data_4HW1 # _entry.id 4HW1 # _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 4HW1 pdb_00004hw1 10.2210/pdb4hw1/pdb NDB NA2122 ? ? RCSB RCSB075990 ? ? WWPDB D_1000075990 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2013-11-20 2 'Structure model' 1 1 2015-02-25 3 'Structure model' 1 2 2024-02-28 4 'Structure model' 1 3 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_site 5 4 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4HW1 _pdbx_database_status.recvd_initial_deposition_date 2012-11-07 _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Acosta-Reyes, F.' 1 'Subirana, J.A.' 2 'Pous, J.' 3 'Condom, N.' 4 'Malinina, L.' 5 'Campos, J.L.' 6 # _citation.id primary _citation.title 'Polymorphic crystal structures of an all-AT DNA dodecamer.' _citation.journal_abbrev Biopolymers _citation.journal_volume 103 _citation.page_first 123 _citation.page_last 133 _citation.year 2015 _citation.journal_id_ASTM BIPMAA _citation.country US _citation.journal_id_ISSN 0006-3525 _citation.journal_id_CSD 0161 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 25257185 _citation.pdbx_database_id_DOI 10.1002/bip.22565 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Acosta-Reyes, F.J.' 1 ? primary 'Subirana, J.A.' 2 ? primary 'Pous, J.' 3 ? primary 'Sanchez-Giraldo, R.' 4 ? primary 'Condom, N.' 5 ? primary 'Baldini, R.' 6 ? primary 'Malinina, L.' 7 ? primary 'Campos, J.L.' 8 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*AP*AP*TP*AP*AP*AP*TP*TP*TP*AP*TP*T)-3') ; 3659.440 4 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 14 ? ? ? ? # _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 '(DA)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DT)(DA)(DT)(DT)' _entity_poly.pdbx_seq_one_letter_code_can AATAAATTTATT _entity_poly.pdbx_strand_id A,B,C,D _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 DA n 1 2 DA n 1 3 DT n 1 4 DA n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DT n 1 10 DA n 1 11 DT n 1 12 DT 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 oligonucleotide.' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 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 DA 1 1 1 DA DA A . n A 1 2 DA 2 2 2 DA DA A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DA 10 10 10 DA DA A . n A 1 11 DT 11 11 11 DT DT A . n A 1 12 DT 12 12 12 DT DT A . n B 1 1 DA 1 13 13 DA DA B . n B 1 2 DA 2 14 14 DA DA B . n B 1 3 DT 3 15 15 DT DT B . n B 1 4 DA 4 16 16 DA DA B . n B 1 5 DA 5 17 17 DA DA B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 DT 8 20 20 DT DT B . n B 1 9 DT 9 21 21 DT DT B . n B 1 10 DA 10 22 22 DA DA B . n B 1 11 DT 11 23 23 DT DT B . n B 1 12 DT 12 24 24 DT DT B . n C 1 1 DA 1 1 1 DA DA C . n C 1 2 DA 2 2 2 DA DA C . n C 1 3 DT 3 3 3 DT DT C . n C 1 4 DA 4 4 4 DA DA C . n C 1 5 DA 5 5 5 DA DA C . n C 1 6 DA 6 6 6 DA DA C . n C 1 7 DT 7 7 7 DT DT C . n C 1 8 DT 8 8 8 DT DT C . n C 1 9 DT 9 9 9 DT DT C . n C 1 10 DA 10 10 10 DA DA C . n C 1 11 DT 11 11 11 DT DT C . n C 1 12 DT 12 12 12 DT DT C . n D 1 1 DA 1 13 13 DA DA D . n D 1 2 DA 2 14 14 DA DA D . n D 1 3 DT 3 15 15 DT DT D . n D 1 4 DA 4 16 16 DA DA D . n D 1 5 DA 5 17 17 DA DA D . n D 1 6 DA 6 18 18 DA DA D . n D 1 7 DT 7 19 19 DT DT