data_4NFO # _entry.id 4NFO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 4NFO pdb_00004nfo 10.2210/pdb4nfo/pdb NDB NA2783 ? ? RCSB RCSB083143 ? ? WWPDB D_1000083143 ? ? # 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 2014-07-02 2 'Structure model' 1 1 2014-09-03 3 'Structure model' 1 2 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 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' struct_ncs_dom_lim 5 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_ncs_dom_lim.beg_auth_comp_id' 4 3 'Structure model' '_struct_ncs_dom_lim.beg_label_asym_id' 5 3 'Structure model' '_struct_ncs_dom_lim.beg_label_comp_id' 6 3 'Structure model' '_struct_ncs_dom_lim.beg_label_seq_id' 7 3 'Structure model' '_struct_ncs_dom_lim.end_auth_comp_id' 8 3 'Structure model' '_struct_ncs_dom_lim.end_label_asym_id' 9 3 'Structure model' '_struct_ncs_dom_lim.end_label_comp_id' 10 3 'Structure model' '_struct_ncs_dom_lim.end_label_seq_id' 11 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 12 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 13 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4NFO _pdbx_database_status.recvd_initial_deposition_date 2013-10-31 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4NFP . unspecified PDB 4NFQ . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Beal, P.A.' 1 'Fisher, A.J.' 2 'Phelps, K.J.' 3 'Ibarra-Soza, J.M.' 4 'Zheng, Y.' 5 # _citation.id primary _citation.title 'Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.' _citation.journal_abbrev 'Acs Chem.Biol.' _citation.journal_volume 9 _citation.page_first 1780 _citation.page_last 1787 _citation.year 2014 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1554-8929 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24896732 _citation.pdbx_database_id_DOI 10.1021/cb500270x # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Phelps, K.J.' 1 ? primary 'Ibarra-Soza, J.M.' 2 ? primary 'Tran, K.' 3 ? primary 'Fisher, A.J.' 4 ? primary 'Beal, P.A.' 5 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn GCAGACUUAAGUCUGC 5098.079 3 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 water nat water 18.015 22 ? ? ? ? # _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 GCAGACUUAAGUCUGC _entity_poly.pdbx_seq_one_letter_code_can GCAGACUUAAGUCUGC _entity_poly.pdbx_strand_id A,B,C _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMINE SPM 3 water HOH # 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 C n 1 3 A n 1 4 G n 1 5 A n 1 6 C n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 G n 1 12 U n 1 13 C n 1 14 U n 1 15 G n 1 16 C n # 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 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 A . n A 1 2 C 2 2 2 C C A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 C 16 16 16 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 A 3 3 3 A A B . n B 1 4 G 4 4 4 G G B . n B 1 5 A 5 5 5 A A B . n B 1 6 C 6 6 6 C C B . n B 1 7 U 7 7 7 U U B . n B 1 8 U 8 8 8 U U B . n B 1 9 A 9 9 9 A A B . n B 1 10 A 10 10 10 A A B . n B 1 11 G 11 11 11 G G B . n B 1 12 U 12 12 12 U U B . n B 1 13 C 13 13 13 C C B . n B 1 14 U 14 14 14 U U B . n B 1 15 G 15 15 15 G G B . n B 1 16 C 16 16 16 C C B . n C 1 1 G 1 1 1 G G C . n C 1 2 C 2 2 2 C C C . n C 1 3 A 3 3 3 A A C . n C 1 4 G 4 4 4 G G C . n C 1 5 A 5 5 5 A A C . n C 1 6 C 6 6 6 C C C . n C 1 7 U 7 7 7 U U C . n C 1 8 U 8 8 8 U U C . n C 1 9 A 9 9 9 A A C . n C 1 10 A 10 10 10 A A C . n C 1 11 G 11 11 11 G G C . n C 1 12 U 12 12 12 U U C . n C 1 13 C 13 13 13 C C C . n C 1 14 U 14 14 14 U U C . n C 1 15 G 15 15 15 G G C . n C 1 16 C 16 16 16 C C C . 