data_1P54 # _entry.id 1P54 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1P54 pdb_00001p54 10.2210/pdb1p54/pdb NDB UD0030 ? ? RCSB RCSB019018 ? ? WWPDB D_1000019018 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1P4Y 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' unspecified PDB 1P4Z 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1P54 _pdbx_database_status.recvd_initial_deposition_date 2003-04-25 _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_ _audit_author.name _audit_author.pdbx_ordinal 'Hays, F.A.' 1 'Vargason, J.M.' 2 'Ho, P.S.' 3 # _citation.id primary _citation.title 'Effect of Sequence on the Conformation of DNA Holliday Junctions' _citation.journal_abbrev Biochemistry _citation.journal_volume 42 _citation.page_first 9586 _citation.page_last 9597 _citation.year 2003 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12911300 _citation.pdbx_database_id_DOI 10.1021/bi0346603 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hays, F.A.' 1 ? primary 'Vargason, J.M.' 2 ? primary 'Ho, P.S.' 3 ? # _cell.entry_id 1P54 _cell.length_a 64.840 _cell.length_b 22.580 _cell.length_c 38.070 _cell.angle_alpha 90.00 _cell.angle_beta 106.78 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1P54 _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 # 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*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3'" 3109.874 2 ? ? ? ? 2 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 3 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 4 water nat water 18.015 87 ? ? ? ? # _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 '(DC)(DC)(DA)(DG)(DT)(DA)(DC)(BRU)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAGTACUGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # 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 DA n 1 4 DG n 1 5 DT n 1 6 DA n 1 7 DC n 1 8 BRU 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 ;DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. ; # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1P54 _struct_ref.pdbx_db_accession 1P54 _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 1P54 A 1 ? 10 ? 1P54 1 ? 10 ? 1 10 2 1 1P54 B 1 ? 10 ? 1P54 11 ? 20 ? 11 20 # 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 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # _exptl.entry_id 1P54 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.93 _exptl_crystal.density_percent_sol 35.87 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.50 _exptl_crystal_grow.pdbx_details ;0.6mM DNA, 5mM Tris-HCL, 120mM calcium acetate, 16% 2-methyl-2,4-pentane diol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.50 ; _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 Tris-HCL ? ? ? 1 2 1 'calcium acetate' ? ? ? 1 3 1 '2-methyl-2,4-pentane diol' ? ? ? 1 4 1 H2O ? ? ? 1 5 2 'calcium acetate' ? ? ? 1 6 2 Tris-HCL ? ? ? 1 7 2 '2-methyl-2,4-pentane diol' ? ? ? 1 8 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 103.