D . n D 1 8 DT 8 20 20 DT DT D . n D 1 9 DT 9 21 21 DT DT D . n D 1 10 DA 10 22 22 DA DA D . n D 1 11 DT 11 23 23 DT DT D . n D 1 12 DT 12 24 24 DT DT D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 MG 1 101 1 MG MG B . F 3 HOH 1 101 12 HOH HOH A . G 3 HOH 1 201 1 HOH HOH B . G 3 HOH 2 202 3 HOH HOH B . G 3 HOH 3 203 5 HOH HOH B . G 3 HOH 4 204 8 HOH HOH B . G 3 HOH 5 205 9 HOH HOH B . H 3 HOH 1 101 2 HOH HOH C . H 3 HOH 2 102 3 HOH HOH C . H 3 HOH 3 103 6 HOH HOH C . I 3 HOH 1 101 2 HOH HOH D . I 3 HOH 2 102 4 HOH HOH D . I 3 HOH 3 103 7 HOH HOH D . I 3 HOH 4 104 10 HOH HOH D . I 3 HOH 5 105 11 HOH HOH D . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 PHASER phasing . ? 2 REFMAC refinement 5.7.0029 ? 3 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # _cell.entry_id 4HW1 _cell.length_a 50.431 _cell.length_b 61.155 _cell.length_c 80.601 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 32 _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 4HW1 _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4HW1 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.12 _exptl_crystal.density_percent_sol 42.06 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details 'Mg, MPD, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K' _exptl_crystal_grow.pdbx_pH_range ? # _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 210r' _diffrn_detector.pdbx_collection_date 2007-03-02 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator MIRRORS _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9796 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM16' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM16 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9796 # _reflns.entry_id 4HW1 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 24.36 _reflns.d_resolution_high 3.099 _reflns.number_obs 2433 _reflns.number_all 2435 _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.184 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 9.7952 _reflns.B_iso_Wilson_estimate 58.7 _reflns.pdbx_redundancy 10.25 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _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.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 3.10 3.27 98.99 0.55 ? ? 9.75 ? 344 ? ? ? ? 1 1 3.27 3.46 99.66 0.80 ? ? 10.74 ? 319 ? ? ? ? 2 1 3.46 3.70 100.00 0.48 ? ? 10.49 ? 315 ? ? ? ? 3 1 3.70 4.00 100.00 0.50 ? ? 10.65 ? 292 ? ? ? ? 4 1 4.00 4.38 100.00 0.30 ? ? 10.55 ? 270 ? ? ? ? 5 1 4.38 4.90 100.00 0.17 ? ? 10.54 ? 243 ? ? ? ? 6 1 4.90 5.66 100.00 0.12 ? ? 10.27 ? 226 ? ? ? ? 7 1 5.66 6.93 100.00 0.08 ? ? 9.86 ? 185 ? ? ? ? 8 1 6.93 9.80 100.00 0.05 ? ? 9.58 ? 151 ? ? ? ? 9 1 9.80 24.36 93.65 0.04 ? ? 8.30 ? 88 ? ? ? ? 10 1 # _refine.entry_id 4HW1 _refine.ls_number_reflns_obs 2311 _refine.ls_number_reflns_all 2435 _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 24.36 _refine.ls_d_res_high 3.10 _refine.ls_percent_reflns_obs 99.42 _refine.ls_R_factor_obs 0.26262 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.26196 _refine.ls_R_factor_R_free 0.27659 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.5 _refine.ls_number_reflns_R_free 109 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.936 _refine.correlation_coeff_Fo_to_Fc_free 0.931 _refine.B_iso_mean 55.486 _refine.aniso_B[1][1] -7.64 _refine.aniso_B[2][2] 4.69 _refine.aniso_B[3][3] 2.94 _refine.aniso_B[1][2] -0.00 _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 'theoretic model of B-DNA' _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_Free 0.570 _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_ESU_R ? _refine.pdbx_overall_phase_error ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 972 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 14 _refine_hist.number_atoms_total 987 _refine_hist.d_res_high 3.10 _refine_hist.d_res_low 24.36 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.007 0.011 ? 1088 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.001 0.020 ? 556 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.040 1.188 ? 1672 ? 'X-RAY DIFFRACTION' r_angle_other_deg 6.478 3.000 ? 1324 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 52.716 20.000 ? 232 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 33.541 20.000 ? 192 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_chiral_restr 0.036 0.200 ? 144 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.001 0.020 ? 544 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.002 0.020 ? 184 ? 'X-RAY DIFFRACTION' r_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_other ? ? ? ? ? '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 3.099 _refine_ls_shell.d_res_low 3.179 _refine_ls_shell.number_reflns_R_work 162 _refine_ls_shell.R_factor_R_work 0.380 _refine_ls_shell.percent_reflns_obs 97.77 _refine_ls_shell.R_factor_R_free 0.651 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 13 _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 4HW1 _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 4HW1 _struct.title 'Multiple Crystal structures of an all-AT DNA dodecamer stabilized by weak interactions.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4HW1 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Oligonucleotide, weak interactions, B form DNA, 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 1 ? D N N 1 ? E N N 2 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4HW1 _struct_ref.pdbx_db_accession 4HW1 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code AATAAATTTATT _struct_ref.pdbx_db_isoform ? # 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 4HW1 A 1 ? 12 ? 4HW1 1 ? 12 ? 1 12 2 1 4HW1 B 1 ? 12 ? 4HW1 13 ? 24 ? 13 24 3 1 4HW1 C 1 ? 12 ? 4HW1 1 ? 12 ? 1 12 4 1 4HW1 D 1 ? 12 ? 4HW1 13 ? 24 ? 13 24 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1050 ? 1 MORE -10 ? 1 'SSA (A^2)' 4710 ? 2 'ABSA (A^2)' 1000 ? 2 MORE -7 ? 2 'SSA (A^2)' 4640 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,G 2 1 C,D,H,I # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? E MG . MG ? ? ? 1_555 G HOH . O ? ? B MG 101 B HOH 201 1_555 ? ? ? ? ? ? ? 2.191 ? ? metalc2 metalc ? ? E MG . MG ? ? ? 1_555 G HOH . O ? ? B MG 101 B HOH 202 1_555 ? ? ? ? ? ? ? 2.377 ? ? metalc3 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 101 C HOH 101 1_555 ? ? ? ? ? ? ? 