data_2QEG # _entry.id 2QEG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 2QEG pdb_00002qeg 10.2210/pdb2qeg/pdb NDB BD0103 ? ? RCSB RCSB043495 ? ? WWPDB D_1000043495 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2QEF _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2QEG _pdbx_database_status.recvd_initial_deposition_date 2007-06-25 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wang, F.' 1 'Li, F.' 2 'Ganguly, M.' 3 'Marky, L.A.' 4 'Gold, B.' 5 'Egli, M.' 6 'Stone, M.P.' 7 # _citation.id primary _citation.title ;A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 47 _citation.page_first 7147 _citation.page_last 7157 _citation.year 2008 _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 18549246 _citation.pdbx_database_id_DOI 10.1021/bi800375m # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wang, F.' 1 ? primary 'Li, F.' 2 ? primary 'Ganguly, M.' 3 ? primary 'Marky, L.A.' 4 ? primary 'Gold, B.' 5 ? primary 'Egli, M.' 6 ? primary 'Stone, M.P.' 7 ? # _cell.entry_id 2QEG _cell.length_a 24.185 _cell.length_b 40.328 _cell.length_c 65.686 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 2QEG _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 ;DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DTP*DCP*(7GU)P*DCP*DG)-3') ; 3662.404 2 ? ? ? DDDZ10 2 water nat water 18.015 110 ? ? ? ? # _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)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(7GU)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _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 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 7GU n 1 11 DC n 1 12 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 ;The 7-zG was introduced as the phosphoramidite (Glenn Research, Sterling, VA). The on-column oxidation of the phosphite to phosphate when a 7-zG is present requires (1S)-(+)-(10-camphorsulfonyl)oxaziridine rather than I2 according to the manufacturers protocols (Glenn Research, Sterling, VA). The dry oligomers were then dissolved in the appropriate buffer. ; # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2QEG _struct_ref.pdbx_db_accession 2QEG _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CGCGAATTCGCG _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 2QEG A 1 ? 12 ? 2QEG 1 ? 12 ? 1 12 2 1 2QEG B 1 ? 12 ? 2QEG 1 ? 12 ? 1 12 # 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 7GU 'DNA linking' n "7-DEAZA-2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C11 H15 N4 O7 P' 346.233 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 # _exptl.entry_id 2QEG _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.10 _exptl_crystal.density_percent_sol 41.54 _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 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;Droplets containing 0.6 mM oligonucleotide, 5% 2-methyl-2,4-pentanediol (MPD), 20 mM sodium cacodylate (pH 6.0), 6 mM spermine tetrahydrochloride, 40 mM KCl and 10 mM MgCl2 were equilibrated against a reservoir of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _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 2-methyl-2,4-pentanediol ? ? ? 1 2 1 'sodium cacodylate' ? ? ? 1 3 1 'spermine tetrahydrochloride' ? ? ? 1 4 1 KCl ? ? ? 