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2002-12-19 _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 'NI FILTER' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.542 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU300' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.542 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1P54 _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 19.180 _reflns.d_resolution_high 1.800 _reflns.number_obs 4177 _reflns.number_all ? _reflns.percent_possible_obs 82.0 _reflns.pdbx_Rmerge_I_obs 0.041 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 4.05 _reflns.B_iso_Wilson_estimate 4.3 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.80 _reflns_shell.d_res_low 1.86 _reflns_shell.percent_possible_all 34.9 _reflns_shell.Rmerge_I_obs 0.189 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1P54 _refine.ls_number_reflns_obs 3745 _refine.ls_number_reflns_all 4011 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.18 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 86.7 _refine.ls_R_factor_obs 0.215 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.215 _refine.ls_R_factor_R_free 0.242 _refine.ls_R_factor_R_free_error 0.012 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.4 _refine.ls_number_reflns_R_free 388 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 9.50 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model '1L6B USED FOR INITIAL SOLUTION VIA MOLECULAR REPLACEMENT' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _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_analyze.entry_id 1P54 _refine_analyze.Luzzati_coordinate_error_obs 0.22 _refine_analyze.Luzzati_sigma_a_obs 0.14 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.26 _refine_analyze.Luzzati_sigma_a_free 0.18 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 404 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 87 _refine_hist.number_atoms_total 493 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 19.18 # 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 c_bond_d 0.005 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.9 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 18.30 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.37 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.90 _refine_ls_shell.d_res_low 2.02 _refine_ls_shell.number_reflns_R_work 385 _refine_ls_shell.R_factor_R_work 0.259 _refine_ls_shell.percent_reflns_obs 60.10 _refine_ls_shell.R_factor_R_free 0.248 _refine_ls_shell.R_factor_R_free_error 0.041 _refine_ls_shell.percent_reflns_R_free 8.8 _refine_ls_shell.number_reflns_R_free 37 _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 ? # _struct.entry_id 1P54 _struct.title 'Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1P54 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA Holliday Junction, Four-Way Junction, stacked-X junction, brominated uracil, 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 3 ? E N N 4 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details ;This entry contains the crystallographic asymmetric unit which consists of two chains A and B. The full four stranded Holliday junction structure can be generated by the following: matrix = (-1.00000 0.00001 0.00000) (0.00001 1.00000 -0.00002) (0.00000 -0.00002 -1.00000) translation = (0.00022 0.00018 -0.00034) ; _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 both ? A DC 7 "O3'" ? ? ? 1_555 A BRU 8 P ? ? A DC 7 A BRU 8 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale2 covale both ? A BRU 8 "O3'" ? ? ? 1_555 A DG 9 P ? ? A BRU 8 A DG 9 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale3 covale both ? B DC 7 "O3'" ? ? ? 