2.429 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 12 N3 ? ? A DA 1 B DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 12 O4 ? ? A DA 1 B DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 11 N3 ? ? A DA 2 B DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 11 O4 ? ? A DA 2 B DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 10 N6 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 7 B DA 17 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog14 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 9 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 9 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 10 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 10 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 11 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 11 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 11 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 11 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 12 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 12 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 12 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 12 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C DA 1 N1 ? ? ? 1_555 D DT 12 N3 ? ? C DA 1 D DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C DA 1 N6 ? ? ? 1_555 D DT 12 O4 ? ? C DA 1 D DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C DA 2 N1 ? ? ? 1_555 D DT 11 N3 ? ? C DA 2 D DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C DA 2 N6 ? ? ? 1_555 D DT 11 O4 ? ? C DA 2 D DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C DT 3 N3 ? ? ? 1_555 D DA 10 N1 ? ? C DT 3 D DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C DT 3 O4 ? ? ? 1_555 D DA 10 N6 ? ? C DT 3 D DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DA 4 N1 ? ? ? 1_555 D DT 9 N3 ? ? C DA 4 D DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C DA 4 N6 ? ? ? 1_555 D DT 9 O4 ? ? C DA 4 D DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DA 5 N1 ? ? ? 1_555 D DT 8 N3 ? ? C DA 5 D DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C DA 5 N6 ? ? ? 1_555 D DT 8 O4 ? ? C DA 5 D DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C DA 6 N1 ? ? ? 1_555 D DT 7 N3 ? ? C DA 6 D DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C DA 6 N6 ? ? ? 1_555 D DT 7 O4 ? ? C DA 6 D DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C DT 7 N3 ? ? ? 1_555 D DA 6 N1 ? ? C DT 7 D DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C DT 7 O4 ? ? ? 1_555 D DA 6 N6 ? ? C DT 7 D DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C DT 8 N3 ? ? ? 1_555 D DA 5 N1 ? ? C DT 8 D DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C DT 8 O4 ? ? ? 1_555 D DA 5 N6 ? ? C DT 8 D DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C DT 9 N3 ? ? ? 1_555 D DA 4 N1 ? ? C DT 9 D DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C DT 9 O4 ? ? ? 1_555 D DA 4 N6 ? ? C DT 9 D DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C DA 10 N1 ? ? ? 1_555 D DT 3 N3 ? ? C DA 10 D DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C DA 10 N6 ? ? ? 1_555 D DT 3 O4 ? ? C DA 10 D DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C DT 11 N3 ? ? ? 1_555 D DA 2 N1 ? ? C DT 11 D DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C DT 11 O4 ? ? ? 