1 5 1 MgCl2 ? ? ? 1 6 2 MPD ? ? ? # _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 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2007-04-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 22-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 22-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1 # _reflns.entry_id 2QEG _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 34.36 _reflns.number_all 9994 _reflns.number_obs 8678 _reflns.percent_possible_obs 96.4 _reflns.pdbx_Rmerge_I_obs 0.049 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.2 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.68 _reflns_shell.percent_possible_all 86.7 _reflns_shell.Rmerge_I_obs 0.118 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 4.6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 153 _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 2QEG _refine.ls_number_reflns_obs 7824 _refine.ls_number_reflns_all 9994 _refine.pdbx_ls_sigma_I 2.0 _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.36 _refine.ls_d_res_high 1.60 _refine.ls_percent_reflns_obs 96.59 _refine.ls_R_factor_obs 0.18855 _refine.ls_R_factor_all 0.18855 _refine.ls_R_factor_R_work 0.18205 _refine.ls_R_factor_R_free 0.25957 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.6 _refine.ls_number_reflns_R_free 831 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.962 _refine.correlation_coeff_Fo_to_Fc_free 0.926 _refine.B_iso_mean 22.428 _refine.aniso_B[1][1] 0.48 _refine.aniso_B[2][2] -0.77 _refine.aniso_B[3][3] 0.29 _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 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 355D _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.152 _refine.pdbx_overall_ESU_R_Free 0.121 _refine.overall_SU_ML 0.064 _refine.overall_SU_B 3.985 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _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 486 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 110 _refine_hist.number_atoms_total 596 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 34.36 # 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_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.006 0.021 ? 542 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 220 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.618 3.000 ? 826 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.144 3.000 ? 558 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.056 0.200 ? 94 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.023 0.020 ? 248 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.402 0.200 ? 64 'X-RAY DIFFRACTION' ? r_nbd_other 0.249 0.200 ? 262 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.244 0.200 ? 196 'X-RAY DIFFRACTION' ? r_nbtor_other 0.083 0.200 ? 130 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.167 0.200 ? 58 '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 0.048 0.200 ? 2 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.148 0.200 ? 12 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.077 0.200 ? 10 '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 3.217 3.000 ? 783 'X-RAY DIFFRACTION' ? r_scangle_it 4.040 4.500 ? 