 1 Y 1 X DG 13 ? N7 ? A DG 13 N7 11 1 Y 1 X DG 13 ? C5 ? A DG 13 C5 12 1 Y 1 X DG 13 ? C6 ? A DG 13 C6 13 1 Y 1 X DG 13 ? O6 ? A DG 13 O6 14 1 Y 1 X DG 13 ? N1 ? A DG 13 N1 15 1 Y 1 X DG 13 ? C2 ? A DG 13 C2 16 1 Y 1 X DG 13 ? N2 ? A DG 13 N2 17 1 Y 1 X DG 13 ? N3 ? A DG 13 N3 18 1 Y 1 X DG 13 ? C4 ? A DG 13 C4 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.24 ? 1 HKL-2000 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing . ? 4 # _cell.entry_id 1P1Y _cell.length_a 40.630 _cell.length_b 40.630 _cell.length_c 55.270 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1P1Y _symmetry.space_group_name_H-M 'P 64' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1P1Y _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.97 _exptl_crystal.density_percent_sol 58.52 _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 295.5 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'magnesium formate, mpd, lithium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K' _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 'magnesium formate' ? ? ? 1 2 1 mpd ? ? ? 1 3 1 LiCl ? ? ? 1 4 2 mpd ? ? ? 1 5 2 LiCl ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2002-08-04 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.92002 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X8C' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X8C _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.92002 # _reflns.entry_id 1P1Y _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 1.8 _reflns.d_resolution_low 50 _reflns.number_all 5957 _reflns.number_obs 3066 _reflns.percent_possible_obs 99 _reflns.pdbx_Rmerge_I_obs 0.071 _reflns.pdbx_Rsym_value 0.071 _reflns.pdbx_netI_over_sigmaI 20.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.10 _reflns_shell.d_res_low 2.18 _reflns_shell.percent_possible_all 99.4 _reflns_shell.Rmerge_I_obs 0.22 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 13.76 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 307 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1P1Y _refine.ls_number_reflns_obs 2870 _refine.ls_number_reflns_all 2907 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 35.14 _refine.ls_d_res_high 2.10 _refine.ls_percent_reflns_obs 98.70 _refine.ls_R_factor_obs 0.20485 _refine.ls_R_factor_all 0.20485 _refine.ls_R_factor_R_work 0.20332 _refine.ls_R_factor_R_free 0.23256 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.3 _refine.ls_number_reflns_R_free 161 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.956 _refine.correlation_coeff_Fo_to_Fc_free 0.940 _refine.B_iso_mean 39.727 _refine.aniso_B[1][1] -1.50 _refine.aniso_B[2][2] -1.50 _refine.aniso_B[3][3] 2.24 _refine.aniso_B[1][2] -0.75 _refine.aniso_B[1][3] 0.00 _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 ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.163 _refine.pdbx_overall_ESU_R_Free 0.156 _refine.overall_SU_ML 0.096 _refine.overall_SU_B 3.627 _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 257 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 23 _refine_hist.number_atoms_total 281 _refine_hist.d_res_high 2.10 _refine_hist.d_res_low 35.14 # 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 0.020 0.021 ? 