data_3D0M # _entry.id 3D0M # _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 3D0M pdb_00003d0m 10.2210/pdb3d0m/pdb NDB AR0099 ? ? RCSB RCSB047441 ? ? WWPDB D_1000047441 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3CZW _pdbx_database_related.details 'The same molecule in different crystal form' _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3D0M _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-05-02 _pdbx_database_status.SG_entry N _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Rypniewski, W.' 1 'Adamiak, D.A.' 2 'Milecki, J.' 3 'Adamiak, R.W.' 4 # _citation.id primary _citation.title 'Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.' _citation.journal_abbrev Rna _citation.journal_volume 14 _citation.page_first 1845 _citation.page_last 1851 _citation.year 2008 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18658118 _citation.pdbx_database_id_DOI 10.1261/rna.1164308 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Rypniewski, W.' 1 ? primary 'Adamiak, D.A.' 2 ? primary 'Milecki, J.' 3 ? primary 'Adamiak, R.W.' 4 ? # _cell.entry_id 3D0M _cell.length_a 46.653 _cell.length_b 46.653 _cell.length_c 126.397 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _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 3D0M _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 155 _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 ;RNA (5'-R(*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3') ; 5170.103 1 ? ? 'duplex formed by the shorter strands of hammerhead ribozyme' ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 water nat water 18.015 19 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GUGGUCUGAUGAGGCC _entity_poly.pdbx_seq_one_letter_code_can GUGGUCUGAUGAGGCC _entity_poly.pdbx_strand_id X _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 G n 1 2 U n 1 3 G n 1 4 G n 1 5 U n 1 6 C n 1 7 U n 1 8 G n 1 9 A n 1 10 U n 1 11 G n 1 12 A n 1 13 G n 1 14 G n 1 15 C n 1 16 C n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3D0M _struct_ref.pdbx_db_accession 3D0M _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3D0M _struct_ref_seq.pdbx_strand_id X _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 16 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3D0M _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 16 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 16 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 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 HOH non-polymer . WATER ? 'H2 O' 18.015 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 3D0M _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.56 _exptl_crystal.density_percent_sol 51.95 _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 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '1.7 M ammonium sulphate, 50 mM cacodylate buffer, 15 mM magnesium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K' # 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.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 '(NH4)2SO4' ? ? ? 1 2 1 'magnesium acetate' ? ? ? 1 3 1 cacodylate ? ? ? 1 4 2 '(NH4)2SO4' ? ? ? 