826 '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 1.600 _refine_ls_shell.d_res_low 1.641 _refine_ls_shell.number_reflns_R_work 471 _refine_ls_shell.R_factor_R_work 0.133 _refine_ls_shell.percent_reflns_obs 82.12 _refine_ls_shell.R_factor_R_free 0.207 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 48 _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' # _struct.entry_id 2QEG _struct.title 'B-DNA with 7-deaza-dG modification' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2QEG _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, 7-deaza-dG, 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 2 ? # _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 covale1 covale both ? A DC 9 "O3'" ? ? ? 1_555 A 7GU 10 P ? ? A DC 9 A 7GU 10 1_555 ? ? ? ? ? ? ? 1.594 ? ? covale2 covale both ? A 7GU 10 "O3'" ? ? ? 1_555 A DC 11 P ? ? A 7GU 10 A DC 11 1_555 ? ? ? ? ? ? ? 1.645 ? ? covale3 covale both ? B DC 9 "O3'" ? ? ? 1_555 B 7GU 10 P ? ? B DC 9 B 7GU 10 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale4 covale both ? B 7GU 10 "O3'" ? ? ? 1_555 B DC 11 P ? ? B 7GU 10 B DC 11 1_555 ? ? ? ? ? ? ? 1.610 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B 7GU 10 N1 ? ? A DC 3 B 7GU 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B 7GU 10 O6 ? ? A DC 3 B 7GU 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B 7GU 10 N2 ? ? A DC 3 B 7GU 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A 7GU 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A 7GU 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A 7GU 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A 7GU 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A 7GU 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A 7GU 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 2QEG _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 2QEG _atom_sites.fract_transf_matrix[1][1] 0.041348 _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] 0.024797 _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] 0.015224 _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 N 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 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 7GU 10 10 10 7GU 7DG A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 1 13 DC C B . n B 1 2 DG 2 2 14 DG G B . n B 1 3 DC 3 3 15 DC C B . n B 1 4 DG 4 4 16 DG G B . n B 1 5 DA 5 5 17 DA A B . n B 1 6 DA 6 6 18 DA A B . n B 1 7 DT 7 7 19 DT T B . n B 1 8 DT 8 8 20 DT T B . n B 1 9 DC 9 9 21 DC C B . n B 1 10 7GU 10 10 22 7GU 7DG B . n B 1 11 DC 11 11 23 DC C B . n B 1 12 DG 12 12 24 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 HOH 1 13 101 HOH HOH A . C 2 HOH 2 14 104 HOH HOH A . C 2 HOH 3 15 112 HOH HOH A . C 2 HOH 4 16 113 HOH HOH A . C 2 HOH 5 17 114 HOH HOH A . C 2 HOH 6 18 115 HOH HOH A . C 2 HOH 7 19 119 HOH HOH A . C 2 HOH 8 20 120 HOH HOH A . C 2 HOH 9 21 122 HOH HOH A . C 2 HOH 10 22 123 HOH HOH A . C 2 HOH 11 23 125 HOH HOH A . C 2 HOH 12 24 126 HOH HOH A . C 2 HOH 13 25 131 HOH HOH A . C 2 HOH 14 26 133 HOH HOH A . C 2 HOH 15 27 134 HOH HOH A . C 2 HOH 16 28 136 HOH HOH A . C 2 HOH 17 29 137 HOH HOH A . C 2 HOH 18 30 138 HOH HOH A . C 2 HOH 19 31 139 HOH HOH A . C 2 HOH 20 32 140 HOH HOH A . C 2 HOH 21 33 142 HOH HOH A . C 2 HOH 22 34 143 HOH HOH A . C 2 HOH 