292 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.133 3.000 ? 451 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.120 0.200 ? 36 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.013 0.020 ? 142 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.381 0.200 ? 74 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.187 0.200 ? 11 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.113 0.200 ? 20 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.065 0.200 ? 5 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.100 _refine_ls_shell.d_res_low 2.155 _refine_ls_shell.number_reflns_R_work 217 _refine_ls_shell.R_factor_R_work 0.228 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.258 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 16 _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 1P1Y _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 1P1Y _struct.title 'Crystal structure of a continuous three-dimensional DNA lattice from d(GGACAGATGGGAG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1P1Y _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'continuous three-dimensional dna lattice, parallel-stranded base pairs, 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1P1Y _struct_ref.pdbx_db_accession 1P1Y _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 1P1Y _struct_ref_seq.pdbx_strand_id X _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 13 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1P1Y _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 13 _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 13 # _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 # 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' 4_435 -x-1,-y-2,z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 -70.3732243115 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 ? A DA 3 "O3'" ? ? ? 1_555 A CBR 4 P ? ? X DA 3 X CBR 4 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale2 covale both ? A CBR 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? X CBR 4 X DA 5 1_555 ? ? ? ? ? ? ? 1.593 ? ? covale3 covale both ? A DA 7 "O3'" ? ? ? 1_555 A BRU 8 P ? ? X DA 7 X BRU 8 1_555 ? ? ? ? ? ? ? 1.574 ? ? covale4 covale both ? A BRU 8 "O3'" ? ? ? 1_555 A DG 9 P ? ? X BRU 8 X DG 9 1_555 ? ? ? ? ? ? ? 1.565 ? ? metalc1 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? X MG 51 X HOH 71 1_555 ? ? ? ? ? ? ? 2.159 ? ? metalc2 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? X MG 51 X HOH 72 1_555 ? ? ? ? ? ? ? 2.168 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? X MG 51 X HOH 73 1_555 ? ? ? ? ? ? ? 2.167 ? ? metalc4 metalc ? ? B MG . MG ? ? ? 