1_555 D DA 2 N6 ? ? C DT 11 D DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C DT 12 N3 ? ? ? 1_555 D DA 1 N1 ? ? C DT 12 D DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C DT 12 O4 ? ? ? 1_555 D DA 1 N6 ? ? C DT 12 D DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? G HOH . ? B HOH 201 ? 1_555 MG ? E MG . ? B MG 101 ? 1_555 O ? G HOH . ? B HOH 202 ? 1_555 79.8 ? 2 O ? G HOH . ? B HOH 201 ? 1_555 MG ? E MG . ? B MG 101 ? 1_555 O ? H HOH . ? C HOH 101 ? 1_555 72.0 ? 3 O ? G HOH . ? B HOH 202 ? 1_555 MG ? E MG . ? B MG 101 ? 1_555 O ? H HOH . ? C HOH 101 ? 1_555 97.2 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE MG B 101' # 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 DA B 4 ? DA B 16 . ? 1_555 ? 2 AC1 4 HOH G . ? HOH B 201 . ? 1_555 ? 3 AC1 4 HOH G . ? HOH B 202 . ? 1_555 ? 4 AC1 4 HOH H . ? HOH C 101 . ? 1_555 ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DT OP3 O N N 37 DT P P N N 38 DT OP1 O N N 39 DT OP2 O N N 40 DT "O5'" O N N 41 DT "C5'" C N N 42 DT "C4'" C N R 43 DT "O4'" O N N 44 DT "C3'" C N S 45 DT "O3'" O N N 46 DT "C2'" C N N 47 DT "C1'" C N R 48 DT N1 N N N 49 DT C2 C N N 50 DT O2 O N N 51 DT N3 N N N 52 DT C4 C N N 53 DT O4 O N N 54 DT C5 C N N 55 DT C7 C N N 56 DT C6 C N N 57 DT HOP3 H N N 58 DT HOP2 H N N 59 DT "H5'" H N N 60 DT "H5''" H N N 61 DT "H4'" H N N 62 DT "H3'" H N N 63 DT "HO3'" H N N 64 DT "H2'" H N N 65 DT "H2''" H N N 66 DT "H1'" H N N 67 DT H3 H N N 68 DT H71 H N N 69 DT H72 H N N 70 DT H73 H N N 71 DT H6 H N N 72 HOH O O N N 73 HOH H1 H N N 74 HOH H2 H N N 75 MG MG MG N N 76 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DT OP3 P sing N N 39 DT OP3 HOP3 sing N N 40 DT P OP1 doub N N 41 DT P OP2 sing N N 42 DT P "O5'" sing N N 43 DT OP2 HOP2 sing N N 44 DT "O5'" "C5'" sing N N 45 DT "C5'" "C4'" sing N N 46 DT "C5'" "H5'" sing N N 47 DT "C5'" "H5''" sing N N 48 DT "C4'" "O4'" sing N N 49 DT "C4'" "C3'" sing N N 50 DT "C4'" "H4'" sing N N 51 DT "O4'" "C1'" sing N N 52 DT "C3'" "O3'" sing N N 53 DT "C3'" "C2'" sing N N 54 DT "C3'" "H3'" sing N N 55 DT "O3'" "HO3'" sing N N 56 DT "C2'" "C1'" sing N N 57 DT "C2'" "H2'" sing N N 58 DT "C2'" "H2''" sing N N 59 DT "C1'" N1 sing N N 60 DT "C1'" "H1'" sing N N 61 DT N1 C2 sing N N 62 DT N1 C6 sing N N 63 DT C2 O2 doub N N 64 DT C2 N3 sing N N 65 DT N3 C4 sing N N 66 DT N3 H3 sing N N 67 DT C4 O4 doub N N 68 DT C4 C5 sing N N 69 DT C5 C7 sing N N 70 DT C5 C6 doub N N 71 DT C7 H71 sing N N 72 DT C7 H72 sing N N 73 DT C7 H73 sing N N 74 DT C6 H6 sing N N 75 HOH O H1 sing N N 76 HOH O H2 sing N N 77 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4HW1 'double helix' 4HW1 '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 DA 1 1_555 B DT 12 1_555 0.300 -0.183 -0.452 -5.320 -9.286 1.651 1 A_DA1:DT24_B A 1 ? B 24 ? 20 1 1 A DA 2 1_555 B DT 11 1_555 0.146 -0.140 0.021 2.425 -10.210 0.419 2 A_DA2:DT23_B A 2 ? B 23 ? 20 1 1 A DT 3 1_555 B DA 10 1_555 -0.658 -0.110 0.014 10.987 -17.212 -3.318 3 A_DT3:DA22_B A 3 ? B 22 ? 20 1 1 A DA 4 1_555 B DT 9 1_555 -0.019 -0.163 0.475 10.155 -17.571 -4.108 4 A_DA4:DT21_B A 4 ? B 21 ? 