1_555 B BRU 8 P ? ? B DC 17 B BRU 18 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale4 covale both ? B BRU 8 "O3'" ? ? ? 1_555 B DG 9 P ? ? B BRU 18 B DG 19 1_555 ? ? ? ? ? ? ? 1.612 ? ? metalc1 metalc ? ? A DA 6 OP2 ? ? ? 1_555 C NA . NA ? ? A DA 6 A NA 37 1_555 ? ? ? ? ? ? ? 2.777 ? ? metalc2 metalc ? ? E HOH . O ? ? ? 1_555 D CA . CA ? ? A HOH 27 A CA 67 1_555 ? ? ? ? ? ? ? 2.303 ? ? metalc3 metalc ? ? D CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 67 A HOH 80 1_555 ? ? ? ? ? ? ? 2.278 ? ? metalc4 metalc ? ? D CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 67 A HOH 81 1_555 ? ? ? ? ? ? ? 2.242 ? ? metalc5 metalc ? ? D CA . CA ? ? ? 1_555 E HOH . O ? ? A CA 67 A HOH 82 1_555 ? ? ? ? ? ? ? 2.948 ? ? metalc6 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 67 B HOH 69 2_555 ? ? ? ? ? ? ? 3.119 ? ? metalc7 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 67 B HOH 75 2_555 ? ? ? ? ? ? ? 3.011 ? ? metalc8 metalc ? ? D CA . CA ? ? ? 1_555 F HOH . O ? ? A CA 67 B HOH 93 2_555 ? ? ? ? ? ? ? 3.261 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B BRU 8 N3 ? ? A DA 3 B BRU 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B BRU 8 O4 ? ? A DA 3 B BRU 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 5 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A NA 37 ? 2 'BINDING SITE FOR RESIDUE NA A 37' AC2 Software A CA 67 ? 5 'BINDING SITE FOR RESIDUE CA A 67' # 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 2 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 2 DA A 6 ? DA A 6 . ? 2_555 ? 3 AC2 5 HOH E . ? HOH A 27 . ? 1_555 ? 4 AC2 5 HOH E . ? HOH A 80 . ? 1_555 ? 5 AC2 5 HOH E . ? HOH A 81 . ? 1_555 ? 6 AC2 5 HOH E . ? HOH A 82 . ? 1_555 ? 7 AC2 5 HOH F . ? HOH B 75 . ? 2_555 ? # _database_PDB_matrix.entry_id 1P54 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1P54 _atom_sites.fract_transf_matrix[1][1] 0.015423 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.004649 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.044293 _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] 0.027436 _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 CA N NA O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DA 3 3 3 DA A 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 BRU 8 8 8 BRU +U 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 11 11 DC C B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DA 3 13 13 DA A B . n B 1 4 DG 4 14 14 DG G B . n B 1 5 DT 5 15 15 DT T B . n B 1 6 DA 6 16 16 DA A B . n B 1 7 DC 7 17 17 DC C B . n B 1 8 BRU 8 18 18 BRU +U B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DG 10 20 20 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 NA 1 37 37 NA NA A . D 3 CA 1 67 67 CA CA A . E 4 HOH 1 21 21 HOH HOH A . E 4 HOH 2 23 23 HOH HOH A . E 4 HOH 3 24 24 HOH HOH A . E 4 HOH 4 25 25 HOH HOH A . E 4 HOH 5 26 26 HOH HOH A . E 4 HOH 6 27 27 HOH HOH A . E 4 HOH 7 29 29 HOH HOH A . E 4 HOH 8 30 30 HOH HOH A . E 4 HOH 9 32 32 HOH HOH A . E 4 HOH 10 33 33 HOH HOH A . E 4 HOH 11 34 34 HOH HOH A . E 4 HOH 12 36 36 HOH HOH A . E 4 HOH 13 38 38 HOH HOH A . E 4 HOH 14 39 39 HOH HOH A . E 4 HOH 15 40 40 HOH HOH A . E 4 HOH 16 42 42 HOH HOH A . E 4 HOH 17 43 43 HOH HOH A . E 4 HOH 18 44 44 HOH HOH A . E 4 HOH 19 46 46 HOH HOH A . E 4 HOH 20 50 50 HOH HOH A . E 4 HOH 21 52 52 HOH HOH A . E 4 HOH 22 53 53 HOH HOH A . E 4 HOH 23 54 54 HOH HOH A . E 4 HOH 24 55 55 HOH HOH A . E 4 HOH 25 