1_555 C HOH . O ? ? X MG 51 X HOH 74 1_555 ? ? ? ? ? ? ? 2.164 ? ? hydrog1 hydrog ? ? A DG 1 N7 ? ? ? 1_555 A DG 10 N1 ? ? X DG 1 X DG 10 6_454 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog2 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DG 10 N2 ? ? X DG 1 X DG 10 6_454 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog3 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DG 11 N3 ? ? X DG 2 X DG 11 6_454 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog4 hydrog ? ? A DG 2 N3 ? ? ? 1_555 A DG 11 N2 ? ? X DG 2 X DG 11 6_454 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog5 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DA 12 N7 ? ? X DA 3 X DA 12 6_454 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog6 hydrog ? ? A DA 3 N7 ? ? ? 1_555 A DA 12 N6 ? ? X DA 3 X DA 12 6_454 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 ? C HOH . ? X HOH 71 ? 1_555 MG ? B MG . ? X MG 51 ? 1_555 O ? C HOH . ? X HOH 72 ? 1_555 178.7 ? 2 O ? C HOH . ? X HOH 71 ? 1_555 MG ? B MG . ? X MG 51 ? 1_555 O ? C HOH . ? X HOH 73 ? 1_555 93.5 ? 3 O ? C HOH . ? X HOH 72 ? 1_555 MG ? B MG . ? X MG 51 ? 1_555 O ? C HOH . ? X HOH 73 ? 1_555 87.0 ? 4 O ? C HOH . ? X HOH 71 ? 1_555 MG ? B MG . ? X MG 51 ? 1_555 O ? C HOH . ? X HOH 74 ? 1_555 83.8 ? 5 O ? C HOH . ? X HOH 72 ? 1_555 MG ? B MG . ? X MG 51 ? 1_555 O ? C HOH . ? X HOH 74 ? 1_555 95.0 ? 6 O ? C HOH . ? X HOH 73 ? 1_555 MG ? B MG . ? X MG 51 ? 1_555 O ? C HOH . ? X HOH 74 ? 1_555 93.7 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id X _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 51 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE MG X 51' # 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 4 HOH C . ? HOH X 71 . ? 1_555 ? 2 AC1 4 HOH C . ? HOH X 72 . ? 1_555 ? 3 AC1 4 HOH C . ? HOH X 73 . ? 1_555 ? 4 AC1 4 HOH C . ? HOH X 74 . ? 1_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 N3 X DA 3 ? ? C4 X DA 3 ? ? 1.296 1.344 -0.048 0.006 N 2 1 "O3'" X DG 9 ? ? "C3'" X DG 9 ? ? 1.378 1.419 -0.041 0.006 N 3 1 N3 X DA 12 ? ? C4 X DA 12 ? ? 1.305 1.344 -0.039 0.006 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'" X DG 1 ? ? "C1'" X DG 1 ? ? N9 X DG 1 ? ? 110.19 108.30 1.89 0.30 N 2 1 "O4'" X DG 2 ? ? "C1'" X DG 2 ? ? "C2'" X DG 2 ? ? 99.75 105.90 -6.15 0.80 N 3 1 "O4'" X DA 3 ? ? "C4'" X DA 3 ? ? "C3'" X DA 3 ? ? 96.80 104.50 -7.70 0.40 N 4 1 "C1'" X DA 3 ? ? "O4'" X DA 3 ? ? "C4'" X DA 3 ? ? 118.99 110.30 8.69 0.70 N 5 1 "O4'" X DA 3 ? ? "C1'" X DA 3 ? ? "C2'" X DA 3 ? ? 98.39 105.90 -7.51 0.80 N 6 1 "O4'" X DA 3 ? ? "C1'" X DA 3 ? ? N9 X DA 3 ? ? 99.65 108.00 -8.35 0.70 N 7 1 N1 X DA 3 ? ? C2 X DA 3 ? ? N3 X DA 3 ? ? 125.18 129.30 -4.12 0.50 N 8 1 C2 X DA 3 ? ? N3 X DA 3 ? ? C4 X DA 3 ? ? 116.67 110.60 6.07 0.50 N 9 1 C4 X DA 5 ? ? C5 X DA 5 ? ? N7 X DA 5 ? ? 107.58 110.70 -3.12 0.50 N 10 1 N1 X DA 5 ? ? C6 X DA 5 ? ? N6 X DA 5 ? ? 114.19 118.60 -4.41 0.60 N 11 1 "C3'" X DG 6 ? ? "C2'" X DG 6 ? ? "C1'" X DG 6 ? ? 