data_1N6S # _entry.id 1N6S # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1N6S NDB ZD0009 RCSB RCSB017589 WWPDB D_1000017589 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2005-04-19 _pdbx_database_PDB_obs_spr.pdb_id 1VRO _pdbx_database_PDB_obs_spr.replace_pdb_id 1N6S _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 1N6S _pdbx_database_status.recvd_initial_deposition_date 2002-11-12 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wilds, C.J.' 1 'Pattanayek, R.' 2 'Pan, C.' 3 'Wawrzak, Z.' 4 'Egli, M.' 5 # _citation.id primary _citation.title 'Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 124 _citation.page_first 14910 _citation.page_last 14916 _citation.year 2002 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12475332 _citation.pdbx_database_id_DOI 10.1021/ja021058b # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Wilds, C.J.' 1 primary 'Pattanayek, R.' 2 primary 'Pan, C.' 3 primary 'Wawrzak, Z.' 4 primary 'Egli, M.' 5 # _cell.entry_id 1N6S _cell.length_a 17.778 _cell.length_b 31.348 _cell.length_c 44.116 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 # _symmetry.entry_id 1N6S _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 19 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # 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*(GMS)P*CP*GP*CP*G)-3'" 1953.166 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 73 ? ? ? ? # _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 'C(GMS)CGCG' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _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 C n 1 2 GMS n 1 3 C n 1 4 G n 1 5 C n 1 6 G 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 ;synthesized with a solid-phase oligonucleotide synthesizer using DNA phosphoramidites and potassium selenocyanide for introducing the phosphoroselenoate linkage ; # 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GMS 'DNA linking' n "2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE" ? 'C10 H14 N5 O6 P Se' 410.182 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # _exptl.entry_id 1N6S _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.32 _exptl_crystal.density_percent_sol 5.98 _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 291.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;0.5mM DNA, 4mM-15mM magnesium chloride, 50mM sodium cacodylate, 2mM-8mM spermine tetrahydrochloride and reservoir 30% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K ; _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 DNA ? ? ? 1 2 1 MgCl ? ? ? 1 3 1 'sodium cacodylate' ? ? ? 1 4 1 'spermine tetrahydrochloride' ? ? ? 1 5 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 120 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2002-01-22 _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 graphite _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9561 1.0 2 0.9787 1.0 3 0.9784 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 5IDB' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 5IDB _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9561, 0.9787, 0.9784' # _reflns.entry_id 1N6S _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 1.1 _reflns.d_resolution_low 20.0 _reflns.number_all ? _reflns.number_obs 18919 _reflns.percent_possible_obs 97.7 _reflns.pdbx_Rmerge_I_obs 0.041 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 22.