57 57 HOH HOH A . E 4 HOH 26 61 61 HOH HOH A . E 4 HOH 27 62 62 HOH HOH A . E 4 HOH 28 64 64 HOH HOH A . E 4 HOH 29 65 65 HOH HOH A . E 4 HOH 30 66 66 HOH HOH A . E 4 HOH 31 68 68 HOH HOH A . E 4 HOH 32 70 70 HOH HOH A . E 4 HOH 33 72 72 HOH HOH A . E 4 HOH 34 73 73 HOH HOH A . E 4 HOH 35 76 76 HOH HOH A . E 4 HOH 36 77 77 HOH HOH A . E 4 HOH 37 79 79 HOH HOH A . E 4 HOH 38 80 80 HOH HOH A . E 4 HOH 39 81 81 HOH HOH A . E 4 HOH 40 82 82 HOH HOH A . E 4 HOH 41 85 85 HOH HOH A . E 4 HOH 42 86 86 HOH HOH A . E 4 HOH 43 87 87 HOH HOH A . E 4 HOH 44 88 88 HOH HOH A . E 4 HOH 45 90 90 HOH HOH A . E 4 HOH 46 96 96 HOH HOH A . E 4 HOH 47 100 100 HOH HOH A . E 4 HOH 48 101 101 HOH HOH A . E 4 HOH 49 103 103 HOH HOH A . E 4 HOH 50 107 107 HOH HOH A . F 4 HOH 1 22 22 HOH HOH B . F 4 HOH 2 28 28 HOH HOH B . F 4 HOH 3 31 31 HOH HOH B . F 4 HOH 4 35 35 HOH HOH B . F 4 HOH 5 41 41 HOH HOH B . F 4 HOH 6 45 45 HOH HOH B . F 4 HOH 7 47 47 HOH HOH B . F 4 HOH 8 48 48 HOH HOH B . F 4 HOH 9 49 49 HOH HOH B . F 4 HOH 10 51 51 HOH HOH B . F 4 HOH 11 56 56 HOH HOH B . F 4 HOH 12 58 58 HOH HOH B . F 4 HOH 13 59 59 HOH HOH B . F 4 HOH 14 60 60 HOH HOH B . F 4 HOH 15 63 63 HOH HOH B . F 4 HOH 16 69 69 HOH HOH B . F 4 HOH 17 71 71 HOH HOH B . F 4 HOH 18 74 74 HOH HOH B . F 4 HOH 19 75 75 HOH HOH B . F 4 HOH 20 78 78 HOH HOH B . F 4 HOH 21 83 83 HOH HOH B . F 4 HOH 22 84 84 HOH HOH B . F 4 HOH 23 89 89 HOH HOH B . F 4 HOH 24 91 91 HOH HOH B . F 4 HOH 25 92 92 HOH HOH B . F 4 HOH 26 93 93 HOH HOH B . F 4 HOH 27 94 94 HOH HOH B . F 4 HOH 28 95 95 HOH HOH B . F 4 HOH 29 97 97 HOH HOH B . F 4 HOH 30 98 98 HOH HOH B . F 4 HOH 31 99 99 HOH HOH B . F 4 HOH 32 102 102 HOH HOH B . F 4 HOH 33 104 104 HOH HOH B . F 4 HOH 34 105 105 HOH HOH B . F 4 HOH 35 106 106 HOH HOH B . F 4 HOH 36 108 108 HOH HOH B . F 4 HOH 37 109 109 HOH HOH B . # 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 BRU 8 A BRU 8 ? DU ? 2 B BRU 8 B BRU 18 ? DU ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # 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_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 # 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 NA 37 ? C NA . 2 1 A HOH 68 ? E HOH . 3 1 A HOH 86 ? E HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 27 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? E HOH . ? A HOH 80 ? 1_555 83.5 ? 2 O ? E HOH . ? A HOH 27 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? E HOH . ? A HOH 81 ? 1_555 106.8 ? 3 O ? E HOH . ? A HOH 80 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? E HOH . ? A HOH 81 ? 1_555 76.9 ? 4 O ? E HOH . ? A HOH 27 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? E HOH . ? A HOH 82 ? 1_555 71.0 ? 5 O ? E HOH . ? A HOH 80 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? E HOH . ? A HOH 82 ? 1_555 152.0 ? 6 O ? E HOH . ? A HOH 81 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? E HOH . ? A HOH 82 ? 1_555 121.1 ? 7 O ? E HOH . ? A HOH 27 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 69 ? 2_555 136.1 ? 8 O ? E HOH . ? A HOH 80 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 69 ? 2_555 140.0 ? 9 O ? E HOH . ? A HOH 81 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 69 ? 2_555 84.5 ? 10 O ? E HOH . ? A HOH 82 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 69 ? 2_555 67.1 ? 11 O ? E HOH . ? A HOH 27 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 75 ? 