96.61 102.40 -5.79 0.80 N 12 1 "O4'" X DG 6 ? ? "C1'" X DG 6 ? ? N9 X DG 6 ? ? 114.23 108.30 5.93 0.30 N 13 1 N1 X DG 6 ? ? C2 X DG 6 ? ? N3 X DG 6 ? ? 120.03 123.90 -3.87 0.60 N 14 1 "O4'" X DA 7 ? ? "C1'" X DA 7 ? ? N9 X DA 7 ? ? 111.22 108.30 2.92 0.30 N 15 1 "C3'" X DG 9 ? ? "C2'" X DG 9 ? ? "C1'" X DG 9 ? ? 93.48 102.40 -8.92 0.80 N 16 1 "O4'" X DG 9 ? ? "C1'" X DG 9 ? ? N9 X DG 9 ? ? 110.79 108.30 2.49 0.30 N 17 1 C5 X DG 9 ? ? C6 X DG 9 ? ? O6 X DG 9 ? ? 124.76 128.60 -3.84 0.60 N 18 1 "O4'" X DG 11 ? ? "C4'" X DG 11 ? ? "C3'" X DG 11 ? ? 101.70 104.50 -2.80 0.40 N 19 1 "C1'" X DG 11 ? ? "O4'" X DG 11 ? ? "C4'" X DG 11 ? ? 114.74 110.30 4.44 0.70 N 20 1 N1 X DG 11 ? ? C6 X DG 11 ? ? O6 X DG 11 ? ? 113.48 119.90 -6.42 0.60 N 21 1 C5 X DG 11 ? ? C6 X DG 11 ? ? O6 X DG 11 ? ? 132.21 128.60 3.61 0.60 N 22 1 "O5'" X DA 12 ? ? P X DA 12 ? ? OP1 X DA 12 ? ? 118.72 110.70 8.02 1.20 N 23 1 C4 X DA 12 ? ? C5 X DA 12 ? ? N7 X DA 12 ? ? 107.29 110.70 -3.41 0.50 N 24 1 C5 X DA 12 ? ? N7 X DA 12 ? ? C8 X DA 12 ? ? 108.44 103.90 4.54 0.50 N 25 1 N1 X DA 12 ? ? C6 X DA 12 ? ? N6 X DA 12 ? ? 114.57 118.60 -4.03 0.60 N 26 1 OP1 X DG 13 ? ? P X DG 13 ? ? OP2 X DG 13 ? ? 130.12 119.60 10.52 1.50 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A CBR 4 X CBR 4 ? DC ? 2 A BRU 8 X BRU 8 ? DU ? # 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 BRU N1 N N N 1 BRU C2 C N N 2 BRU N3 N N N 3 BRU C4 C N N 4 BRU C5 C N N 5 BRU C6 C N N 6 BRU O2 O N N 7 BRU O4 O N N 8 BRU BR BR N N 9 BRU "C1'" C N R 10 BRU "C2'" C N N 11 BRU "C3'" C N S 12 BRU "C4'" C N R 13 BRU "O3'" O N N 14 BRU "O4'" O N N 15 BRU "C5'" C N N 16 BRU "O5'" O N N 17 BRU P P N N 18 BRU OP1 O N N 19 BRU OP2 O N N 20 BRU OP3 O N N 21 BRU HN3 H N N 22 BRU H6 H N N 23 BRU "H1'" H N N 24 BRU "H2'" H N N 25 BRU "H2''" H N N 26 BRU "H3'" H N N 27 BRU "H4'" H N N 28 BRU "HO3'" H N N 29 BRU "H5'" H N N 30 BRU "H5''" H N N 31 BRU HOP2 H N N 32 BRU HOP3 H N N 33 CBR BR BR N N 34 CBR P P N N 35 CBR OP1 O N N 36 CBR OP2 O N N 37 CBR "O5'" O N N 38 CBR N1 N N N 39 CBR C6 C N N 40 CBR C2 C N N 41 CBR O2 O N N 42 CBR N3 N N N 43 CBR C4 C N N 44 CBR N4 N N N 45 CBR C5 C N N 46 CBR "C2'" C N N 47 CBR "C5'" C N N 48 CBR "C4'" C N R 49 CBR "O4'" O N N 50 CBR "C1'" C N R 51 CBR "C3'" C N S 52 CBR "O3'" O N N 53 CBR OP3 O N N 54 CBR HOP2 H N N 55 CBR H6 H N N 56 CBR H41 H N N 57 CBR H42 H N N 58 CBR "H2'" H N N 59 CBR "H2''" H N N 60 CBR "H5'" H N N 61 CBR "H5''" H N N 62 CBR "H4'" H N N 63 CBR "H1'" H N N 64 CBR "H3'" H N N 65 CBR "HO3'" H N N 66 CBR HOP3 H N N 67 DA OP3 O N N 68 DA P P N N 69 DA OP1 O N N 70 DA OP2 O N N 71 DA "O5'" O N N 72 DA "C5'" C N N 73 DA "C4'" C N R 74 DA "O4'" O N N 75 DA "C3'" C N S 76 DA "O3'" O N N 77 DA "C2'" C N N 78 DA "C1'" C N R 79 DA N9 N Y N 80 DA C8 C Y N 81 DA N7 N Y N 82 DA C5 C Y N 83 DA C6 C Y N 84 DA N6 N N N 85 DA N1 N Y N 86 DA C2 C Y N 87 DA N3 N Y N 88 DA C4 C Y N 89 DA HOP3 H N N 90 DA HOP2 H N N 91 DA "H5'" H N N 92 DA "H5''" H N N 93 DA "H4'" H N N 94 DA "H3'" H N N 95 DA "HO3'" H N N 96 DA "H2'" H N N 97 DA "H2''" H N N 98 DA "H1'" H N N 99 DA H8 H N N 100 DA H61 H N N 101 DA H62 H N N 102 DA H2 H N N 103 DG OP3 O N N 104 DG P P N N 105 DG OP1 O N N 106 DG OP2 O N N 107 DG "O5'" O N N 108 DG "C5'" C N N 109 DG "C4'" C N R 110 DG "O4'" O N N 111 DG "C3'" C N S 112 DG "O3'" O N N 113 DG "C2'" C N N 114 DG "C1'" C N R 115 DG N9 N Y N 116 DG C8 C Y N 117 DG N7 N Y N 118 DG C5 C Y N 119 DG C6 C N N 120 DG O6 O N N 121 DG N1 N N N 122 DG C2 C N N 123 DG N2 N N N 124 DG N3 N N N 125 DG C4 C Y N 126 DG HOP3 H N N 127 DG HOP2 H N N 128 DG "H5'" H N N 129 DG "H5''" H N N 130 DG "H4'" H N N 131 DG "H3'" H N N 132 DG "HO3'" H N N 133 DG "H2'" H N N 134 DG "H2''" H N N 135 DG "H1'" H N N 136 DG H8 H N N 137 DG H1 H N N 138 DG H21 H N N 139 DG H22 H N N 140 HOH O O N N 141 HOH H1 H N N 142 HOH H2 H N N 143 MG MG MG N N 144 # 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 BRU N1 C2 sing N N 1 BRU N1 C6 sing N N 2 BRU N1 "C1'" sing N N 3 BRU C2 N3 sing N N 4 BRU C2 O2 doub N N 5 BRU N3 C4 sing N N 6 BRU N3 HN3 sing N N 7 BRU C4 C5 sing N N 8 BRU C4 O4 doub N N 9 BRU C5 C6 doub N N 10 BRU C5 BR sing N N 11 BRU C6 H6 sing N N 12 BRU "C1'" "C2'" sing N N 13 BRU "C1'" "O4'" sing N N 14 BRU "C1'" "H1'" sing N N 15 BRU "C2'" "C3'" sing N N 16 BRU "C2'" "H2'" sing N N 17 BRU "C2'" "H2''" sing N N 18 BRU "C3'" "C4'" sing N N 19 BRU "C3'" "O3'" sing N N 20 BRU "C3'" "H3'" sing N N 21 BRU "C4'" "O4'" sing N N 22 BRU "C4'" "C5'" sing N N 23 BRU "C4'" "H4'" sing N N 24 BRU "O3'" "HO3'" sing N N 25 BRU "C5'" "O5'" sing N N 26 BRU "C5'" "H5'" sing N N 27 BRU "C5'" "H5''" sing N N 28 BRU "O5'" P sing N N 29 BRU P OP1 doub N N 30 BRU P OP2 sing N N 31 BRU P OP3 sing N N 32 BRU OP2 HOP2 sing N N 33 BRU OP3 HOP3 sing N N 34 CBR BR C5 sing N N 35 CBR P OP1 doub N N 36 CBR P OP2 sing N N 37 CBR P "O5'" sing N N 38 CBR P OP3 sing N N 39 CBR OP2 HOP2 sing N N 40 CBR "O5'" "C5'" sing N N 41 CBR N1 C6 sing N N 42 CBR N1 C2 sing N N 43 CBR N1 "C1'" sing N N 44 CBR C6 C5 doub N N 45 CBR C6 H6 sing N N 46 CBR C2 O2 doub N N 47 CBR C2 N3 sing N N 48 CBR N3 C4 doub N N 49 CBR C4 N4 sing N N 50 CBR C4 C5 sing N N 51 CBR N4 H41 sing N N 52 CBR N4 H42 sing N N 53 CBR "C2'" "C1'" sing N N 54 CBR "C2'" "C3'" sing N N 55 CBR "C2'" "H2'" sing N N 56 CBR "C2'" "H2''" sing N N 57 CBR "C5'" "C4'" sing N N 58 CBR "C5'" "H5'" sing N N 59 CBR "C5'" "H5''" sing N N 60 CBR "C4'" "O4'" sing N N 61 CBR "C4'" "C3'" sing N N 62 CBR "C4'" "H4'" sing N N 63 CBR "O4'" "C1'" sing N N 64 CBR "C1'" "H1'" sing N N 65 CBR "C3'" "O3'" sing N N 66 CBR "C3'" "H3'" sing N N 67 CBR "O3'" "HO3'" sing N N 68 CBR OP3 HOP3 sing N N 69 DA OP3 P sing N N 70 DA OP3 HOP3 sing N N 71 DA P OP1 doub N N 72 DA P OP2 sing N N 73 DA P "O5'" sing N N 74 DA OP2 HOP2 sing N N 75 DA "O5'" "C5'" sing N N 76 DA "C5'" "C4'" sing N N 77 DA "C5'" "H5'" sing N N 78 DA "C5'" "H5''" sing