1 5 2 'magnesium acetate' ? ? ? # _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 2004-01-26 _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 'Si 111' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8020 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X13' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X13 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.8020 # _reflns.entry_id 3D0M _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 2.00 _reflns.number_obs 3434 _reflns.number_all 3434 _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.055 _reflns.pdbx_netI_over_sigmaI 37 _reflns.B_iso_Wilson_estimate 29.00 _reflns.pdbx_redundancy 10.6 _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 2.00 _reflns_shell.d_res_low 2.03 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.463 _reflns_shell.meanI_over_sigI_obs 4.7 _reflns_shell.pdbx_redundancy 8.4 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3D0M _refine.ls_number_reflns_obs 3372 _refine.ls_number_reflns_all 3433 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 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 20.00 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 100.00 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.295 _refine.ls_R_factor_R_free 0.361 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 1.8 _refine.ls_number_reflns_R_free 61 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.947 _refine.correlation_coeff_Fo_to_Fc_free 0.888 _refine.B_iso_mean 60.988 _refine.aniso_B[1][1] 2.93 _refine.aniso_B[2][2] 2.93 _refine.aniso_B[3][3] -4.40 _refine.aniso_B[1][2] 1.47 _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 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'another crystal form (pdb id 3czw)' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model isotropic _refine.pdbx_stereochemistry_target_values 'ENGH & HUBER' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.262 _refine.pdbx_overall_ESU_R_Free 0.248 _refine.overall_SU_ML 0.352 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 18.108 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3D0M _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs 0.262 _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free 0.248 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 341 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 19 _refine_hist.number_atoms_total 365 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 20.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.020 0.021 ? 385 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.978 3.000 ? 600 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.186 0.200 ? 79 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.012 0.020 ? 169 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.231 0.200 ? 119 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.313 0.200 ? 222 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.197 0.200 ? 9 '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 0.239 0.200 ? 37 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.166 0.200 ? 13 '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 2.524 3.000 ? 560 'X-RAY DIFFRACTION' ? r_scangle_it 4.149 4.500 ? 