23 35 146 HOH HOH A . C 2 HOH 24 36 152 HOH HOH A . C 2 HOH 25 37 159 HOH HOH A . C 2 HOH 26 38 160 HOH HOH A . C 2 HOH 27 39 171 HOH HOH A . C 2 HOH 28 40 175 HOH HOH A . C 2 HOH 29 41 176 HOH HOH A . C 2 HOH 30 42 177 HOH HOH A . C 2 HOH 31 43 178 HOH HOH A . C 2 HOH 32 44 179 HOH HOH A . C 2 HOH 33 45 180 HOH HOH A . C 2 HOH 34 46 181 HOH HOH A . C 2 HOH 35 47 182 HOH HOH A . C 2 HOH 36 48 183 HOH HOH A . C 2 HOH 37 49 186 HOH HOH A . C 2 HOH 38 50 187 HOH HOH A . C 2 HOH 39 51 188 HOH HOH A . C 2 HOH 40 52 190 HOH HOH A . C 2 HOH 41 53 193 HOH HOH A . C 2 HOH 42 54 194 HOH HOH A . C 2 HOH 43 55 195 HOH HOH A . C 2 HOH 44 56 197 HOH HOH A . C 2 HOH 45 57 198 HOH HOH A . C 2 HOH 46 58 201 HOH HOH A . C 2 HOH 47 59 202 HOH HOH A . C 2 HOH 48 60 206 HOH HOH A . C 2 HOH 49 61 211 HOH HOH A . C 2 HOH 50 62 212 HOH HOH A . C 2 HOH 51 63 213 HOH HOH A . C 2 HOH 52 64 214 HOH HOH A . C 2 HOH 53 65 215 HOH HOH A . C 2 HOH 54 66 218 HOH HOH A . C 2 HOH 55 67 219 HOH HOH A . C 2 HOH 56 68 210 HOH HOH A . C 2 HOH 57 69 222 HOH HOH A . C 2 HOH 58 70 227 HOH HOH A . D 2 HOH 1 13 102 HOH HOH B . D 2 HOH 2 14 103 HOH HOH B . D 2 HOH 3 15 105 HOH HOH B . D 2 HOH 4 16 107 HOH HOH B . D 2 HOH 5 17 109 HOH HOH B . D 2 HOH 6 18 110 HOH HOH B . D 2 HOH 7 19 111 HOH HOH B . D 2 HOH 8 20 116 HOH HOH B . D 2 HOH 9 21 117 HOH HOH B . D 2 HOH 10 22 118 HOH HOH B . D 2 HOH 11 23 121 HOH HOH B . D 2 HOH 12 24 124 HOH HOH B . D 2 HOH 13 25 127 HOH HOH B . D 2 HOH 14 26 128 HOH HOH B . D 2 HOH 15 27 129 HOH HOH B . D 2 HOH 16 28 130 HOH HOH B . D 2 HOH 17 29 144 HOH HOH B . D 2 HOH 18 30 147 HOH HOH B . D 2 HOH 19 31 148 HOH HOH B . D 2 HOH 20 32 149 HOH HOH B . D 2 HOH 21 33 150 HOH HOH B . D 2 HOH 22 34 153 HOH HOH B . D 2 HOH 23 35 154 HOH HOH B . D 2 HOH 24 36 156 HOH HOH B . D 2 HOH 25 37 157 HOH HOH B . D 2 HOH 26 38 158 HOH HOH B . D 2 HOH 27 39 161 HOH HOH B . D 2 HOH 28 40 162 HOH HOH B . D 2 HOH 29 41 165 HOH HOH B . D 2 HOH 30 42 166 HOH HOH B . D 2 HOH 31 43 167 HOH HOH B . D 2 HOH 32 44 168 HOH HOH B . D 2 HOH 33 45 169 HOH HOH B . D 2 HOH 34 46 170 HOH HOH B . D 2 HOH 35 47 174 HOH HOH B . D 2 HOH 36 48 184 HOH HOH B . D 2 HOH 37 49 185 HOH HOH B . D 2 HOH 38 50 189 HOH HOH B . D 2 HOH 39 51 191 HOH HOH B . D 2 HOH 40 52 192 HOH HOH B . D 2 HOH 41 53 199 HOH HOH B . D 2 HOH 42 54 203 HOH HOH B . D 2 HOH 43 55 204 HOH HOH B . D 2 HOH 44 56 205 HOH HOH B . D 2 HOH 45 57 216 HOH HOH B . D 2 HOH 46 58 217 HOH HOH B . D 2 HOH 47 59 221 HOH HOH B . D 2 HOH 48 60 224 HOH HOH B . D 2 HOH 49 61 226 HOH HOH B . D 2 HOH 50 62 228 HOH HOH B . D 2 HOH 51 63 229 HOH HOH B . D 2 HOH 52 64 231 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 7GU 10 A 7GU 10 ? DG ? 2 B 7GU 10 B 7GU 10 ? DG ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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)' 2370 ? 1 MORE 7.5 ? 