20 1 1 A DA 5 1_555 B DT 8 1_555 -0.460 -0.333 0.527 10.776 -23.514 -5.007 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.680 -0.181 0.440 -0.295 -12.989 -1.483 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.401 -0.252 0.808 -8.328 -14.479 -3.917 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.314 -0.096 0.279 -7.751 -26.435 -9.148 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DT 9 1_555 B DA 4 1_555 -0.165 -0.078 0.731 -20.233 -11.285 -6.685 9 A_DT9:DA16_B A 9 ? B 16 ? 20 1 1 A DA 10 1_555 B DT 3 1_555 0.740 -0.115 0.161 -5.350 -10.117 -2.927 10 A_DA10:DT15_B A 10 ? B 15 ? 20 1 1 A DT 11 1_555 B DA 2 1_555 -1.100 -0.246 0.772 -10.732 -5.172 -1.024 11 A_DT11:DA14_B A 11 ? B 14 ? 20 1 1 A DT 12 1_555 B DA 1 1_555 0.033 -0.159 -0.271 -10.336 -24.428 1.898 12 A_DT12:DA13_B A 12 ? B 13 ? 20 1 1 C DA 1 1_555 D DT 12 1_555 -0.855 -0.414 0.102 -1.682 -11.736 0.255 13 C_DA1:DT24_D C 1 ? D 24 ? 20 1 1 C DA 2 1_555 D DT 11 1_555 0.447 -0.189 0.702 5.207 -8.034 -0.766 14 C_DA2:DT23_D C 2 ? D 23 ? 20 1 1 C DT 3 1_555 D DA 10 1_555 -0.299 -0.264 0.822 3.225 -10.760 -3.360 15 C_DT3:DA22_D C 3 ? D 22 ? 20 1 1 C DA 4 1_555 D DT 9 1_555 0.899 -0.183 0.316 11.744 -16.524 -2.016 16 C_DA4:DT21_D C 4 ? D 21 ? 20 1 1 C DA 5 1_555 D DT 8 1_555 0.846 -0.096 0.393 8.392 -22.720 -6.446 17 C_DA5:DT20_D C 5 ? D 20 ? 20 1 1 C DA 6 1_555 D DT 7 1_555 0.358 -0.177 0.142 7.742 -19.462 1.015 18 C_DA6:DT19_D C 6 ? D 19 ? 20 1 1 C DT 7 1_555 D DA 6 1_555 -0.732 -0.157 -0.393 6.667 -20.764 -0.398 19 C_DT7:DA18_D C 7 ? D 18 ? 20 1 1 C DT 8 1_555 D DA 5 1_555 -0.831 -0.246 0.781 -8.480 -24.788 -8.380 20 C_DT8:DA17_D C 8 ? D 17 ? 20 1 1 C DT 9 1_555 D DA 4 1_555 -0.483 -0.133 0.821 -15.930 -19.020 -10.046 21 C_DT9:DA16_D C 9 ? D 16 ? 20 1 1 C DA 10 1_555 D DT 3 1_555 -0.330 -0.204 -0.108 -13.272 2.500 1.633 22 C_DA10:DT15_D C 10 ? D 15 ? 20 1 1 C DT 11 1_555 D DA 2 1_555 -0.141 -0.094 0.359 -9.235 -5.527 -3.112 23 C_DT11:DA14_D C 11 ? D 14 ? 20 1 1 C DT 12 1_555 D DA 1 1_555 0.429 -0.250 0.439 -12.844 -11.105 -0.073 24 C_DT12:DA13_D C 12 ? D 13 ? 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 DA 1 1_555 B DT 12 1_555 A DA 2 1_555 B DT 11 1_555 -0.445 -0.002 2.901 -4.250 -3.155 33.621 0.448 0.154 2.922 -5.413 7.291 34.023 1 AA_DA1DA2:DT23DT24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DA 2 1_555 B DT 11 1_555 A DT 3 1_555 B DA 10 1_555 0.320 -0.880 2.935 0.834 2.864 29.781 -2.230 -0.468 2.848 5.555 -1.617 29.926 2 AA_DA2DT3:DA22DT23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DT 3 1_555 B DA 10 1_555 A DA 4 1_555 B DT 9 1_555 -0.455 -0.047 3.437 -2.001 3.271 38.295 -0.499 0.429 3.440 4.970 3.041 38.479 3 AA_DT3DA4:DT21DA22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DA 4 1_555 B DT 9 1_555 A DA 5 1_555 B DT 8 1_555 0.215 -0.714 3.261 -1.359 -5.152 32.101 -0.363 -0.624 3.320 -9.237 2.437 32.528 4 AA_DA4DA5:DT20DT21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.121 -0.696 3.554 -1.346 -6.644 44.246 -0.247 -0.294 3.612 -8.760 1.774 44.737 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.150 -1.545 3.369 -2.224 -1.827 26.987 -2.811 -0.266 3.464 -3.901 4.747 27.138 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.256 -0.730 2.954 5.503 -7.281 39.518 -0.306 0.935 2.977 -10.597 -8.010 40.518 