600 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.033 _refine_ls_shell.d_res_low 2.085 _refine_ls_shell.number_reflns_R_work 249 _refine_ls_shell.R_factor_R_work 0.466 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.379 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 4 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3D0M _struct.title 'X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3D0M _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, duplex, base pairing, G(syn) - G(anti), sulphate anion' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_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 hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 16 O2 ? ? X G 3 X C 16 16_545 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog2 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 15 N3 ? ? X G 4 X C 15 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 15 O2 ? ? X G 4 X C 15 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 15 N4 ? ? X G 4 X C 15 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 5 N3 ? ? ? 1_555 A G 14 O6 ? ? X U 5 X G 14 16_545 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A U 5 O2 ? ? ? 1_555 A G 14 N1 ? ? X U 5 X G 14 16_545 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog7 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 13 N1 ? ? X C 6 X G 13 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 13 O6 ? ? X C 6 X G 13 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 13 N2 ? ? X C 6 X G 13 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 12 N1 ? ? X U 7 X A 12 16_545 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog11 hydrog ? ? A G 8 N7 ? ? ? 1_555 A G 11 N2 ? ? X G 8 X G 11 16_545 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A G 8 O6 ? ? ? 1_555 A G 11 N1 ? ? X G 8 X G 11 16_545 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A A 9 N1 ? ? ? 1_555 A U 10 N3 ? ? X A 9 X U 10 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 9 N6 ? ? ? 1_555 A U 10 O4 ? ? X A 9 X U 10 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 9 N1 ? ? X U 10 X A 9 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 10 O4 ? ? ? 1_555 A A 9 N6 ? ? X U 10 X A 9 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 11 N1 ? ? ? 1_555 A G 8 O6 ? ? X G 11 X G 8 16_545 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A G 11 N2 ? ? ? 1_555 A G 8 N7 ? ? X G 11 X G 8 16_545 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A A 12 N1 ? ? ? 1_555 A U 7 N3 ? ? X A 12 X U 7 16_545 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog20 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 6 N3 ? ? X G 13 X C 6 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 6 O2 ? ? X G 13 X C 6 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 6 N4 ? ? X G 13 X C 6 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 14 N1 ? ? ? 1_555 A U 5 O2 ? ? X G 14 X U 5 16_545 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A G 14 O6 ? ? ? 1_555 A U 5 N3 ? ? X G 14 X U 5 16_545 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog25 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 4 N1 ? ? X C 15 X G 4 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 4 O6 ? ? X C 15 X G 4 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 4 N2 ? ? X C 15 X G 4 16_545 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 3 N1 ? ? X C 16 X G 3 16_545 ? ? ? ? ? ? 