1 'SSA (A^2)' 4250 ? # _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 # 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 2008-05-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-08-30 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 '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' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn # 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_conn.pdbx_leaving_atom_flag' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 21.7550 _pdbx_refine_tls.origin_y 39.5050 _pdbx_refine_tls.origin_z 41.3730 _pdbx_refine_tls.T[1][1] 0.0174 _pdbx_refine_tls.T[2][2] -0.0409 _pdbx_refine_tls.T[3][3] -0.0095 _pdbx_refine_tls.T[1][2] -0.0145 _pdbx_refine_tls.T[1][3] -0.0122 _pdbx_refine_tls.T[2][3] 0.0068 _pdbx_refine_tls.L[1][1] 0.9331 _pdbx_refine_tls.L[2][2] 0.3362 _pdbx_refine_tls.L[3][3] 6.6049 _pdbx_refine_tls.L[1][2] -0.2709 _pdbx_refine_tls.L[1][3] -0.5480 _pdbx_refine_tls.L[2][3] -1.0341 _pdbx_refine_tls.S[1][1] 0.1614 _pdbx_refine_tls.S[1][2] -0.0850 _pdbx_refine_tls.S[1][3] -0.0026 _pdbx_refine_tls.S[2][1] -0.0428 _pdbx_refine_tls.S[2][2] 0.1041 _pdbx_refine_tls.S[2][3] 0.0652 _pdbx_refine_tls.S[3][1] 0.0282 _pdbx_refine_tls.S[3][2] 0.0129 _pdbx_refine_tls.S[3][3] -0.2655 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 A 1 A 1 A 12 A 12 ? 'X-RAY DIFFRACTION' ? 2 1 B 1 B 1 B 12 B 12 ? 'X-RAY DIFFRACTION' ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 HKL-2000 'data collection' . ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 EPMR phasing . ? 5 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 DC _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 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 DC _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 DC _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 112.03 _pdbx_validate_rmsd_angle.angle_target_value 108.30 _pdbx_validate_rmsd_angle.angle_deviation 3.73 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.30 _pdbx_validate_rmsd_angle.linker_flag N # 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 7GU P P N N 1 7GU OP1 O N N 2 7GU OP2 O N N 3 7GU "O5'" O N N 4 7GU N9 N Y N 5 7GU C4 C Y N 6 7GU N3 N N N 7 7GU C2 C N N 8 7GU N2 N N N 9 7GU N1 N N N 10 7GU C6 C N N 11 7GU O6 O N N 12 7GU C5 C Y N 13 7GU C7 C Y N 14 7GU C8 C Y N 15 7GU "C2'" C N N 16 7GU "C5'" C N N 17 7GU "C4'" C N R 18 7GU "O4'" O N N 19 7GU "C1'" C N R 20 7GU "C3'" C N S 21 7GU "O3'" O N N 22 7GU OP3 O N N 23 7GU HOP2 H N N 24 7GU HN21 H N N 25 7GU HN22 H N N 26 7GU HN1 H N N 27 7GU H7 H N N 28 7GU H8 H N N 29 7GU "H2'" H N N 30 7GU "H2''" H N N 31 7GU "H5'" H N N 32 7GU "H5''" H N N 33 7GU "H4'" H N N 34 7GU "H1'" H N N 35 7GU "H3'" H N N 36 7GU "HO3'" H N N 37 7GU HOP3 H N N 38 DA OP3 O N N 39 DA P P N N 40 DA OP1 O N N 41 DA OP2 O N N 42 DA "O5'" O N N 43 DA "C5'" C N N 44 DA "C4'" C N R 45 DA "O4'" O N N 46 DA "C3'" C N S 47 DA "O3'" O N N 48 DA "C2'" C N N 49 DA "C1'" C N R 50 DA N9 N Y N 51 DA C8 C Y N 52 DA N7 N Y N 53 DA C5 C Y N 54 DA C6 C Y N 55 DA N6 N N N 56 DA N1 N Y N 57 DA C2 C Y N 58 DA N3 N Y N 59 DA C4 C Y N 60 DA HOP3 H N N 61 DA HOP2 H N N 62 DA "H5'" H N N 63 DA "H5''" H N N 64 DA "H4'" H N N 65 DA "H3'" H N N 66 DA "HO3'" H N N 67 DA "H2'" H N N 68 DA "H2''" H N N 69 DA "H1'" H N N 70 DA H8 H N N 71 DA H61 H N N 72 DA H62 H N N 73 DA H2 H N N 74 DC OP3 O N N 75 DC P P N N 76 DC OP1 O N N 77 DC OP2 O N N 78 DC "O5'" O N N 79 DC "C5'" C N N 80 DC "C4'" C N R 81 DC "O4'" O N N 82 DC "C3'" C N S 83 DC "O3'" O N N 84 DC "C2'" C N N 85 DC "C1'" C N R 86 DC N1 N N N 87 DC C2 C N N 88 DC O2 O N N 89 DC N3 N N N 90 DC C4 C