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DT 9 1_555 B DA 4 1_555 0.774 -0.465 3.468 1.841 -4.823 40.485 -0.096 -0.893 3.529 -6.936 -2.647 40.799 8 AA_DT8DT9:DA16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DT 9 1_555 B DA 4 1_555 A DA 10 1_555 B DT 3 1_555 -0.104 -0.256 2.944 0.652 3.582 31.749 -1.047 0.294 2.896 6.521 -1.187 31.951 9 AA_DT9DA10:DT15DA16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DA 10 1_555 B DT 3 1_555 A DT 11 1_555 B DA 2 1_555 -0.085 -1.061 3.368 -3.528 -0.463 26.440 -2.174 -0.768 3.368 -1.007 7.669 26.674 10 AA_DA10DT11:DA14DT15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DT 11 1_555 B DA 2 1_555 A DT 12 1_555 B DA 1 1_555 0.129 -0.387 3.148 9.780 0.361 40.216 -0.585 0.833 3.091 0.516 -13.974 41.342 11 AA_DT11DT12:DA13DA14_BB A 11 ? B 14 ? A 12 ? B 13 ? 1 C DA 1 1_555 D DT 12 1_555 C DA 2 1_555 D DT 11 1_555 -0.414 -0.188 2.994 -5.905 -3.284 44.337 0.030 0.047 3.028 -4.321 7.771 44.823 12 CC_DA1DA2:DT23DT24_DD C 1 ? D 24 ? C 2 ? D 23 ? 1 C DA 2 1_555 D DT 11 1_555 C DT 3 1_555 D DA 10 1_555 -0.105 -1.372 3.326 -3.070 -3.131 25.716 -2.147 -0.644 3.454 -6.969 6.835 26.080 13 CC_DA2DT3:DA22DT23_DD C 2 ? D 23 ? C 3 ? D 22 ? 1 C DT 3 1_555 D DA 10 1_555 C DA 4 1_555 D DT 9 1_555 0.449 -0.188 3.099 6.597 -2.977 40.347 0.043 0.051 3.136 -4.274 -9.472 40.965 14 CC_DT3DA4:DT21DA22_DD C 3 ? D 22 ? C 4 ? D 21 ? 1 C DA 4 1_555 D DT 9 1_555 C DA 5 1_555 D DT 8 1_555 -0.315 -0.185 3.284 -1.444 -5.036 36.182 0.406 0.302 3.289 -8.056 2.310 36.546 15 CC_DA4DA5:DT20DT21_DD C 4 ? D 21 ? C 5 ? D 20 ? 1 C DA 5 1_555 D DT 8 1_555 C DA 6 1_555 D DT 7 1_555 -0.152 -0.898 3.166 0.924 2.737 34.270 -1.928 0.395 3.082 4.634 -1.564 34.388 16 CC_DA5DA6:DT19DT20_DD C 5 ? D 20 ? C 6 ? D 19 ? 1 C DA 6 1_555 D DT 7 1_555 C DT 7 1_555 D DA 6 1_555 -0.236 -0.895 3.203 4.160 -1.620 26.495 -1.517 1.558 3.177 -3.503 -8.995 26.862 17 CC_DA6DT7:DA18DT19_DD C 6 ? D 19 ? C 7 ? D 18 ? 1 C DT 7 1_555 D DA 6 1_555 C DT 8 1_555 D DA 5 1_555 0.020 -0.700 3.691 -7.704 -3.032 36.291 -0.639 -1.197 3.656 -4.791 12.174 37.193 18 CC_DT7DT8:DA17DA18_DD C 7 ? D 18 ? C 8 ? D 17 ? 1 C DT 8 1_555 D DA 5 1_555 C DT 9 1_555 D DA 4 1_555 -0.070 -0.508 3.331 0.603 -5.535 41.048 -0.111 0.166 3.367 -7.850 -0.855 41.407 19 CC_DT8DT9:DA16DA17_DD C 8 ? D 17 ? C 9 ? D 16 ? 1 C DT 9 1_555 D DA 4 1_555 C DA 10 1_555 D DT 3 1_555 0.465 -0.022 3.300 5.049 -3.367 37.920 0.395 -0.066 3.322 -5.141 -7.710 38.385 20 CC_DT9DA10:DT15DA16_DD C 9 ? D 16 ? C 10 ? D 15 ? 1 C DA 10 1_555 D DT 3 1_555 C DT 11 1_555 D DA 2 1_555 -0.233 -0.722 3.285 -3.626 1.734 31.658 -1.629 -0.237 3.247 3.162 6.613 31.906 21 CC_DA10DT11:DA14DT15_DD C 10 ? D 15 ? C 11 ? D 14 ? 1 C DT 11 1_555 D DA 2 1_555 C DT 12 1_555 D DA 1 1_555 0.504 -0.744 3.245 2.702 1.191 38.562 -1.269 -0.430 3.248 1.800 -4.084 38.671 22 CC_DT11DT12:DA13DA14_DD C 11 ? D 14 ? C 12 ? D 13 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'theoretical model of B-DNA' # _atom_sites.entry_id 4HW1 _atom_sites.fract_transf_matrix[1][1] 0.019829 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.016352 _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] 0.012407 _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 MG N O P # loop_