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 D 2 SPM 1 101 1 SPM SPM C . E 3 HOH 1 101 6 HOH HOH A . E 3 HOH 2 102 11 HOH HOH A . E 3 HOH 3 103 16 HOH HOH A . E 3 HOH 4 104 29 HOH HOH A . E 3 HOH 5 105 30 HOH HOH A . E 3 HOH 6 106 31 HOH HOH A . F 3 HOH 1 101 8 HOH HOH B . F 3 HOH 2 102 9 HOH HOH B . F 3 HOH 3 103 10 HOH HOH B . F 3 HOH 4 104 12 HOH HOH B . F 3 HOH 5 105 15 HOH HOH B . F 3 HOH 6 106 26 HOH HOH B . F 3 HOH 7 107 32 HOH HOH B . G 3 HOH 1 201 2 HOH HOH C . G 3 HOH 2 202 4 HOH HOH C . G 3 HOH 3 203 20 HOH HOH C . G 3 HOH 4 204 21 HOH HOH C . G 3 HOH 5 205 22 HOH HOH C . G 3 HOH 6 206 24 HOH HOH C . G 3 HOH 7 207 25 HOH HOH C . G 3 HOH 8 208 27 HOH HOH C . G 3 HOH 9 209 28 HOH HOH C . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal Blu-Ice 'data collection' . ? 1 PHASER phasing . ? 2 REFMAC refinement 5.7.0029 ? 3 # _cell.entry_id 4NFO _cell.length_a 74.980 _cell.length_b 43.080 _cell.length_c 48.760 _cell.angle_alpha 90.00 _cell.angle_beta 120.98 _cell.angle_gamma 90.00 _cell.Z_PDB 12 _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 4NFO _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4NFO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.21 _exptl_crystal.density_percent_sol 44.27 _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 294.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details ;10% MPD(v/v)(Drop), 35% MPD(v/v)(reservoir), 40mM Na-cacodylate trihydrate (pH 7), 12mM spermine tetrahydrochloride, 80mM SrCl2, 20mM MgCl2 hexahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.details ? _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2012-04-19 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ;Si(111) Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg ; _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.148 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL7-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL7-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.148 # _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.limit_k_max ? _reflns.d_resolution_high 1.96 _reflns.observed_criterion_F_min ? _reflns.pdbx_netI_over_sigmaI 17.06 _reflns.observed_criterion_F_max ? _reflns.pdbx_Rmerge_I_obs .020 _reflns.limit_l_max ? _reflns.limit_k_min ? _reflns.entry_id 4NFO _reflns.B_iso_Wilson_estimate ? _reflns.percent_possible_obs 93.4 _reflns.pdbx_Rsym_value ? _reflns.observed_criterion_sigma_I 0. _reflns.observed_criterion_sigma_F 0. _reflns.limit_l_min ? _reflns.limit_h_min ? _reflns.R_free_details ? _reflns.number_all 9759 _reflns.d_resolution_low 35.81 _reflns.pdbx_redundancy 2.0 _reflns.number_obs 9115 _reflns.limit_h_max ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.96 _reflns_shell.d_res_low 2.01 _reflns_shell.percent_possible_all 96.7 _reflns_shell.Rmerge_I_obs 0.310 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.19 _reflns_shell.pdbx_redundancy 1.87 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 706 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.ls_percent_reflns_R_free 4.9 _refine.overall_SU_B 13.127 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_R_Free_selection_details RANDOM _refine.overall_FOM_free_R_set ? _refine.pdbx_data_cutoff_low_absF ? _refine.entry_id 4NFO _refine.aniso_B[2][3] 0.00 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_ML 0.160 _refine.aniso_B[1][3] -0.93 _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.aniso_B[3][3] -1.92 _refine.solvent_model_param_ksol ? _refine.ls_number_restraints ? _refine.aniso_B[1][1] 2.06 _refine.pdbx_overall_ESU_R 0.214 _refine.ls_R_factor_obs 0.21839 _refine.occupancy_min ? _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_starting_model ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.occupancy_max ? _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.correlation_coeff_Fo_to_Fc 0.971 _refine.ls_number_reflns_R_free 443 _refine.correlation_coeff_Fo_to_Fc_free 