N N 91 DC N4 N N N 92 DC C5 C N N 93 DC C6 C N N 94 DC HOP3 H N N 95 DC HOP2 H N N 96 DC "H5'" H N N 97 DC "H5''" H N N 98 DC "H4'" H N N 99 DC "H3'" H N N 100 DC "HO3'" H N N 101 DC "H2'" H N N 102 DC "H2''" H N N 103 DC "H1'" H N N 104 DC H41 H N N 105 DC H42 H N N 106 DC H5 H N N 107 DC H6 H N N 108 DG OP3 O N N 109 DG P P N N 110 DG OP1 O N N 111 DG OP2 O N N 112 DG "O5'" O N N 113 DG "C5'" C N N 114 DG "C4'" C N R 115 DG "O4'" O N N 116 DG "C3'" C N S 117 DG "O3'" O N N 118 DG "C2'" C N N 119 DG "C1'" C N R 120 DG N9 N Y N 121 DG C8 C Y N 122 DG N7 N Y N 123 DG C5 C Y N 124 DG C6 C N N 125 DG O6 O N N 126 DG N1 N N N 127 DG C2 C N N 128 DG N2 N N N 129 DG N3 N N N 130 DG C4 C Y N 131 DG HOP3 H N N 132 DG HOP2 H N N 133 DG "H5'" H N N 134 DG "H5''" H N N 135 DG "H4'" H N N 136 DG "H3'" H N N 137 DG "HO3'" H N N 138 DG "H2'" H N N 139 DG "H2''" H N N 140 DG "H1'" H N N 141 DG H8 H N N 142 DG H1 H N N 143 DG H21 H N N 144 DG H22 H N N 145 DT OP3 O N N 146 DT P P N N 147 DT OP1 O N N 148 DT OP2 O N N 149 DT "O5'" O N N 150 DT "C5'" C N N 151 DT "C4'" C N R 152 DT "O4'" O N N 153 DT "C3'" C N S 154 DT "O3'" O N N 155 DT "C2'" C N N 156 DT "C1'" C N R 157 DT N1 N N N 158 DT C2 C N N 159 DT O2 O N N 160 DT N3 N N N 161 DT C4 C N N 162 DT O4 O N N 163 DT C5 C N N 164 DT C7 C N N 165 DT C6 C N N 166 DT HOP3 H N N 167 DT HOP2 H N N 168 DT "H5'" H N N 169 DT "H5''" H N N 170 DT "H4'" H N N 171 DT "H3'" H N N 172 DT "HO3'" H N N 173 DT "H2'" H N N 174 DT "H2''" H N N 175 DT "H1'" H N N 176 DT H3 H N N 177 DT H71 H N N 178 DT H72 H N N 179 DT H73 H N N 180 DT H6 H N N 181 HOH O O N N 182 HOH H1 H N N 183 HOH H2 H N N 184 # 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 7GU P OP1 doub N N 1 7GU P OP2 sing N N 2 7GU P "O5'" sing N N 3 7GU P OP3 sing N N 4 7GU OP2 HOP2 sing N N 5 7GU "O5'" "C5'" sing N N 6 7GU N9 C4 sing Y N 7 7GU N9 C8 sing Y N 8 7GU N9 "C1'" sing N N 9 7GU C4 N3 sing N N 10 7GU C4 C5 doub Y N 11 7GU N3 C2 doub N N 12 7GU C2 N2 sing N N 13 7GU C2 N1 sing N N 14 7GU N2 HN21 sing N N 15 7GU N2 HN22 sing N N 16 7GU N1 C6 sing N N 17 7GU N1 HN1 sing N N 18 7GU C6 O6 doub N N 19 7GU C6 C5 sing N N 20 7GU C5 C7 sing Y N 21 7GU C7 C8 doub Y N 22 7GU C7 H7 sing N N 23 7GU C8 H8 sing N N 24 7GU "C2'" "C1'" sing N N 25 7GU "C2'" "C3'" sing N N 26 7GU "C2'" "H2'" sing N N 27 7GU "C2'" "H2''" sing N N 28 7GU "C5'" "C4'" sing N N 29 7GU "C5'" "H5'" sing N N 30 7GU "C5'" "H5''" sing N N 31 7GU "C4'" "O4'" sing N N 32 7GU "C4'" "C3'" sing N N 33 7GU "C4'" "H4'" sing N N 34 7GU "O4'" "C1'" sing N N 35 7GU "C1'" "H1'" sing N N 36 7GU "C3'" "O3'" sing N N 37 7GU "C3'" "H3'" sing N N 38 7GU "O3'" "HO3'" sing N N 39 7GU OP3 HOP3 sing N N 40 DA OP3 P sing N N 41 DA OP3 HOP3 sing N N 42 DA P OP1 doub N N 43 DA P OP2 sing N N 44 DA P "O5'" sing N N 45 DA OP2 HOP2 sing N N 46 DA "O5'" "C5'" sing N N 47 DA "C5'" "C4'" sing N N 48 DA "C5'" "H5'" sing N N 49 DA "C5'" "H5''" sing N N 50 DA "C4'" "O4'" sing N N 51 DA "C4'" "C3'" sing N N 52 DA "C4'" "H4'" sing N N 53 DA "O4'" "C1'" sing N N 54 DA "C3'" "O3'" sing N N 55 DA "C3'" "C2'" sing N N 56 DA "C3'" "H3'" sing N N 57 DA "O3'" "HO3'" sing N N 58 DA "C2'" "C1'" sing N N 59 DA "C2'" "H2'" sing N N 60 DA "C2'" "H2''" sing N N 61 DA "C1'" N9 