2_555 90.3 ? 12 O ? E HOH . ? A HOH 80 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 75 ? 2_555 97.6 ? 13 O ? E HOH . ? A HOH 81 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 75 ? 2_555 161.0 ? 14 O ? E HOH . ? A HOH 82 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 75 ? 2_555 71.7 ? 15 O ? F HOH . ? B HOH 69 ? 2_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 75 ? 2_555 88.8 ? 16 O ? E HOH . ? A HOH 27 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 93 ? 2_555 150.1 ? 17 O ? E HOH . ? A HOH 80 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 93 ? 2_555 89.4 ? 18 O ? E HOH . ? A HOH 81 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 93 ? 2_555 99.7 ? 19 O ? E HOH . ? A HOH 82 ? 1_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 93 ? 2_555 106.7 ? 20 O ? F HOH . ? B HOH 69 ? 2_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 93 ? 2_555 59.1 ? 21 O ? F HOH . ? B HOH 75 ? 2_555 CA ? D CA . ? A CA 67 ? 1_555 O ? F HOH . ? B HOH 93 ? 2_555 61.8 ? # 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 2003-09-02 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-16 5 'Structure model' 1 4 2023-08-16 # _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' 'Atomic model' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 5 '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 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_initial_refinement_model 5 5 'Structure model' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 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_asym_id' 11 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 12 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 13 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 14 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 15 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 16 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 17 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 18 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 19 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 20 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 21 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 22 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 23 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 24 5 'Structure model' '_struct_conn.ptnr2_symmetry' 25 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 26 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 27 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 EPMR phasing . ? 3 CNS refinement 1.0 ? 4 # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DG _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 19 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.054 _pdbx_validate_planes.type 'SIDE CHAIN' # 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 CA CA CA N N 34 DA OP3 O N N 35 DA P P N N 36 DA OP1 O N N 37 DA OP2 O N N 38 DA "O5'" O N N 39 DA "C5'" C N N 40 DA "C4'" C N R 41 DA "O4'" O N N 42 DA "C3'" C N S 43 DA "O3'" O N N 44 DA "C2'" C N N 45 DA "C1'" C N R 46 DA N9 N Y N 47 DA C8 C Y N 48 DA N7 N Y N 49 DA C5 C Y N 50 DA C6 C Y N 51 DA N6 N N N 52 DA N1 N Y N 53 DA C2 C Y N 54 DA N3 N Y N 55 DA C4 C Y N 56 DA HOP3 H N N 57 DA HOP2 H N N 58 DA "H5'" H N N 59 DA "H5''" H N N 60 DA "H4'" H N N 61 DA "H3'" H N N 62 DA "HO3'" H N N 63 DA "H2'" H