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.47 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_netI_over_sigmaI ? # _reflns_shell.d_res_high 1.10 _reflns_shell.d_res_low 1.14 _reflns_shell.percent_possible_all 95.4 _reflns_shell.Rmerge_I_obs 0.075 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 15.85 _reflns_shell.pdbx_redundancy 7.47 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1802 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1N6S _refine.ls_d_res_high 1.10 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I 0.0 _refine.ls_number_reflns_all 9718 _refine.ls_number_reflns_obs 9718 _refine.ls_number_reflns_R_free 508 _refine.ls_percent_reflns_obs 97.7 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.097 _refine.ls_R_factor_R_free 0.129 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters 3005 _refine.ls_number_restraints 5144 _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean 6.9 _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details Shelx-97 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 245 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 73 _refine_hist.number_atoms_total 333 _refine_hist.d_res_high 1.10 _refine_hist.d_res_low 20.0 _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' # 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 s_bond_d 0.028 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.022 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1N6S _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.097 _pdbx_refine.number_reflns_obs_no_cutoff 9718 _pdbx_refine.free_R_factor_no_cutoff 0.129 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 508 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff 0.096 _pdbx_refine.number_reflns_obs_4sig_cutoff 9692 _pdbx_refine.free_R_factor_4sig_cutoff 0.129 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 508 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 1N6S _struct.title 'Selenium-Assisted Nucleic Acid Crystallography: Use of Phosphoroselenoates for MAD Phasing of a DNA Structure' _struct.pdbx_descriptor "5'-D(*CP*(GMS)P*CP*GP*CP*G)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1N6S _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;Left-handed Z-DNA, phosphoroselenoate, multiwavelength anomalous dispersion (MAD), covalent modification of oligonucleotides, oligonucleotide analogue, phasing strategy, synchrotron, 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 ? # _struct_biol.id 1 _struct_biol.details 'Asymmetric unit consists of a single duplex' _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 hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 1 B G 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 1 B G 