'C-G PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 3D0M _atom_sites.fract_transf_matrix[1][1] 0.021435 _atom_sites.fract_transf_matrix[1][2] 0.012375 _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] 0.024751 _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] 0.007912 _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 S # 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 G 1 1 1 G G X . n A 1 2 U 2 2 2 U U X . n A 1 3 G 3 3 3 G G X . n A 1 4 G 4 4 4 G G X . n A 1 5 U 5 5 5 U U X . n A 1 6 C 6 6 6 C C X . n A 1 7 U 7 7 7 U U X . n A 1 8 G 8 8 8 G G X . n A 1 9 A 9 9 9 A A X . n A 1 10 U 10 10 10 U U X . n A 1 11 G 11 11 11 G G X . n A 1 12 A 12 12 12 A A X . n A 1 13 G 13 13 13 G G X . n A 1 14 G 14 14 14 G G X . n A 1 15 C 15 15 15 C C X . n A 1 16 C 16 16 16 C C X . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SO4 1 501 501 SO4 SO4 X . C 3 HOH 1 502 1 HOH HOH X . C 3 HOH 2 503 2 HOH HOH X . C 3 HOH 3 504 3 HOH HOH X . C 3 HOH 4 505 4 HOH HOH X . C 3 HOH 5 506 5 HOH HOH X . C 3 HOH 6 507 6 HOH HOH X . C 3 HOH 7 508 7 HOH HOH X . C 3 HOH 8 509 8 HOH HOH X . C 3 HOH 9 510 9 HOH HOH X . C 3 HOH 10 511 10 HOH HOH X . C 3 HOH 11 512 11 HOH HOH X . C 3 HOH 12 513 12 HOH HOH X . C 3 HOH 13 514 13 HOH HOH X . C 3 HOH 14 515 14 HOH HOH X . C 3 HOH 15 516 15 HOH HOH X . C 3 HOH 16 517 16 HOH HOH X . C 3 HOH 17 518 17 HOH HOH X . C 3 HOH 18 519 19 HOH HOH X . C 3 HOH 19 520 20 HOH HOH X . # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # 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)' 1810 ? 1 MORE -44 ? 1 'SSA (A^2)' 6010 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 16_545 y+1/3,x-1/3,-z+2/3 -0.5000000000 0.8660254038 0.0000000000 23.3265000000 0.8660254038 0.5000000000 0.0000000000 -13.4675610543 0.0000000000 0.0000000000 -1.0000000000 84.2646666667 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 X SO4 501 ? B SO4 . 2 1 X HOH 504 ? C HOH . 3 1 X HOH 505 ? C HOH . 4 1 X HOH 516 ? C HOH . 5 1 X HOH 518 ? C 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 2008-09-09 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 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' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 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' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' diffrn_source 6 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' '_software.name' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345 'data collection' CCD ? 1 MOLREP phasing . ? 2 REFMAC refinement 5.1 ? 3 DENZO 'data reduction' . ? 4 SCALEPACK 'data scaling' . ? 5 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C2 X G 1 ? ? N3 X G 1 ? ? 1.377 1.323 0.054 0.008 N 2 1 "C2'" X C 6 ? ? "C1'" X C 6 ? ? 1.452 1.526 -0.074 0.008 N 3 1 C5 X G 13 ? ? N7 X G 13 ? ? 1.427 1.388 0.039 0.006 N 4 1 C5 X G 14 ? ? N7 X G 14 ? ? 1.425 1.388 0.037 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" X G 1 ? ? "C4'" X G 1 ? ? "C3'" X G 1 ? ? 92.54 104.00 -11.46 1.00 N 2 1 "C5'" X G 1 ? ? "C4'" X G 1 ? ? "O4'" X G 1 ? ? 96.67 109.10 -12.43 1.20 N 3 1 "C4'" X G 1 ? ? "C3'" X G 1 ? ? "C2'" X G 1 ? ? 110.59 102.60 7.99 1.00 N 4 1 "C3'" X G 1 ? ? "C2'" X G 1 ? ? "C1'" X G 1 ? ? 92.77 101.30 -8.53 0.70 N 5 1 N1 X G 1 ? ? C2 X G 1 ? ? N3 X G 1 ? ? 120.21 123.90 -3.69 0.60 N 6 1 C2 X G 1 ? ? N3 X G 1 ? ? C4 X G 1 ? ? 115.18 111.90 3.28 0.50 N 7 1 "O4'" X U 2 ? ? "C4'" X U 2 ? ? "C3'" X U 2 ? ? 