N N 64 DA "H2''" H N N 65 DA "H1'" H N N 66 DA H8 H N N 67 DA H61 H N N 68 DA H62 H N N 69 DA H2 H N N 70 DC OP3 O N N 71 DC P P N N 72 DC OP1 O N N 73 DC OP2 O N N 74 DC "O5'" O N N 75 DC "C5'" C N N 76 DC "C4'" C N R 77 DC "O4'" O N N 78 DC "C3'" C N S 79 DC "O3'" O N N 80 DC "C2'" C N N 81 DC "C1'" C N R 82 DC N1 N N N 83 DC C2 C N N 84 DC O2 O N N 85 DC N3 N N N 86 DC C4 C N N 87 DC N4 N N N 88 DC C5 C N N 89 DC C6 C N N 90 DC HOP3 H N N 91 DC HOP2 H N N 92 DC "H5'" H N N 93 DC "H5''" H N N 94 DC "H4'" H N N 95 DC "H3'" H N N 96 DC "HO3'" H N N 97 DC "H2'" H N N 98 DC "H2''" H N N 99 DC "H1'" H N N 100 DC H41 H N N 101 DC H42 H N N 102 DC H5 H N N 103 DC H6 H N N 104 DG OP3 O N N 105 DG P P N N 106 DG OP1 O N N 107 DG OP2 O N N 108 DG "O5'" O N N 109 DG "C5'" C N N 110 DG "C4'" C N R 111 DG "O4'" O N N 112 DG "C3'" C N S 113 DG "O3'" O N N 114 DG "C2'" C N N 115 DG "C1'" C N R 116 DG N9 N Y N 117 DG C8 C Y N 118 DG N7 N Y N 119 DG C5 C Y N 120 DG C6 C N N 121 DG O6 O N N 122 DG N1 N N N 123 DG C2 C N N 124 DG N2 N N N 125 DG N3 N N N 126 DG C4 C Y N 127 DG HOP3 H N N 128 DG HOP2 H N N 129 DG "H5'" H N N 130 DG "H5''" H N N 131 DG "H4'" H N N 132 DG "H3'" H N N 133 DG "HO3'" H N N 134 DG "H2'" H N N 135 DG "H2''" H N N 136 DG "H1'" H N N 137 DG H8 H N N 138 DG H1 H N N 139 DG H21 H N N 140 DG H22 H N N 141 DT OP3 O N N 142 DT P P N N 143 DT OP1 O N N 144 DT OP2 O N N 145 DT "O5'" O N N 146 DT "C5'" C N N 147 DT "C4'" C N R 148 DT "O4'" O N N 149 DT "C3'" C N S 150 DT "O3'" O N N 151 DT "C2'" C N N 152 DT "C1'" C N R 153 DT N1 N N N 154 DT C2 C N N 155 DT O2 O N N 156 DT N3 N N N 157 DT C4 C N N 158 DT O4 O N N 159 DT C5 C N N 160 DT C7 C N N 161 DT C6 C N N 162 DT HOP3 H N N 163 DT HOP2 H N N 164 DT "H5'" H N N 165 DT "H5''" H N N 166 DT "H4'" H N N 167 DT "H3'" H N N 168 DT "HO3'" H N N 169 DT "H2'" H N N 170 DT "H2''" H N N 171 DT "H1'" H N N 172 DT H3 H N N 173 DT H71 H N N 174 DT H72 H N N 175 DT H73 H N N 176 DT H6 H N N 177 HOH O O N N 178 HOH H1 H N N 179 HOH H2 H N N 180 NA NA NA N N 181 # 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 DA OP3 P sing N N 35 DA OP3 HOP3 sing N N 36 DA P OP1 doub N N 37 DA P OP2 sing N N 38 DA P "O5'" sing N N 39 DA OP2 HOP2 sing N N 40 DA "O5'" "C5'" sing N N 41 DA "C5'" "C4'" sing N N 42 DA "C5'" "H5'" sing N N 43 DA "C5'" "H5''" sing N N 44 DA "C4'" "O4'" sing N N 45 DA "C4'" "C3'" sing N N 46 DA "C4'" "H4'" sing N N 47 DA "O4'" "C1'" sing N N 48 DA "C3'" "O3'" sing N N 49 DA "C3'" "C2'" sing N N 50 DA "C3'" "H3'" sing N N 51 DA "O3'" "HO3'" sing N N 52 DA "C2'" "C1'" sing N N 53 DA "C2'" "H2'" sing N N 54 DA "C2'" "H2''" sing N N 55 DA "C1'" N9 sing N N 56 DA "C1'" "H1'" sing N N 57 DA N9 C8 sing Y N 58 DA N9 C4 sing Y N 59 DA C8 N7 doub Y N 60 DA C8 H8 sing N N 61 DA N7 C5 sing Y N 62 DA C5 C6 sing Y N 63 DA C5 C4 doub Y N 64 DA C6 N6 sing N N 65 DA C6 N1 doub Y N 66 DA N6 H61 sing N N 67 DA N6 H62 sing N N 68 DA N1 C2 sing Y N 69 DA C2 N3 doub Y N 70 DA C2 H2 sing N N 71 DA N3 C4 sing Y N 72 DC OP3 P sing N N 73 DC OP3 HOP3 sing N N 74 DC P OP1 doub N N 75 DC P OP2 sing N N 76 DC P "O5'" sing N N 77 DC OP2 HOP2 sing N N 78 DC "O5'" "C5'" sing N N 79 DC "C5'" "C4'" sing N N 80 DC "C5'" "H5'" sing N N 81 DC "C5'" "H5''" sing N N 82 DC "C4'" "O4'" sing N N 83 DC "C4'" "C3'" sing N N 84 DC "C4'" "H4'" sing N N 85 DC "O4'" "C1'" sing N N 86 DC "C3'" "O3'" sing N N 