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 1 B G 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 3 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 3 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 3 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 4 B C 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 4 B C 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 4 B C 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 6 B C 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 6 B C 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 6 B C 107 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1N6S _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 1N6S _atom_sites.fract_transf_matrix[1][1] 0.056249 _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] 0.031900 _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] 0.022668 _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 SE # 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 C 1 1 1 C CYT A . n A 1 2 GMS 2 2 2 GMS GUA A . n A 1 3 C 3 3 3 C CYT A . n A 1 4 G 4 4 4 G GUA A . n A 1 5 C 5 5 5 C CYT A . n A 1 6 G 6 6 6 G GUA A . n B 1 1 C 1 107 107 C CYT B . n B 1 2 GMS 2 108 108 GMS GUA B . n B 1 3 C 3 109 109 C CYT B . n B 1 4 G 4 110 110 G GUA B . n B 1 5 C 5 111 111 C CYT B . n B 1 6 G 6 112 112 G GUA 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 SPM 1 201 201 SPM SPM ? . D 3 MG 1 301 301 MG MG ? . E 4 HOH 1 401 401 HOH HOH ? . E 4 HOH 2 402 402 HOH HOH ? . E 4 HOH 3 403 403 HOH HOH ? . E 4 HOH 4 404 404 HOH HOH ? . E 4 HOH 5 405 405 HOH HOH ? . E 4 HOH 6 406 406 HOH HOH ? . E 4 HOH 7 407 407 HOH HOH ? . E 4 HOH 8 408 408 HOH HOH ? . E 4 HOH 9 409 409 HOH HOH ? . E 4 HOH 10 410 410 HOH HOH ? . E 4 HOH 11 411 411 HOH HOH ? . E 4 HOH 12 412 412 HOH HOH ? . E 4 HOH 13 413 413 HOH HOH ? . E 4 HOH 14 414 414 HOH HOH ? . E 4 HOH 15 415 415 HOH HOH ? . E 4 HOH 16 416 416 HOH HOH ? . E 4 HOH 17 417 417 HOH HOH ? . E 4 HOH 18 418 418 HOH HOH ? . E 4 HOH 19 419 419 HOH HOH ? . E 4 HOH 20 420 420 HOH HOH ? . E 4 HOH 21 421 421 HOH HOH ? . E 4 HOH 22 422 422 HOH HOH ? . E 4 HOH 23 423 423 HOH HOH ? . E 4 HOH 24 424 424 HOH HOH ? . E 4 HOH 25 425 425 HOH HOH ? . E 4 HOH 26 426 426 HOH HOH ? . E 4 HOH 27 427 427 HOH HOH ? . E 4 HOH 28 428 428 HOH HOH ? . E 4 HOH 29 429 429 HOH HOH ? . E 4 HOH 30 430 430 HOH HOH ? . E 4 HOH 31 431 431 HOH HOH ? . E 4 HOH 32 432 432 HOH HOH ? . E 4 HOH 33 433 433 HOH HOH ? . E 4 HOH 34 434 434 HOH HOH ? . E 4 HOH 35 435 435 HOH HOH ? . E 4 HOH 36 436 436 HOH HOH ? . E 4 HOH 37 437 437 HOH HOH ? . E 4 HOH 38 438 438 HOH HOH ? . E 4 HOH 39 439 439 HOH HOH ? . E 4 HOH 40 440 440 HOH HOH ? . E 4 HOH 41 441 441 HOH HOH ? . E 4 HOH 42 442 442 HOH HOH ? . E 4 HOH 43 443 443 HOH HOH ? . E 4 HOH 44 444 444 HOH HOH ? . E 4 HOH 45 445 445 HOH HOH ? . E 4 HOH 46 446 446 HOH HOH ? . E 4 HOH 47 447 447 HOH HOH ? . E 4 HOH 48 448 448 HOH HOH ? . E 4 HOH 49 449 449 HOH HOH ? . E 4 HOH 50 450 450 HOH HOH ? . E 4 HOH 51 451 451 HOH HOH ? . E 4 HOH 52 452 452 HOH HOH ? . E 4 HOH 53 453 453 HOH HOH ? . E 