93.98 104.00 -10.02 1.00 N 8 1 "C1'" X U 2 ? ? "O4'" X U 2 ? ? "C4'" X U 2 ? ? 114.96 109.90 5.06 0.80 N 9 1 "C4'" X U 2 ? ? "C3'" X U 2 ? ? "C2'" X U 2 ? ? 108.67 102.60 6.07 1.00 N 10 1 "C3'" X U 2 ? ? "C2'" X U 2 ? ? "C1'" X U 2 ? ? 96.63 101.30 -4.67 0.70 N 11 1 C6 X U 2 ? ? N1 X U 2 ? ? C2 X U 2 ? ? 124.83 121.00 3.83 0.60 N 12 1 C5 X U 2 ? ? C4 X U 2 ? ? O4 X U 2 ? ? 121.60 125.90 -4.30 0.60 N 13 1 "O4'" X G 3 ? ? "C4'" X G 3 ? ? "C3'" X G 3 ? ? 97.30 104.00 -6.70 1.00 N 14 1 "C4'" X G 3 ? ? "C3'" X G 3 ? ? "C2'" X G 3 ? ? 95.38 102.60 -7.22 1.00 N 15 1 "C3'" X G 3 ? ? "C2'" X G 3 ? ? "C1'" X G 3 ? ? 95.03 101.30 -6.27 0.70 N 16 1 "O4'" X G 3 ? ? "C1'" X G 3 ? ? N9 X G 3 ? ? 100.73 108.20 -7.47 0.80 N 17 1 N1 X G 4 ? ? C6 X G 4 ? ? O6 X G 4 ? ? 115.47 119.90 -4.43 0.60 N 18 1 C5 X G 4 ? ? C6 X G 4 ? ? O6 X G 4 ? ? 132.90 128.60 4.30 0.60 N 19 1 "C3'" X U 5 ? ? "C2'" X U 5 ? ? "C1'" X U 5 ? ? 97.00 101.30 -4.30 0.70 N 20 1 C4 X U 5 ? ? C5 X U 5 ? ? C6 X U 5 ? ? 115.33 119.70 -4.37 0.60 N 21 1 "O4'" X C 6 ? ? "C4'" X C 6 ? ? "C3'" X C 6 ? ? 97.35 104.00 -6.65 1.00 N 22 1 "C3'" X C 6 ? ? "C2'" X C 6 ? ? "C1'" X C 6 ? ? 93.49 101.30 -7.81 0.70 N 23 1 C6 X C 6 ? ? N1 X C 6 ? ? C2 X C 6 ? ? 123.13 120.30 2.83 0.40 N 24 1 N3 X C 6 ? ? C4 X C 6 ? ? C5 X C 6 ? ? 125.32 121.90 3.42 0.40 N 25 1 C4 X C 6 ? ? C5 X C 6 ? ? C6 X C 6 ? ? 113.77 117.40 -3.63 0.50 N 26 1 "C3'" X C 6 ? ? "O3'" X C 6 ? ? P X U 7 ? ? 128.63 119.70 8.93 1.20 Y 27 1 OP1 X U 7 ? ? P X U 7 ? ? OP2 X U 7 ? ? 132.47 119.60 12.87 1.50 N 28 1 "O5'" X U 7 ? ? P X U 7 ? ? OP1 X U 7 ? ? 99.37 105.70 -6.33 0.90 N 29 1 P X U 7 ? ? "O5'" X U 7 ? ? "C5'" X U 7 ? ? 133.79 120.90 12.89 1.60 N 30 1 "C3'" X U 7 ? ? "C2'" X U 7 ? ? "C1'" X U 7 ? ? 92.47 101.30 -8.83 0.70 N 31 1 C2 X U 7 ? ? N3 X U 7 ? ? C4 X U 7 ? ? 123.12 127.00 -3.88 0.60 N 32 1 "C3'" X U 7 ? ? "O3'" X U 7 ? ? P X G 8 ? ? 127.93 119.70 8.23 1.20 Y 33 1 P X G 8 ? ? "O5'" X G 8 ? ? "C5'" X G 8 ? ? 132.75 120.90 11.85 1.60 N 34 1 "O4'" X G 8 ? ? "C4'" X G 8 ? ? "C3'" X G 8 ? ? 88.46 104.00 -15.54 1.00 N 35 1 "C5'" X G 8 ? ? "C4'" X G 8 ? ? "O4'" X G 8 ? ? 118.08 109.80 8.28 0.90 N 36 1 "C3'" X G 8 ? ? "C2'" X G 8 ? ? "C1'" X G 8 ? ? 93.20 101.30 -8.10 0.70 N 37 1 "O4'" X G 8 ? ? "C1'" X G 8 ? ? N9 X G 8 ? ? 118.18 108.50 9.68 0.70 N 38 1 "C3'" X G 8 ? ? "O3'" X G 8 ? ? P X A 9 ? ? 129.48 119.70 9.78 1.20 Y 39 1 "C3'" X A 12 ? ? "C2'" X A 12 ? ? "C1'" X A 12 ? ? 90.90 101.30 -10.40 0.70 N 40 1 "C3'" X G 13 ? ? "C2'" X G 13 ? ? "C1'" X G 13 ? ? 94.96 101.30 -6.34 0.70 N 41 1 N1 X G 13 ? ? C2 X G 13 ? ? N3 X G 13 ? ? 120.23 123.90 -3.67 0.60 N 42 1 C4 X G 13 ? ? C5 X G 13 ? ? C6 X G 13 ? ? 114.67 118.80 -4.13 0.60 N 43 1 C5 X G 13 ? ? C6 X G 13 ? ? N1 X G 13 ? ? 114.61 111.50 3.11 0.50 N 44 1 "C3'" X G 13 ? ? "O3'" X G 13 ? ? P X G 14 ? ? 112.41 119.70 -7.29 1.20 Y 45 1 "C1'" X G 14 ? ? "O4'" X G 14 ? ? "C4'" X G 14 ? ? 104.85 109.70 -4.85 0.70 N 46 1 "C3'" X G 14 ? ? "C2'" X G 14 ? ? "C1'" X G 14 ? ? 94.18 101.30 -7.12 0.70 N 47 1 N3 X G 14 ? ? C4 X G 14 ? ? C5 X G 14 ? ? 132.10 128.60 3.50 0.50 N 48 1 C4 X G 14 ? ? C5 X G 14 ? ? C6 X G 14 ? ? 113.26 118.80 -5.54 0.60 N 49 1 C4 X G 14 ? ? C5 X G 14 ? ? N7 X G 14 ? ? 113.58 110.80 2.78 0.40 N 50 1 "O5'" X C 15 ? ? "C5'" X C 15 ? ? "C4'" X C 15 ? ? 