N N 79 DA "C4'" "O4'" sing N N 80 DA "C4'" "C3'" sing N N 81 DA "C4'" "H4'" sing N N 82 DA "O4'" "C1'" sing N N 83 DA "C3'" "O3'" sing N N 84 DA "C3'" "C2'" sing N N 85 DA "C3'" "H3'" sing N N 86 DA "O3'" "HO3'" sing N N 87 DA "C2'" "C1'" sing N N 88 DA "C2'" "H2'" sing N N 89 DA "C2'" "H2''" sing N N 90 DA "C1'" N9 sing N N 91 DA "C1'" "H1'" sing N N 92 DA N9 C8 sing Y N 93 DA N9 C4 sing Y N 94 DA C8 N7 doub Y N 95 DA C8 H8 sing N N 96 DA N7 C5 sing Y N 97 DA C5 C6 sing Y N 98 DA C5 C4 doub Y N 99 DA C6 N6 sing N N 100 DA C6 N1 doub Y N 101 DA N6 H61 sing N N 102 DA N6 H62 sing N N 103 DA N1 C2 sing Y N 104 DA C2 N3 doub Y N 105 DA C2 H2 sing N N 106 DA N3 C4 sing Y N 107 DG OP3 P sing N N 108 DG OP3 HOP3 sing N N 109 DG P OP1 doub N N 110 DG P OP2 sing N N 111 DG P "O5'" sing N N 112 DG OP2 HOP2 sing N N 113 DG "O5'" "C5'" sing N N 114 DG "C5'" "C4'" sing N N 115 DG "C5'" "H5'" sing N N 116 DG "C5'" "H5''" sing N N 117 DG "C4'" "O4'" sing N N 118 DG "C4'" "C3'" sing N N 119 DG "C4'" "H4'" sing N N 120 DG "O4'" "C1'" sing N N 121 DG "C3'" "O3'" sing N N 122 DG "C3'" "C2'" sing N N 123 DG "C3'" "H3'" sing N N 124 DG "O3'" "HO3'" sing N N 125 DG "C2'" "C1'" sing N N 126 DG "C2'" "H2'" sing N N 127 DG "C2'" "H2''" sing N N 128 DG "C1'" N9 sing N N 129 DG "C1'" "H1'" sing N N 130 DG N9 C8 sing Y N 131 DG N9 C4 sing Y N 132 DG C8 N7 doub Y N 133 DG C8 H8 sing N N 134 DG N7 C5 sing Y N 135 DG C5 C6 sing N N 136 DG C5 C4 doub Y N 137 DG C6 O6 doub N N 138 DG C6 N1 sing N N 139 DG N1 C2 sing N N 140 DG N1 H1 sing N N 141 DG C2 N2 sing N N 142 DG C2 N3 doub N N 143 DG N2 H21 sing N N 144 DG N2 H22 sing N N 145 DG N3 C4 sing N N 146 HOH O H1 sing N N 147 HOH O H2 sing N N 148 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1P1Y 'double helix' 1P1Y 'parallel strands' 1P1Y 'mismatched base pair' # 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 DG 1 1_555 A DG 10 6_454 -5.716 -0.518 -0.213 -2.683 -6.650 -112.497 1 X_DG1:DG10_X X 1 ? X 10 ? 7 4 1 A DG 2 1_555 A DG 11 6_454 3.179 8.009 -0.574 -0.455 24.789 174.581 2 X_DG2:DG11_X X 2 ? X 11 ? 4 12 1 A DA 3 1_555 A DA 12 6_454 -5.402 5.487 0.167 -7.038 29.923 -179.699 3 X_DA3:DA12_X X 3 ? X 12 ? 2 7 # 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 DG 1 1_555 A DG 10 6_454 A DG 2 1_555 A DG 11 6_454 4.877 -0.870 1.701 -111.194 131.801 26.996 0.048 -2.035 -3.306 68.114 57.465 172.650 1 XX_DG1DG2:DG11DG10_XX X 1 ? X 10 ? X 2 ? X 11 ? 1 A DG 2 1_555 A DG 11 6_454 A DA 3 1_555 A DA 12 6_454 0.032 0.071 4.480 -0.242 1.746 173.703 0.034 -0.016 4.480 0.875 0.121 173.704 2 XX_DG2DA3:DA12DG11_XX X 2 ? X 11 ? X 3 ? X 12 ? # _atom_sites.entry_id 1P1Y _atom_sites.fract_transf_matrix[1][1] 0.024612 _atom_sites.fract_transf_matrix[1][2] 0.014210 _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] 0.028420 _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] 0.018093 _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 BR C MG N O P # loop_