4 HOH 54 454 454 HOH HOH ? . E 4 HOH 55 455 455 HOH HOH ? . E 4 HOH 56 456 456 HOH HOH ? . E 4 HOH 57 457 457 HOH HOH ? . E 4 HOH 58 458 458 HOH HOH ? . E 4 HOH 59 459 459 HOH HOH ? . E 4 HOH 60 460 460 HOH HOH ? . E 4 HOH 61 461 461 HOH HOH ? . E 4 HOH 62 462 462 HOH HOH ? . E 4 HOH 63 463 463 HOH HOH ? . E 4 HOH 64 464 464 HOH HOH ? . E 4 HOH 65 465 465 HOH HOH ? . E 4 HOH 66 466 466 HOH HOH ? . E 4 HOH 67 467 467 HOH HOH ? . E 4 HOH 68 468 468 HOH HOH ? . E 4 HOH 69 469 469 HOH HOH ? . E 4 HOH 70 470 470 HOH HOH ? . E 4 HOH 71 471 471 HOH HOH ? . E 4 HOH 72 472 472 HOH HOH ? . E 4 HOH 73 473 473 HOH HOH ? . # 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 2002-12-20 2 'Structure model' 1 1 2005-04-19 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 2 'Structure model' repository Obsolete ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data collection' . ? 1 SCALEPACK 'data reduction' . ? 2 CNS 'model building' . ? 3 SHELXL-97 refinement . ? 4 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O3* A C 5 ? ? P A G 6 ? ? 1.56 2 1 O3* B G 110 ? ? P B C 111 ? ? 1.58 3 1 O3* B C 107 ? ? P B GMS 108 ? ? 1.59 4 1 O3* A C 1 ? B P A GMS 2 ? B 1.59 5 1 O3* A G 4 ? ? P A C 5 ? ? 1.59 6 1 O3* A C 3 ? ? P A G 4 ? ? 1.59 7 1 O3* B C 109 ? ? P B G 110 ? ? 1.59 8 1 O3* A C 1 ? A P A GMS 2 ? A 1.60 9 1 O3* A GMS 2 ? ? P A C 3 ? ? 1.60 10 1 O3* B C 111 ? ? P B G 112 ? ? 1.60 11 1 O3* B GMS 108 ? ? P B C 109 ? ? 1.64 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 C5 _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 C _pdbx_validate_rmsd_angle.auth_seq_id_1 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 C6 _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 C _pdbx_validate_rmsd_angle.auth_seq_id_2 1 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N1 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 C _pdbx_validate_rmsd_angle.auth_seq_id_3 1 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 124.23 _pdbx_validate_rmsd_angle.angle_target_value 121.00 _pdbx_validate_rmsd_angle.angle_deviation 3.23 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # 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 A C 1 ? "O5'" ? A C 1 "O5'" 2 1 Y 1 A C 1 ? "C5'" ? A C 1 "C5'" 3 1 Y 1 A C 1 ? "C4'" ? A C 1 "C4'" 4 1 Y 1 A C 1 ? "O4'" ? A C 1 "O4'" 5 1 Y 1 A C 1 ? "C3'" ? A C 1 "C3'" 6 1 Y 1 A C 1 ? "O3'" ? A C 1 "O3'" 7 1 Y 1 A C 1 ? "C2'" ? A C 1 "C2'" 8 1 Y 1 A C 1 ? "O2'" ? A C 1 "O2'" 9 1 Y 1 A C 1 ? "C1'" ? A C 1 "C1'" 10 1 Y 1 A GMS 2 ? OP1 ? A GMS 2 OP1 11 1 Y 1 A GMS 2 ? "O5'" ? A GMS 2 "O5'" 12 1 Y 1 A GMS 2 ? "C2'" ? A GMS 2 "C2'" 13 1 Y 1 A GMS 2 ? "C5'" ? A GMS 2 "C5'" 14 1 Y 1 A GMS 2 ? "C4'" ? A GMS 2 "C4'" 15 1 Y 1 A GMS 2 ? "O4'" ? A GMS 2 "O4'" 16 1 Y 1 A GMS 2 ? "C1'" ? A GMS 2 "C1'" 17 1 Y 1 A GMS 2 ? "C3'" ? A GMS 2 "C3'" 18 1 Y 1 A GMS 2 ? "O3'" ? A GMS 2 "O3'" 19 1 Y 1 A GMS 2 ? OP2 ? A GMS 2 OP2 20 1 Y 1 A C 3 ? OP1 ? A C 3 OP1 21 1 Y 1 A C 3 ? OP2 ? A C 3 OP2 22 1 Y 1 A C 3 ? "O5'" ? A C 3 "O5'" 23 1 Y 1 A C 3 ? "C5'" ? A C 3 "C5'" 24 1 Y 1 A C 3 ? "C4'" ? A C 3 "C4'" 25 1 Y 1 A C 3 ? "O4'" ? A C 3 "O4'" 26 1 Y 1 A C 3 ? "C3'" ? A C 3 "C3'" 27 1 Y 1 A C 3 ? "O3'" ? A C 3 "O3'" 28 1 Y 1 A C 3 ? "C2'" ? A C 3 "C2'" 29 1 Y 1 A C 3 ? "O2'" ? A C 3 "O2'" 30 1 Y 1 A C 3 ? "C1'" ? A C 3 "C1'" 31 1 Y 1 A G 4 ? OP1 ? A G 4 OP1 32 1 Y 1 A G 4 ? OP2 ? A G 4 OP2 33 1 Y 1 A G 4 ? "O5'" ? A G 4 "O5'" 34 1 Y 1 A G 4 ? "C5'" ? A G 4 "C5'" 35 1 Y 1 A G 4 ? "C4'" ? A G 4 "C4'" 36 1 Y 1 A G 4 ? "O4'" ? A G 4 "O4'" 37 1 Y 1 A G 4 ? "C3'" ? A G 4 "C3'" 38 1 Y 1 A G 4 ? "O3'" ? A G 4 "O3'" 39 1 Y 1 A G 4 ? "C2'" ? A G 4 "C2'" 40 1 Y 1 A G 4 ? "O2'" ? A G 4 "O2'" 41 1 Y 1 A G 4 ? "C1'" ? A G 4 "C1'" 42 1 Y 1 A C 5 ? OP1 ? A C 5 OP1 43 1 Y 1 A C 5 ? OP2 ? A C 5 OP2 44 1 Y 1 A C 5 ? "O5'" ? A C 5 "O5'" 45 1 Y 1 A C 5 ? "C5'" ? A C 5 "C5'" 46 1 Y 1 A C 5 ? "C4'" ? A C 5 "C4'" 47 1 Y 1 A C 5 ? "O4'" ? A C 5 "O4'" 48 1 Y 1 A C 5 ? "C3'" ? A C 5 "C3'" 49 1 Y 1 A C 5 ? "O3'" ? A C 5 "O3'" 50 1 Y 1 A C 5 ? "C2'" ? A C 5 "C2'" 51 1 Y 1 A C 5 ? "O2'" ? A C 5 "O2'" 52 1 Y 1 A C 5 ? "C1'" ? A C 5 "C1'" 53 1 Y 1 A G 6 ? OP1 ? A G 6 OP1 54 1 Y 1 A G 6 ? OP2 ? A G 6 OP2 55 1 Y 1 A G 6 ? "O5'" ? A G 6 "O5'" 56 1 Y 1 A G 6 ? "C5'" ? A G 6 "C5'" 57 1 Y 1 A G 6 ? "C4'" ? A G 6 "C4'" 58 1 Y 1 A G 6 ? "O4'" ? A G 6 "O4'" 59 1 Y 1 A G 6 ? "C3'" ? A G 6 "C3'" 60 1 Y 1 A G 6 ? "O3'" ? A G 6 "O3'" 61 1 Y 1 A G 6 ? "C2'" ? A G 6 "C2'" 62 1 Y 1 A G 6 ? "O2'" ? A G 6 "O2'" 63 1 Y 1 A G 6 ? "C1'" ? A G 6 "C1'" 64 1 Y 1 B C 107 ? "O5'" ? B C 1 "O5'" 65 1 Y 1 B C 107 ? "C5'" ? B C 1 "C5'" 66 1 Y 1 B C 107 ? "C4'" ? B C 1 "C4'" 67 1 Y 1 B C 107 ? "O4'" ? B C 1 "O4'" 68 1 Y 1 B C 107 ? "C3'" ? B C 1 "C3'" 69 1 Y 1 B C 107 ? "O3'" ? B C 1 "O3'" 70 1 Y 1 B C 107 ? "C2'" ? B C 1 "C2'" 71 1 Y 1 B C 107 ? "O2'" ? B C 1 "O2'" 72 1 Y 1 B C 107 ? "C1'" ? B C 1 "C1'" 73 1 Y 1 B GMS 108 ? OP1 ? B GMS 2 OP1 74 1 Y 1 B GMS 108 ? "O5'" ? B GMS 2 "O5'" 75 1 Y 1 B GMS 108 ? "C2'" ? B GMS 2 "C2'" 76 1 Y 1 B GMS 108 ? "C5'" ? B GMS 2 "C5'" 77 1 Y 1 B GMS 108 ? "C4'" ? B GMS 2 "C4'" 78 1 Y 1 B GMS 108 ? "O4'" ? B GMS 2 "O4'" 79 1 Y 1 B GMS 108 ? "C1'" ? B GMS 2 "C1'" 80 1 Y 1 B GMS 108 ? "C3'" ? B GMS 2 "C3'" 81 1 Y 1 B GMS 108 ? "O3'" ? B GMS 2 "O3'" 82 1 Y 1 B GMS 108 ? OP2 ? B GMS 2 OP2 83 1 Y 1 B C 109 ? OP1 ? B C 3 OP1 84 1 Y 1 B C 109 ? OP2 ? B C 3 OP2 85 1 Y 1 B C 109 ? "O5'" ? B C 3 "O5'" 86 1 Y 1 B C 109 ? "C5'" ? B C 3 "C5'" 87 1 Y 1 B C 109 ? "C4'" ? B C 3 "C4'" 88 1 Y 1 B C 109 ? "O4'" ? B C 3 "O4'" 89 1 Y 1 B C 109 ? "C3'" ? B C 3 "C3'" 90 1 Y 1 B C 109 ? "O3'" ? B C 3 "O3'" 91 1 Y 1 B C 109 ? "C2'" ? B C 3 "C2'" 92 1 Y 1 B C 109 ? "O2'" ? B C 3 "O2'" 93 1 Y 1 B C 109 ? "C1'" ? B C 3 "C1'" 94 1 Y 1 B G 110 ? OP1 ? B G 4 OP1 95 1 Y 1 B G 110 ? OP2 ? B G 4 OP2 96 1 Y 1 B G 110 ? "O5'" ? B G 4 "O5'" 97 1 Y 1 B G 110 ? "C5'" ? B G 4 "C5'" 98 1 Y 1 B G 110 ? "C4'" ? B G 4 "C4'" 99 1 Y 1 B G 110 ? "O4'" ? B G 4 "O4'" 100 1 Y 1 B G 110 ? "C3'" ? B G 4 "C3'" 101 1 Y 1 B G 110 ? "O3'" ? B G 4 "O3'" 102 1 Y 1 B G 110 ? "C2'" ? B G 4 "C2'" 103 1 Y 1 B G 110 ? "O2'" ? B G 4 "O2'" 104 1 Y 1 B G 110 ? "C1'" ? B G 4 "C1'" 105 1 Y 1 B C 111 ? OP1 ? B C 5 OP1 106 1 Y 1 B C 111 ? OP2 ? B C 5 OP2 107 1 Y 1 B C 111 ? "O5'" ? B C 5 "O5'" 108 1 Y 1 B C 111 ? "C5'" ? B C 5 "C5'" 109 1 Y 1 B C 111 ? "C4'" ? B C 5 "C4'" 110 1 Y 1 B C 111 ? "O4'" ? B C 5 "O4'" 111 1 Y 1 B C 111 ? "C3'" ? B C 5 "C3'" 112 1 Y 1 B C 111 ? "O3'" ? B C 5 "O3'" 113 1 Y 1 B C 111 ? "C2'" ? B C 5 "C2'" 114 1 Y 1 B C 111 ? "O2'" ? B C 5 "O2'" 115 1 Y 1 B C 111 ? "C1'" ? B C 5 "C1'" 116 1 Y 1 B G 112 ? OP1 ? B G 6 OP1 117 1 Y 1 B G 112 ? OP2 ? B G 6 OP2 118 1 Y 1 B G 112 ? "O5'" ? B G 6 "O5'" 119 1 Y 1 B G 112 ? "C5'" ? B G 6 "C5'" 120 1 Y 1 B G 112 ? "C4'" ? B G 6 "C4'" 121 1 Y 1 B G 112 ? "O4'" ? B G 6 "O4'" 122 1 Y 1 B G 112 ? "C3'" ? B G 6 "C3'" 123 1 Y 1 B G 112 ? "O3'" ? B G 6 "O3'" 124 1 Y 1 B G 112 ? "C2'" ? B G 6 "C2'" 125 1 Y 1 B G 112 ? "O2'" ? B G 6 "O2'" 126 1 Y 1 B G 112 ? "C1'" ? B G 6 "C1'" # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1N6S 'double helix' 1N6S 'z-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 C 1 1_555 B G 6 1_555 -0.346 -0.169 0.195 -5.715 4.357 2.511 1 A_C1:G112_B A 1 ? B 112 ? 19 1 1 A C 3 1_555 B G 4 1_555 -0.190 -0.154 0.090 7.137 0.355 2.724 2 A_C3:G110_B A 3 ? B 110 ? 19 1 1 A G 4 1_555 B C 3 1_555 0.252 -0.138 -0.016 -4.848 -3.457 1.198 3 A_G4:C109_B A 4 ? B 109 ? 19 1 1 A G 6 1_555 B C 1 1_555 -0.243 -0.141 -0.039 4.017 0.655 -0.434 4 A_G6:C107_B A 6 ? B 107 ? 19 1 # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 A _ndb_struct_na_base_pair_step.i_label_comp_id_1 C _ndb_struct_na_base_pair_step.i_label_seq_id_1 3 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 B _ndb_struct_na_base_pair_step.j_label_comp_id_1 G _ndb_struct_na_base_pair_step.j_label_seq_id_1 4 _ndb_struct_na_base_pair_step.j_symmetry_1 1_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 G _ndb_struct_na_base_pair_step.i_label_seq_id_2 4 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 B _ndb_struct_na_base_pair_step.j_label_comp_id_2 C _ndb_struct_na_base_pair_step.j_label_seq_id_2 3 _ndb_struct_na_base_pair_step.j_symmetry_2 1_555 _ndb_struct_na_base_pair_step.shift 0.009 _ndb_struct_na_base_pair_step.slide 5.458 _ndb_struct_na_base_pair_step.rise 3.769 _ndb_struct_na_base_pair_step.tilt 0.339 _ndb_struct_na_base_pair_step.roll -3.330 _ndb_struct_na_base_pair_step.twist -5.811 _ndb_struct_na_base_pair_step.x_displacement -24.521 _ndb_struct_na_base_pair_step.y_displacement 2.326 _ndb_struct_na_base_pair_step.helical_rise 5.975 _ndb_struct_na_base_pair_step.inclination 29.805 _ndb_struct_na_base_pair_step.tip 3.032 _ndb_struct_na_base_pair_step.helical_twist -6.705 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_C3G4:C109G110_BB _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 3 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 B _ndb_struct_na_base_pair_step.j_auth_seq_id_1 110 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 4 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 B _ndb_struct_na_base_pair_step.j_auth_seq_id_2 109 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMINE SPM 3 'MAGNESIUM ION' MG 4 water HOH #