103.71 109.40 -5.69 0.80 N 51 1 "O4'" X C 15 ? ? "C4'" X C 15 ? ? "C3'" X C 15 ? ? 97.27 104.00 -6.73 1.00 N 52 1 "C3'" X C 15 ? ? "C2'" X C 15 ? ? "C1'" X C 15 ? ? 95.86 101.30 -5.44 0.70 N 53 1 "O4'" X C 15 ? ? "C1'" X C 15 ? ? N1 X C 15 ? ? 103.22 108.20 -4.98 0.80 N 54 1 "O4'" X C 16 ? ? "C1'" X C 16 ? ? N1 X C 16 ? ? 101.65 108.20 -6.55 0.80 N # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag Y _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id X _pdbx_unobs_or_zero_occ_atoms.auth_comp_id G _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id "O5'" _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id A _pdbx_unobs_or_zero_occ_atoms.label_comp_id G _pdbx_unobs_or_zero_occ_atoms.label_seq_id 1 _pdbx_unobs_or_zero_occ_atoms.label_atom_id "O5'" # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 SO4 S S N N 114 SO4 O1 O N N 115 SO4 O2 O N N 116 SO4 O3 O N N 117 SO4 O4 O N N 118 U OP3 O N N 119 U P P N N 120 U OP1 O N N 121 U OP2 O N N 122 U "O5'" O N N 123 U "C5'" C N N 124 U "C4'" C N R 125 U "O4'" O N N 126 U "C3'" C N S 127 U "O3'" O N N 128 U "C2'" C N R 129 U "O2'" O N N 130 U "C1'" C N R 131 U N1 N N N 132 U C2 C N N 133 U O2 O N N 134 U N3 N N N 135 U C4 C N N 136 U O4 O N N 137 U C5 C N N 138 U C6 C N N 139 U HOP3 H N N 140 U HOP2 H N N 141 U "H5'" H N N 142 U "H5''" H N N 143 U "H4'" H N N 144 U "H3'" H N N 145 U "HO3'" H N N 146 U "H2'" H N N 147 U "HO2'" H N N 148 U "H1'" H N N 149 U H3 H N N 150 U H5 H N N 151 U H6 H N N 152 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 SO4 S O1 doub N N 118 SO4 S O2 doub N N 119 SO4 S O3 sing N N 120 SO4 S O4 sing N N 121 U OP3 P sing N N 122 U OP3 HOP3 sing N N 123 U P OP1 doub N N 124 U P OP2 sing N N 125 U P "O5'" sing N N 126 U OP2 HOP2 sing N N 127 U "O5'" "C5'" sing N N 128 U "C5'" "C4'" sing N N 129 U "C5'" "H5'" sing N N 130 U "C5'" "H5''" sing N N 131 U "C4'" "O4'" sing N N 132 U "C4'" "C3'" sing N N 133 U "C4'" "H4'" sing N N 134 U "O4'" "C1'" sing N N 135 U "C3'" "O3'" sing N N 136 U "C3'" "C2'" sing N N 137 U "C3'" "H3'" sing N N 138 U "O3'" "HO3'" sing N N 139 U "C2'" "O2'" sing N N 140 U "C2'" "C1'" sing N N 141 U "C2'" "H2'" sing N N 142 U "O2'" "HO2'" sing N N 143 U "C1'" N1 sing N N 144 U "C1'" "H1'" sing N N 145 U N1 C2 sing N N 146 U N1 C6 sing N N 147 U C2 O2 doub N N 148 U C2 N3 sing N N 149 U N3 C4 sing N N 150 U N3 H3 sing N N 151 U C4 O4 doub N N 152 U C4 C5 sing N N 153 U C5 C6 doub N N 154 U C5 H5 sing N N 155 U C6 H6 sing N N 156 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3D0M 'double helix' 3D0M 'a-form double helix' 3D0M 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 3 1_555 A C 16 16_545 -1.242 -0.049 -0.027 -3.478 -6.414 11.237 1 X_G3:C16_X X 3 ? X 16 ? ? 1 1 A G 4 1_555 A C 15 16_545 -0.142 -0.191 0.204 -4.098 -15.307 -2.194 2 X_G4:C15_X X 4 ? X 15 ? 19 1 1 A U 5 1_555 A G 14 16_545 2.522 -0.379 0.369 -2.594 -17.897 -2.902 3 X_U5:G14_X X 5 ? X 14 ? 28 ? 1 A C 6 1_555 A G 13 16_545 0.216 -0.134 0.359 0.398 -16.149 -0.472 4 X_C6:G13_X X 6 ? X 13 ? 19 1 1 A U 7 1_555 A A 12 16_545 -0.219 0.426 0.171 2.524 -14.861 12.809 5 X_U7:A12_X X 7 ? X 12 ? ? ? 1 A G 8 1_555 A G 11 16_545 -1.533 -3.294 -0.963 26.558 3.306 91.094 6 X_G8:G11_X X 8 ? X 11 ? 6 ? 