sing N N 62 DA "C1'" "H1'" sing N N 63 DA N9 C8 sing Y N 64 DA N9 C4 sing Y N 65 DA C8 N7 doub Y N 66 DA C8 H8 sing N N 67 DA N7 C5 sing Y N 68 DA C5 C6 sing Y N 69 DA C5 C4 doub Y N 70 DA C6 N6 sing N N 71 DA C6 N1 doub Y N 72 DA N6 H61 sing N N 73 DA N6 H62 sing N N 74 DA N1 C2 sing Y N 75 DA C2 N3 doub Y N 76 DA C2 H2 sing N N 77 DA N3 C4 sing Y N 78 DC OP3 P sing N N 79 DC OP3 HOP3 sing N N 80 DC P OP1 doub N N 81 DC P OP2 sing N N 82 DC P "O5'" sing N N 83 DC OP2 HOP2 sing N N 84 DC "O5'" "C5'" sing N N 85 DC "C5'" "C4'" sing N N 86 DC "C5'" "H5'" sing N N 87 DC "C5'" "H5''" sing N N 88 DC "C4'" "O4'" sing N N 89 DC "C4'" "C3'" sing N N 90 DC "C4'" "H4'" sing N N 91 DC "O4'" "C1'" sing N N 92 DC "C3'" "O3'" sing N N 93 DC "C3'" "C2'" sing N N 94 DC "C3'" "H3'" sing N N 95 DC "O3'" "HO3'" sing N N 96 DC "C2'" "C1'" sing N N 97 DC "C2'" "H2'" sing N N 98 DC "C2'" "H2''" sing N N 99 DC "C1'" N1 sing N N 100 DC "C1'" "H1'" sing N N 101 DC N1 C2 sing N N 102 DC N1 C6 sing N N 103 DC C2 O2 doub N N 104 DC C2 N3 sing N N 105 DC N3 C4 doub N N 106 DC C4 N4 sing N N 107 DC C4 C5 sing N N 108 DC N4 H41 sing N N 109 DC N4 H42 sing N N 110 DC C5 C6 doub N N 111 DC C5 H5 sing N N 112 DC C6 H6 sing N N 113 DG OP3 P sing N N 114 DG OP3 HOP3 sing N N 115 DG P OP1 doub N N 116 DG P OP2 sing N N 117 DG P "O5'" sing N N 118 DG OP2 HOP2 sing N N 119 DG "O5'" "C5'" sing N N 120 DG "C5'" "C4'" sing N N 121 DG "C5'" "H5'" sing N N 122 DG "C5'" "H5''" sing N N 123 DG "C4'" "O4'" sing N N 124 DG "C4'" "C3'" sing N N 125 DG "C4'" "H4'" sing N N 126 DG "O4'" "C1'" sing N N 127 DG "C3'" "O3'" sing N N 128 DG "C3'" "C2'" sing N N 129 DG "C3'" "H3'" sing N N 130 DG "O3'" "HO3'" sing N N 131 DG "C2'" "C1'" sing N N 132 DG "C2'" "H2'" sing N N 133 DG "C2'" "H2''" sing N N 134 DG "C1'" N9 sing N N 135 DG "C1'" "H1'" sing N N 136 DG N9 C8 sing Y N 137 DG N9 C4 sing Y N 138 DG C8 N7 doub Y N 139 DG C8 H8 sing N N 140 DG N7 C5 sing Y N 141 DG C5 C6 sing N N 142 DG C5 C4 doub Y N 143 DG C6 O6 doub N N 144 DG C6 N1 sing N N 145 DG N1 C2 sing N N 146 DG N1 H1 sing N N 147 DG C2 N2 sing N N 148 DG C2 N3 doub N N 149 DG N2 H21 sing N N 150 DG N2 H22 sing N N 151 DG N3 C4 sing N N 152 DT OP3 P sing N N 153 DT OP3 HOP3 sing N N 154 DT P OP1 doub N N 155 DT P OP2 sing N N 156 DT P "O5'" sing N N 157 DT OP2 HOP2 sing N N 158 DT "O5'" "C5'" sing N N 159 DT "C5'" "C4'" sing N N 160 DT "C5'" "H5'" sing N N 161 DT "C5'" "H5''" sing N N 162 DT "C4'" "O4'" sing N N 163 DT "C4'" "C3'" sing N N 164 DT "C4'" "H4'" sing N N 165 DT "O4'" "C1'" sing N N 166 DT "C3'" "O3'" sing N N 167 DT "C3'" "C2'" sing N N 168 DT "C3'" "H3'" sing N N 169 DT "O3'" "HO3'" sing N N 170 DT "C2'" "C1'" sing N N 171 DT "C2'" "H2'" sing N N 172 DT "C2'" "H2''" sing N N 173 DT "C1'" N1 sing N N 174 DT "C1'" "H1'" sing N N 175 DT N1 C2 sing N N 176 DT N1 C6 sing N N 177 DT C2 O2 doub N N 178 DT C2 N3 sing N N 179 DT N3 C4 sing N N 180 DT N3 H3 sing N N 181 DT C4 O4 doub N N 182 DT C4 C5 sing N N 183 DT C5 C7 sing N N 184 DT C5 C6 doub N N 185 DT C7 H71 sing N N 186 DT C7 H72 sing N N 187 DT C7 H73 sing N N 188 DT C6 H6 sing N N 189 HOH O H1 sing N N 190 HOH O H2 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2QEG 'double helix' 2QEG '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 12 1_555 0.309 -0.265 -0.234 4.682 1.589 -2.401 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.232 -0.141 0.188 -3.645 -9.000 -3.644 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DC 3 1_555 B 7GU 10 1_555 0.179 -0.122 0.155 0.089 -5.987 1.210 3 A_DC3:7GU10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.242 -0.082 0.040 12.728 -9.053 0.851 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.068 -0.105 -0.050 2.882 -15.362 3.829 5 A_DA5:DT8_B A 5 ? B 8 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.085 -0.075 0.064 1.268 -16.066 3.404 6 A_DA6:DT7_B A 6 ? B 7 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.073 -0.108 0.097 -0.943 -15.853 4.112 7 A_DT7:DA6_B A 7 ? B 6 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.120 -0.167 -0.009 -1.132 -12.434 4.448 8 A_DT8:DA5_B A 8 ? B 5 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.236 -0.148 0.067 -11.090 -9.568 0.320 9 A_DC9:DG4_B A 9 ? B 4 ? 19 1 1 A 7GU 10 1_555 B DC 3 1_555 -0.098 -0.141 0.306 4.960 -6.950 1.766 10 A_7GU10:DC3_B A 10 ? B 3 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.032 -0.142 0.163 0.336 -11.952 -2.818 11 A_DC11:DG2_B A 11 ? B 2 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.120 -0.141 0.735 17.586 -11.955 -4.091 12 A_DG12:DC1_B A 12 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -1.114 -0.291 3.665 -5.346 -7.037 33.104 0.789 0.917 3.775 -12.085 9.180 34.231 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B 7GU 10 1_555 1.035 0.165 3.261 2.485 -1.529 40.864 0.403 -1.207 3.308 -2.186 -3.554 40.964 2 AA_DG2DC3:7GU10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B 7GU 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.483 0.700 3.105 2.694 6.643 27.060 -0.078 1.618 3.123 13.891 -5.633 27.976 3 AA_DC3DG4:DC97GU10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 0.111 -0.174 3.455 0.493 0.305 40.589 -0.286 -0.102 3.455 0.440 -0.710 40.593 4 AA_DG4DA5:DT8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.053 -0.298 3.218 -1.939 -1.705 36.467 -0.243 -0.179 3.227 -2.720 3.093 36.555 5 AA_DA5DA6:DT7DT8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.069 -0.526 3.259 -0.049 -2.328 32.108 -0.532 -0.134 3.288 -4.202 0.088 32.190 6 AA_DA6DT7:DA6DT7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.047 -0.336 3.174 0.697 -1.670 34.377 -0.314 0.186 3.184 -2.824 -1.178 34.423 7 AA_DT7DT8:DA5DA6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 -0.108 -0.158 3.443 0.427 -1.261 43.322 -0.084 0.190 3.445 -1.708 -0.578 43.341 8 AA_DT8DC9:DG4DA5_BB A 8 ? B 5 ? A 9 ? B 4 ? 1 A DC 9 1_555 B DG 4 1_555 A 7GU 10 1_555 B DC 3 1_555 0.589 0.617 3.009 -3.024 2.892 26.881 0.643 -1.951 2.975 6.174 6.455 27.199 9 AA_DC97GU10:DC3DG4_BB A 9 ? B 4 ? A 10 ? B 3 ? 1 A 7GU 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.540 0.577 3.422 -1.954 -6.908 42.876 1.478 1.883 3.358 -9.372 2.650 43.445 10 AA_7GU10DC11:DG2DC3_BB A 10 ? B 3 ? A 11 ? B 2 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 0.886 0.387 2.984 -3.891 0.507 32.704 0.606 -2.158 2.868 0.896 6.878 32.933 11 AA_DC11DG12:DC1DG2_BB A 11 ? B 2 ? A 12 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 355D _pdbx_initial_refinement_model.details ? #