0.972 _refine.pdbx_ls_sigma_F 0. _refine.ls_percent_reflns_obs 93.86 _refine.ls_R_factor_R_work 0.21709 _refine.overall_SU_R_free ? _refine.ls_d_res_high 1.96 _refine.pdbx_overall_ESU_R_Free 0.171 _refine.B_iso_min ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.B_iso_mean 55.364 _refine.pdbx_stereochem_target_val_spec_case ? _refine.ls_R_factor_all 0.21839 _refine.aniso_B[2][2] 1.81 _refine.B_iso_max ? _refine.pdbx_ls_sigma_I 0. _refine.ls_d_res_low 35.81 _refine.pdbx_overall_phase_error ? _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.aniso_B[1][2] 0.00 _refine.ls_R_factor_R_free 0.24200 _refine.ls_R_factor_R_free_error ? _refine.ls_number_reflns_obs 8672 _refine.overall_FOM_work_R_set ? _refine.ls_number_parameters ? _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_number_reflns_all 9115 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.solvent_model_param_bsol ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 4NFO _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.171 _refine_analyze.Luzzati_sigma_a_free ? _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_Luzzati_d_res_high_obs ? _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 1011 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 22 _refine_hist.number_atoms_total 1047 _refine_hist.d_res_high 1.96 _refine_hist.d_res_low 35.81 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.011 0.011 ? 1141 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.009 0.020 ? 497 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.584 1.291 ? 1764 ? 'X-RAY DIFFRACTION' r_angle_other_deg 1.714 3.000 ? 1203 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.082 0.200 ? 192 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.014 0.020 ? 568 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.004 0.020 ? 252 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso _refine_ls_restr_ncs.pdbx_asym_id _refine_ls_restr_ncs.pdbx_rms _refine_ls_restr_ncs.pdbx_weight _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.pdbx_refine_id 1 A 919 0.01 0.05 'interatomic distance' 1 ? ? ? ? ? ? 1 'X-RAY DIFFRACTION' 2 B 919 0.01 0.05 'interatomic distance' 1 ? ? ? ? ? ? 2 'X-RAY DIFFRACTION' 1 A 919 0.01 0.05 'interatomic distance' 2 ? ? ? ? ? ? 3 'X-RAY DIFFRACTION' 2 C 919 0.01 0.05 'interatomic distance' 2 ? ? ? ? ? ? 4 'X-RAY DIFFRACTION' 1 B 923 0.01 0.05 'interatomic distance' 3 ? ? ? ? ? ? 5 'X-RAY DIFFRACTION' 2 C 923 0.01 0.05 'interatomic distance' 3 ? ? ? ? ? ? 6 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.960 _refine_ls_shell.d_res_low 2.011 _refine_ls_shell.number_reflns_R_work 651 _refine_ls_shell.R_factor_R_work 0.379 _refine_ls_shell.percent_reflns_obs 97.13 _refine_ls_shell.R_factor_R_free 0.413 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 27 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 651 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _struct_ncs_dom.id _struct_ncs_dom.details _struct_ncs_dom.pdbx_ens_id 1 A 1 2 B 1 1 A 2 2 C 2 1 B 3 2 C 3 # loop_ _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_comp_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.selection_details 1 1 0 A G 1 . A C 16 . A G 1 A C 16 0 ? 1 2 0 B G 1 . B C 16 . B G 1 B C 16 0 ? 2 1 0 A G 1 . A C 16 . A G 1 A C 16 0 ? 2 2 0 C G 1 . C C 16 . C G 1 C C 16 0 ? 3 1 0 B G 1 . B C 16 . B G 1 B C 16 0 ? 3 2 0 C G 1 . C C 16 . C G 1 C C 16 0 ? # loop_ _struct_ncs_ens.id _struct_ncs_ens.details 1 ? 2 ? 3 ? # _database_PDB_matrix.entry_id 4NFO _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 4NFO _struct.title 'Crystal Structure Analysis of the 16mer GCAGACUUAAGUCUGC' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NFO _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA 16mer oligo, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4NFO _struct_ref.pdbx_db_accession 4NFO _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _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 4NFO A 1 ? 