1 A A 9 1_555 A U 10 16_545 1.298 -0.200 0.350 1.337 -23.246 -15.931 7 X_A9:U10_X X 9 ? X 10 ? 20 1 1 A U 10 1_555 A A 9 16_545 -1.298 -0.200 0.350 -1.337 -23.246 -15.931 8 X_U10:A9_X X 10 ? X 9 ? 20 1 1 A G 11 1_555 A G 8 16_545 1.533 3.294 0.963 -26.558 -3.306 -91.094 9 X_G11:G8_X X 11 ? X 8 ? 6 ? 1 A A 12 1_555 A U 7 16_545 0.219 0.426 0.171 -2.524 -14.861 12.809 10 X_A12:U7_X X 12 ? X 7 ? ? ? 1 A G 13 1_555 A C 6 16_545 -0.216 -0.134 0.359 -0.398 -16.149 -0.472 11 X_G13:C6_X X 13 ? X 6 ? 19 1 1 A G 14 1_555 A U 5 16_545 -2.522 -0.379 0.369 2.594 -17.897 -2.902 12 X_G14:U5_X X 14 ? X 5 ? 28 ? 1 A C 15 1_555 A G 4 16_545 0.142 -0.191 0.204 4.098 -15.307 -2.194 13 X_C15:G4_X X 15 ? X 4 ? 19 1 1 A C 16 1_555 A G 3 16_545 1.242 -0.049 -0.027 3.478 -6.414 11.237 14 X_C16:G3_X X 16 ? X 3 ? ? 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 G 3 1_555 A C 16 16_545 A G 4 1_555 A C 15 16_545 -0.224 -1.870 3.240 -1.486 10.185 32.396 -4.685 0.168 2.560 17.706 2.584 33.950 1 XX_G3G4:C15C16_XX X 3 ? X 16 ? X 4 ? X 15 ? 1 A G 4 1_555 A C 15 16_545 A U 5 1_555 A G 14 16_545 -0.065 -1.256 3.190 1.751 7.305 45.532 -2.195 0.225 2.961 9.364 -2.245 46.115 2 XX_G4U5:G14C15_XX X 4 ? X 15 ? X 5 ? X 14 ? 1 A U 5 1_555 A G 14 16_545 A C 6 1_555 A G 13 16_545 -0.206 -1.905 2.870 2.634 8.946 23.139 -6.472 1.084 1.971 21.229 -6.252 24.924 3 XX_U5C6:G13G14_XX X 5 ? X 14 ? X 6 ? X 13 ? 1 A C 6 1_555 A G 13 16_545 A U 7 1_555 A A 12 16_545 0.449 -1.743 3.094 2.187 6.060 27.463 -4.845 -0.465 2.682 12.547 -4.528 28.195 4 XX_C6U7:A12G13_XX X 6 ? X 13 ? X 7 ? X 12 ? 1 A U 7 1_555 A A 12 16_545 A G 8 1_555 A G 11 16_545 0.945 3.046 -0.465 173.397 -30.760 -61.943 -1.575 0.181 -0.581 15.545 87.629 -176.660 5 XX_U7G8:G11A12_XX X 7 ? X 12 ? X 8 ? X 11 ? 1 A G 8 1_555 A G 11 16_545 A A 9 1_555 A U 10 16_545 -1.562 -2.431 -3.584 114.059 -120.096 82.815 -2.112 -0.062 -1.868 -61.802 -58.695 169.232 6 XX_G8A9:U10G11_XX X 8 ? X 11 ? X 9 ? X 10 ? 1 A A 9 1_555 A U 10 16_545 A U 10 1_555 A A 9 16_545 0.000 -2.398 3.196 0.000 9.023 16.867 -10.890 0.000 1.699 28.280 0.000 19.114 7 XX_A9U10:A9U10_XX X 9 ? X 10 ? X 10 ? X 9 ? 1 A U 10 1_555 A A 9 16_545 A G 11 1_555 A G 8 16_545 1.856 -3.143 2.807 10.780 9.506 92.954 -2.300 -1.103 2.706 6.525 -7.399 93.806 8 XX_U10G11:G8A9_XX X 10 ? X 9 ? X 11 ? X 8 ? 1 A G 11 1_555 A G 8 16_545 A A 12 1_555 A U 7 16_545 -0.581 0.194 3.164 3.341 2.005 -20.119 -1.417 -0.180 3.182 -5.671 9.448 -20.489 9 XX_G11A12:U7G8_XX X 11 ? X 8 ? X 12 ? X 7 ? 1 A A 12 1_555 A U 7 16_545 A G 13 1_555 A C 6 16_545 -0.449 -1.743 3.094 -2.187 6.060 27.463 -4.845 0.465 2.682 12.547 4.528 28.195 10 XX_A12G13:C6U7_XX X 12 ? X 7 ? X 13 ? X 6 ? 1 A G 13 1_555 A C 6 16_545 A G 14 1_555 A U 5 16_545 0.206 -1.905 2.870 -2.634 8.946 23.139 -6.472 -1.084 1.971 21.229 6.252 24.924 11 XX_G13G14:U5C6_XX X 13 ? X 6 ? X 14 ? X 5 ? 1 A G 14 1_555 A U 5 16_545 A C 15 1_555 A G 4 16_545 0.065 -1.256 3.190 -1.751 7.305 45.532 -2.195 -0.225 2.961 9.364 2.245 46.115 12 XX_G14C15:G4U5_XX X 14 ? X 5 ? X 15 ? X 4 ? 1 A C 15 1_555 A G 4 16_545 A C 16 1_555 A G 3 16_545 0.224 -1.870 3.240 1.486 10.185 32.396 -4.685 -0.168 2.560 17.706 -2.584 33.950 13 XX_C15C16:G3G4_XX X 15 ? X 4 ? X 16 ? X 3 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3CZW _pdbx_initial_refinement_model.details 'another crystal form (pdb id 3czw)' #