87 DC "C3'" "C2'" sing N N 88 DC "C3'" "H3'" sing N N 89 DC "O3'" "HO3'" sing N N 90 DC "C2'" "C1'" sing N N 91 DC "C2'" "H2'" sing N N 92 DC "C2'" "H2''" sing N N 93 DC "C1'" N1 sing N N 94 DC "C1'" "H1'" sing N N 95 DC N1 C2 sing N N 96 DC N1 C6 sing N N 97 DC C2 O2 doub N N 98 DC C2 N3 sing N N 99 DC N3 C4 doub N N 100 DC C4 N4 sing N N 101 DC C4 C5 sing N N 102 DC N4 H41 sing N N 103 DC N4 H42 sing N N 104 DC C5 C6 doub N N 105 DC C5 H5 sing N N 106 DC C6 H6 sing N 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 DT OP3 P sing N N 147 DT OP3 HOP3 sing N N 148 DT P OP1 doub N N 149 DT P OP2 sing N N 150 DT P "O5'" sing N N 151 DT OP2 HOP2 sing N N 152 DT "O5'" "C5'" sing N N 153 DT "C5'" "C4'" sing N N 154 DT "C5'" "H5'" sing N N 155 DT "C5'" "H5''" sing N N 156 DT "C4'" "O4'" sing N N 157 DT "C4'" "C3'" sing N N 158 DT "C4'" "H4'" sing N N 159 DT "O4'" "C1'" sing N N 160 DT "C3'" "O3'" sing N N 161 DT "C3'" "C2'" sing N N 162 DT "C3'" "H3'" sing N N 163 DT "O3'" "HO3'" sing N N 164 DT "C2'" "C1'" sing N N 165 DT "C2'" "H2'" sing N N 166 DT "C2'" "H2''" sing N N 167 DT "C1'" N1 sing N N 168 DT "C1'" "H1'" sing N N 169 DT N1 C2 sing N N 170 DT N1 C6 sing N N 171 DT C2 O2 doub N N 172 DT C2 N3 sing N N 173 DT N3 C4 sing N N 174 DT N3 H3 sing N N 175 DT C4 O4 doub N N 176 DT C4 C5 sing N N 177 DT C5 C7 sing N N 178 DT C5 C6 doub N N 179 DT C7 H71 sing N N 180 DT C7 H72 sing N N 181 DT C7 H73 sing N N 182 DT C6 H6 sing N N 183 HOH O H1 sing N N 184 HOH O H2 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1P54 'double helix' 1P54 '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 0.041 -0.058 0.058 -0.110 -13.775 0.485 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.469 -0.121 0.543 -1.830 -16.662 -0.482 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DA 3 1_555 B BRU 8 1_555 -0.085 -0.067 0.417 -3.669 -6.015 1.743 3 A_DA3:BRU18_B A 3 ? B 18 ? 20 1 1 A DG 4 1_555 B DC 7 1_555 -0.843 -0.485 0.221 4.459 -16.673 -6.000 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 1 A DT 5 1_555 B DA 6 1_555 0.106 -0.055 0.178 4.364 -0.040 4.769 5 A_DT5:DA16_B A 5 ? B 16 ? 20 1 1 A DA 6 1_555 B DT 5 1_555 0.217 0.159 0.205 14.311 -16.557 3.463 6 A_DA6:DT15_B A 6 ? B 15 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.200 2.022 3.646 6.057 2.540 45.082 2.359 0.346 3.743 3.292 -7.850 45.533 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DA 3 1_555 B BRU 8 1_555 0.263 2.820 3.276 2.188 -15.048 42.898 4.811 -0.173 2.226 -19.845 -2.885 45.393 2 AA_DC2DA3:BRU18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DA 3 1_555 B BRU 8 1_555 A DG 4 1_555 B DC 7 1_555 0.383 0.066 3.132 -0.576 6.329 34.058 -0.823 -0.728 3.088 10.690 0.973 34.629 3 AA_DA3DG4:DC17BRU18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DG 4 1_555 B DC 7 1_555 A DT 5 1_555 B DA 6 1_555 0.806 -0.076 3.204 3.047 8.337 29.301 -1.779 -0.931 3.130 16.024 -5.856 30.588 4 AA_DG4DT5:DA16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DT 5 1_555 B DA 6 1_555 A DA 6 1_555 B DT 5 1_555 -0.797 0.824 3.175 1.202 2.485 38.339 0.951 1.356 3.194 3.777 -1.828 38.435 5 AA_DT5DA6:DT15DA16_BB A 5 ? B 16 ? A 6 ? B 15 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 'CALCIUM ION' CA 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1L6B _pdbx_initial_refinement_model.details '1L6B USED FOR INITIAL SOLUTION VIA MOLECULAR REPLACEMENT' #