16 ? 4NFO 1 ? 16 ? 1 16 2 1 4NFO B 1 ? 16 ? 4NFO 1 ? 16 ? 1 16 3 1 4NFO C 1 ? 16 ? 4NFO 1 ? 16 ? 1 16 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1510 ? 1 MORE -8 ? 1 'SSA (A^2)' 5870 ? 2 'ABSA (A^2)' 1810 ? 2 MORE -9 ? 2 'SSA (A^2)' 5980 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,E 2 1 B,C,D,F,G # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_756 -x+2,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 124.8613343710 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 41.8042412160 # _struct_biol.id 1 _struct_biol.details 'Asymmetric unit contains 1.5 RNA duplexes' # 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 ? ? B G 1 N1 ? ? ? 1_555 C C 16 N3 ? ? B G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? B G 1 N2 ? ? ? 1_555 C C 16 O2 ? ? B G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? B G 1 O6 ? ? ? 1_555 C C 16 N4 ? ? B G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? B C 2 N3 ? ? ? 1_555 C G 15 N1 ? ? B C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? B C 2 N4 ? ? ? 1_555 C G 15 O6 ? ? B C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? B C 2 O2 ? ? ? 1_555 C G 15 N2 ? ? B C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? B A 3 N1 ? ? ? 1_555 C U 14 N3 ? ? B A 3 C U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? B A 3 N6 ? ? ? 1_555 C U 14 O4 ? ? B A 3 C U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? B G 4 N1 ? ? ? 1_555 C C 13 N3 ? ? B G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? B G 4 N2 ? ? ? 1_555 C C 13 O2 ? ? B G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? B G 4 O6 ? ? ? 1_555 C C 13 N4 ? ? B G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? B A 5 N1 ? ? ? 1_555 C U 12 N3 ? ? B A 5 C U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B A 5 N6 ? ? ? 1_555 C U 12 O4 ? ? B A 5 C U 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? B C 6 N3 ? ? ? 1_555 C G 11 N1 ? ? B C 6 C G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? B C 6 N4 ? ? ? 1_555 C G 11 O6 ? ? B C 6 C G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? B C 6 O2 ? ? ? 1_555 C G 11 N2 ? ? B C 6 C G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? B U 7 N3 ? ? ? 1_555 C A 10 N1 ? ? B U 7 C A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? B U 7 O4 ? ? ? 1_555 C A 10 N6 ? ? B U 7 C A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? B U 8 N3 ? ? ? 1_555 C A 9 N1 ? ? B U 8 C A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B U 8 O4 ? ? ? 1_555 C A 9 N6 ? ? B U 8 C A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? B A 9 N1 ? ? ? 1_555 C U 8 N3 ? ? B A 9 C U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B A 9 N6 ? ? ? 1_555 C U 8 O4 ? ? B A 9 C U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B A 10 N1 ? ? ? 1_555 C U 7 N3 ? ? B A 10 C U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B A 10 N6 ? ? ? 1_555 C U 7 O4 ? ? B A 10 C U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B G 11 N1 ? ? ? 1_555 C C 6 N3 ? ? B G 11 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B G 11 N2 ? ? ? 1_555 C C 6 O2 ? ? B G 11 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B G 11 O6 ? ? ? 1_555 C C 6 N4 ? ? B G 11 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B U 12 N3 ? ? ? 1_555 C A 5 N1 ? ? B U 12 C A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B U 12 O4 ? ? ? 1_555 C A 5 N6 ? ? B U 12 C A 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B C 13 N3 ? ? ? 1_555 C G 4 N1 ? ? B C 13 C G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 13 N4 ? ? ? 1_555 C G 4 O6 ? ? B C 13 C G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B C 13 O2 ? ? ? 1_555 C G 4 N2 ? ? B C 13 C G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B U 14 N3 ? ? ? 1_555 C A 3 N1 ? ? B U 14 C A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B U 14 O4 ? ? ? 1_555 C A 3 N6 ? ? B U 14 C A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 15 N1 ? ? ? 1_555 C C 2 N3 ? ? B G 15 C C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B G 15 N2 ? ? ? 1_555 C C 2 O2 ? ? B G 15 C C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B G 15 O6 ? ? ? 1_555 C C 2 N4 ? ? B G 15 C C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B C 16 N3 ? ? ? 1_555 C G 1 N1 ? ? B C 16 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B C 16 N4 ? ? ? 1_555 C G 1 O6 ? ? B C 16 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B C 16 O2 ? ? ? 1_555 C G 1 N2 ? ? B C 16 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 1 A C 16 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 1 A C 16 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 1 A C 16 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 2 A G 15 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 2 A G 15 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 2 A G 15 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 14 N3 ? ? A A 3 A U 14 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 14 O4 ? ? A A 3 A U 14 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 4 A C 13 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 4 A C 13 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 4 A C 13 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 12 N3 ? ? A A 5 A U 12 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 12 O4 ? ? A A 5 A U 12 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 11 N1 ? ? A C 6 A G 11 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 11 O6 ? ? A C 6 A G 11 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 11 N2 ? ? A C 6 A G 11 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 10 N1 ? ? A U 7 A A 10 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 10 N6 ? ? A U 7 A A 10 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 9 N1 ? ? A U 8 A A 9 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 9 N6 ? ? A U 8 A A 9 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A A 9 N1 ? ? ? 1_555 A U 8 N3 ? ? A A 9 A U 8 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A A 9 N6 ? ? ? 1_555 A U 8 O4 ? ? A A 9 A U 8 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 7 N3 ? ? A A 10 A U 7 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 7 O4 ? ? A A 10 A U 7 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 6 N3 ? ? A G 11 A C 6 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 6 O2 ? ? A G 11 A C 6 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 6 N4 ? ? A G 11 A C 6 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A U 12 N3 ? ? ? 1_555 A A 5 N1 ? ? A U 12 A A 5 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A U 12 O4 ? ? ? 1_555 A A 5 N6 ? ? A U 12 A A 5 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 4 N1 ? ? A C 13 A G 4 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 4 O6 ? ? A C 13 A G 4 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 4 N2 ? ? A C 13 A G 4 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 3 N1 ? ? A U 14 A A 3 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 3 N6 ? ? A U 14 A A 3 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A G 15 N1 ? ? ? 1_555 A C 2 N3 ? ? A G 15 A C 2 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A G 15 N2 ? ? ? 1_555 A C 2 O2 ? ? A G 15 A C 2 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? A G 15 O6 ? ? ? 1_555 A C 2 N4 ? ? A G 15 A C 2 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 1 N1 ? ? A C 16 A G 1 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 1 O6 ? ? A C 16 A G 1 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 1 N2 ? ? A C 16 A G 1 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id C _struct_site.pdbx_auth_comp_id SPM _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'BINDING SITE FOR RESIDUE SPM C 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 G A 4 ? G A 4 . ? 2_756 ? 2 AC1 9 C A 13 ? C A 13 . ? 1_555 ? 3 AC1 9 U A 14 ? U A 14 . ? 1_555 ? 4 AC1 9 G B 4 ? G B 4 . ? 1_555 ? 5 AC1 9 U B 12 ? U B 12 . ? 4_646 ? 6 AC1 9 C B 13 ? C B 13 . ? 4_646 ? 7 AC1 9 A C 5 ? A C 5 . ? 4_646 ? 8 AC1 9 U C 12 ? U C 12 . ? 1_555 ? 9 AC1 9 C C 13 ? C C 13 . ? 1_555 ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 N2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 G _pdbx_validate_symm_contact.auth_seq_id_1 4 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 N14 _pdbx_validate_symm_contact.auth_asym_id_2 C _pdbx_validate_symm_contact.auth_comp_id_2 SPM _pdbx_validate_symm_contact.auth_seq_id_2 101 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 2_756 _pdbx_validate_symm_contact.dist 2.11 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 A _pdbx_validate_rmsd_bond.auth_seq_id_1 5 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 P _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 C _pdbx_validate_rmsd_bond.auth_seq_id_2 6 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.684 _pdbx_validate_rmsd_bond.bond_target_value 1.607 _pdbx_validate_rmsd_bond.bond_deviation 0.077 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.012 _pdbx_validate_rmsd_bond.linker_flag Y # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 58.6865 21.5710 34.9369 0.0838 0.1938 0.0935 0.0208 -0.0126 0.0864 5.4243 13.6947 8.5952 2.8779 -1.3108 -1.1238 0.3661 0.6166 0.2664 -0.1220 0.1065 0.5342 0.3670 -0.1017 -0.4726 'X-RAY DIFFRACTION' 2 ? refined 69.0100 20.4944 24.1121 0.1981 0.1438 0.1060 0.0255 0.0065 0.0466 5.8119 6.2044 3.2463 -1.6194 -2.0387 4.3827 0.6580 0.7217 0.2870 -0.3007 -0.4622 -0.0774 -0.3226 -0.3688 -0.1958 'X-RAY DIFFRACTION' 3 ? refined 59.2287 12.7382 14.1039 0.1355 0.1466 0.1487 0.0512 -0.1288 -0.0739 4.2617 1.1055 4.7873 1.3669 3.5732 0.0537 0.2894 0.5431 -0.5184 0.1700 0.1552 -0.1562 0.1087 0.4677 -0.4446 'X-RAY DIFFRACTION' 4 ? refined 58.5523 22.9726 2.8659 0.2142 0.1853 0.1279 -0.0047 0.1055 -0.0742 9.0010 5.6258 0.2098 -4.0006 -0.4780 1.0523 0.0177 0.2041 0.0351 -0.8122 0.1469 -0.6664 -0.1692 0.0461 -0.1646 'X-RAY DIFFRACTION' 5 ? refined 42.9416 37.3465 6.8236 0.1829 0.2529 0.1322 0.0473 0.0708 0.0539 5.6874 8.6227 10.5975 2.7092 -0.3886 -4.5551 -0.1359 -0.2864 0.3892 0.4563 0.7714 0.7618 -0.2014 0.2724 -0.6355 'X-RAY DIFFRACTION' 6 ? refined 48.9669 28.9711 17.6931 0.0555 0.1864 0.1036 -0.0481 0.0275 -0.0229 3.2022 5.1833 6.1270 -2.0505 4.2921 -1.5582 -0.1510 -0.4979 -0.1484 0.0437 0.4130 0.1817 -0.1292 -0.6040 -0.2620 'X-RAY DIFFRACTION' 7 ? refined 50.7333 41.2979 27.7183 0.0373 0.1864 0.1187 -0.0056 -0.0108 -0.1143 1.9354 10.0583 3.3509 -2.4339 -2.5179 3.8909 -0.2373 -0.2556 0.2245 0.1399 0.5691 -0.5867 0.2823 0.3552 -0.3318 'X-RAY DIFFRACTION' 8 ? refined 41.5126 36.7694 38.9492 0.1581 0.2431 0.1528 -0.0545 -0.1419 0.0985 5.9655 4.4590 1.0101 -3.4008 -1.3010 2.0945 0.2269 -0.7063 -0.4523 0.3633 -0.0176 -0.2589 0.2164 -0.0546 -0.2093 'X-RAY DIFFRACTION' 9 ? refined 46.5490 30.9096 34.9746 0.1393 0.1277 0.0995 -0.0067 -0.0696 -0.0027 13.7105 2.4588 11.4311 -0.5854 5.7247 -0.3850 0.5088 0.1884 -0.5963 -0.4297 -0.0569 0.0062 0.0004 0.3605 -0.4519 'X-RAY DIFFRACTION' 10 ? refined 42.3512 40.3155 24.1143 0.1935 0.2106 0.0900 -0.0642 -0.0470 -0.0430 4.7247 5.6347 5.3618 -0.8921 -2.2926 -4.3848 -0.0905 -0.1392 -0.0494 -1.0221 0.3529 0.2427 0.9184 -0.2655 -0.2625 'X-RAY DIFFRACTION' 11 ? refined 53.9785 35.7666 14.1123 0.1580 0.1811 0.1348 -0.0750 0.0925 -0.0523 4.3163 6.9547 6.4784 -4.7728 -4.2331 6.6510 0.5277 -0.1580 0.4594 -0.6878 0.0483 -0.6249 -0.6097 -0.0302 -0.5760 'X-RAY DIFFRACTION' 12 ? refined 45.5475 30.0459 2.8223 0.0943 0.2090 0.1472 -0.0015 -0.0045 0.1514 1.8008 9.8060 2.6803 -0.1782 -0.4836 1.1170 -0.0060 0.5732 0.4773 -0.4505 0.1621 0.3071 -0.0877 0.0158 -0.1560 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _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.selection_details 'X-RAY DIFFRACTION' 1 1 A 1 ? ? A 4 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 5 ? ? A 8 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 9 ? ? A 12 ? ? ? ? 'X-RAY DIFFRACTION' 4 4 A 13 ? ? A 16 ? ? ? ? 'X-RAY DIFFRACTION' 5 5 B 1 ? ? B 4 ? ? ? ? 'X-RAY DIFFRACTION' 6 6 B 5 ? ? B 8 ? ? ? ? 'X-RAY DIFFRACTION' 7 7 B 9 ? ? B 12 ? ? ? ? 'X-RAY DIFFRACTION' 8 8 B 13 ? ? B 16 ? ? ? ? 'X-RAY DIFFRACTION' 9 9 C 1 ? ? C 4 ? ? ? ? 'X-RAY DIFFRACTION' 10 10 C 5 ? ? C 8 ? ? ? ? 'X-RAY DIFFRACTION' 11 11 C 9 ? ? C 12 ? ? ? ? 'X-RAY DIFFRACTION' 12 12 C 13 ? ? C 16 ? ? ? ? # 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 SPM N1 N N N 114 SPM C2 C N N 115 SPM C3 C N N 116 SPM C4 C N N 117 SPM N5 N N N 118 SPM C6 C N N 119 SPM C7 C N N 120 SPM C8 C N N 121 SPM C9 C N N 122 SPM N10 N N N 123 SPM C11 C N N 124 SPM C12 C N N 125 SPM C13 C N N 126 SPM N14 N N N 127 SPM HN11 H N N 128 SPM HN12 H N N 129 SPM H21 H N N 130 SPM H22 H N N 131 SPM H31 H N N 132 SPM H32 H N N 133 SPM H41 H N N 134 SPM H42 H N N 135 SPM HN5 H N N 136 SPM H61 H N N 137 SPM H62 H N N 138 SPM H71 H N N 139 SPM H72 H N N 140 SPM H81 H N N 141 SPM H82 H N N 142 SPM H91 H N N 143 SPM H92 H N N 144 SPM HN0 H N N 145 SPM H111 H N N 146 SPM H112 H N N 147 SPM H121 H N N 148 SPM H122 H N N 149 SPM H131 H N N 150 SPM H132 H N N 151 SPM HN41 H N N 152 SPM HN42 H N N 153 U OP3 O N N 154 U P P N N 155 U OP1 O N N 156 U OP2 O N N 157 U "O5'" O N N 158 U "C5'" C N N 159 U "C4'" C N R 160 U "O4'" O N N 161 U "C3'" C N S 162 U "O3'" O N N 163 U "C2'" C N R 164 U "O2'" O N N 165 U "C1'" C N R 166 U N1 N N N 167 U C2 C N N 168 U O2 O N N 169 U N3 N N N 170 U C4 C N N 171 U O4 O N N 172 U C5 C N N 173 U C6 C N N 174 U HOP3 H N N 175 U HOP2 H N N 176 U "H5'" H N N 177 U "H5''" H N N 178 U "H4'" H N N 179 U "H3'" H N N 180 U "HO3'" H N N 181 U "H2'" H N N 182 U "HO2'" H N N 183 U "H1'" H N N 184 U H3 H N N 185 U H5 H N N 186 U H6 H N N 187 # 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 SPM N1 C2 sing N N 118 SPM N1 HN11 sing N N 119 SPM N1 HN12 sing N N 120 SPM C2 C3 sing N N 121 SPM C2 H21 sing N N 122 SPM C2 H22 sing N N 123 SPM C3 C4 sing N N 124 SPM C3 H31 sing N N 125 SPM C3 H32 sing N N 126 SPM C4 N5 sing N N 127 SPM C4 H41 sing N N 128 SPM C4 H42 sing N N 129 SPM N5 C6 sing N N 130 SPM N5 HN5 sing N N 131 SPM C6 C7 sing N N 132 SPM C6 H61 sing N N 133 SPM C6 H62 sing N N 134 SPM C7 C8 sing N N 135 SPM C7 H71 sing N N 136 SPM C7 H72 sing N N 137 SPM C8 C9 sing N N 138 SPM C8 H81 sing N N 139 SPM C8 H82 sing N N 140 SPM C9 N10 sing N N 141 SPM C9 H91 sing N N 142 SPM C9 H92 sing N N 143 SPM N10 C11 sing N N 144 SPM N10 HN0 sing N N 145 SPM C11 C12 sing N N 146 SPM C11 H111 sing N N 147 SPM C11 H112 sing N N 148 SPM C12 C13 sing N N 149 SPM C12 H121 sing N N 150 SPM C12 H122 sing N N 151 SPM C13 N14 sing N N 152 SPM C13 H131 sing N N 153 SPM C13 H132 sing N N 154 SPM N14 HN41 sing N N 155 SPM N14 HN42 sing N N 156 U OP3 P sing N N 157 U OP3 HOP3 sing N N 158 U P OP1 doub N N 159 U P OP2 sing N N 160 U P "O5'" sing N N 161 U OP2 HOP2 sing N N 162 U "O5'" "C5'" sing N N 163 U "C5'" "C4'" sing N N 164 U "C5'" "H5'" sing N N 165 U "C5'" "H5''" sing N N 166 U "C4'" "O4'" sing N N 167 U "C4'" "C3'" sing N N 168 U "C4'" "H4'" sing N N 169 U "O4'" "C1'" sing N N 170 U "C3'" "O3'" sing N N 171 U "C3'" "C2'" sing N N 172 U "C3'" "H3'" sing N N 173 U "O3'" "HO3'" sing N N 174 U "C2'" "O2'" sing N N 175 U "C2'" "C1'" sing N N 176 U "C2'" "H2'" sing N N 177 U "O2'" "HO2'" sing N N 178 U "C1'" N1 sing N N 179 U "C1'" "H1'" sing N N 180 U N1 C2 sing N N 181 U N1 C6 sing N N 182 U C2 O2 doub N N 183 U C2 N3 sing N N 184 U N3 C4 sing N N 185 U N3 H3 sing N N 186 U C4 O4 doub N N 187 U C4 C5 sing N N 188 U C5 C6 doub N N 189 U C5 H5 sing N N 190 U C6 H6 sing N N 191 # _ndb_struct_conf_na.entry_id 4NFO _ndb_struct_conf_na.feature 'a-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 B G 1 1_555 C C 16 1_555 -0.391 -0.148 0.262 1.675 -9.138 1.397 1 B_G1:C16_C B 1 ? C 16 ? 19 1 1 B C 2 1_555 C G 15 1_555 0.357 -0.037 0.112 3.350 -16.830 4.086 2 B_C2:G15_C B 2 ? C 15 ? 19 1 1 B A 3 1_555 C U 14 1_555 0.048 -0.138 0.122 -0.030 -9.386 0.551 3 B_A3:U14_C B 3 ? C 14 ? 20 1 1 B G 4 1_555 C C 13 1_555 -0.423 -0.199 0.054 2.977 -8.739 -0.795 4 B_G4:C13_C B 4 ? C 13 ? 19 1 1 B A 5 1_555 C U 12 1_555 -0.321 -0.114 0.156 -0.431 -8.974 3.197 5 B_A5:U12_C B 5 ? C 12 ? 20 1 1 B C 6 1_555 C G 11 1_555 0.353 -0.303 -0.020 1.093 -14.344 -2.842 6 B_C6:G11_C B 6 ? C 11 ? 19 1 1 B U 7 1_555 C A 10 1_555 -0.097 -0.099 0.004 -4.871 -15.795 1.541 7 B_U7:A10_C B 7 ? C 10 ? 20 1 1 B U 8 1_555 C A 9 1_555 -0.119 -0.107 0.002 -0.894 -9.972 1.756 8 B_U8:A9_C B 8 ? C 9 ? 20 1 1 B A 9 1_555 C U 8 1_555 0.082 -0.116 0.005 0.763 -9.722 1.189 9 B_A9:U8_C B 9 ? C 8 ? 20 1 1 B A 10 1_555 C U 7 1_555 0.005 -0.049 -0.025 4.768 -15.444 2.221 10 B_A10:U7_C B 10 ? C 7 ? 20 1 1 B G 11 1_555 C C 6 1_555 -0.395 -0.324 -0.090 0.257 -13.281 -2.266 11 B_G11:C6_C B 11 ? C 6 ? 19 1 1 B U 12 1_555 C A 5 1_555 0.245 -0.160 0.075 1.123 -10.135 2.439 12 B_U12:A5_C B 12 ? C 5 ? 20 1 1 B C 13 1_555 C G 4 1_555 0.395 -0.182 0.048 -1.987 -9.606 -0.751 13 B_C13:G4_C B 13 ? C 4 ? 19 1 1 B U 14 1_555 C A 3 1_555 0.022 -0.128 0.114 -0.414 -9.047 1.268 14 B_U14:A3_C B 14 ? C 3 ? 20 1 1 B G 15 1_555 C C 2 1_555 -0.287 -0.064 -0.003 -2.495 -16.295 2.797 15 B_G15:C2_C B 15 ? C 2 ? 19 1 1 B C 16 1_555 C G 1 1_555 0.374 -0.207 0.152 0.002 -8.368 0.133 16 B_C16:G1_C B 16 ? C 1 ? 19 1 1 A G 1 1_555 A C 16 2_756 -0.424 -0.134 0.267 1.450 -8.509 0.544 17 A_G1:C16_A A 1 ? A 16 ? 19 1 1 A C 2 1_555 A G 15 2_756 0.314 -0.028 0.080 3.315 -15.749 3.057 18 A_C2:G15_A A 2 ? A 15 ? 19 1 1 A A 3 1_555 A U 14 2_756 0.003 -0.101 0.127 1.479 -9.102 1.470 19 A_A3:U14_A A 3 ? A 14 ? 20 1 1 A G 4 1_555 A C 13 2_756 -0.472 -0.157 0.050 2.870 -9.745 0.020 20 A_G4:C13_A A 4 ? A 13 ? 19 1 1 A A 5 1_555 A U 12 2_756 -0.283 -0.117 0.119 -0.121 -8.593 2.612 21 A_A5:U12_A A 5 ? A 12 ? 20 1 1 A C 6 1_555 A G 11 2_756 0.399 -0.293 -0.048 0.445 -14.807 -2.661 22 A_C6:G11_A A 6 ? A 11 ? 19 1 1 A U 7 1_555 A A 10 2_756 -0.047 -0.081 -0.014 -5.884 -15.233 1.473 23 A_U7:A10_A A 7 ? A 10 ? 20 1 1 A U 8 1_555 A A 9 2_756 -0.079 -0.047 -0.030 -0.975 -9.625 1.330 24 A_U8:A9_A A 8 ? A 9 ? 20 1 1 A A 9 1_555 A U 8 2_756 0.079 -0.047 -0.030 0.975 -9.625 1.330 25 A_A9:U8_A A 9 ? A 8 ? 20 1 1 A A 10 1_555 A U 7 2_756 0.047 -0.081 -0.014 5.884 -15.233 1.473 26 A_A10:U7_A A 10 ? A 7 ? 20 1 1 A G 11 1_555 A C 6 2_756 -0.399 -0.293 -0.048 -0.445 -14.807 -2.661 27 A_G11:C6_A A 11 ? A 6 ? 19 1 1 A U 12 1_555 A A 5 2_756 0.283 -0.117 0.119 0.121 -8.593 2.612 28 A_U12:A5_A A 12 ? A 5 ? 20 1 1 A C 13 1_555 A G 4 2_756 0.472 -0.157 0.050 -2.870 -9.745 0.020 29 A_C13:G4_A A 13 ? A 4 ? 19 1 1 A U 14 1_555 A A 3 2_756 -0.003 -0.101 0.127 -1.479 -9.102 1.470 30 A_U14:A3_A A 14 ? A 3 ? 20 1 1 A G 15 1_555 A C 2 2_756 -0.314 -0.028 0.080 -3.315 -15.749 3.057 31 A_G15:C2_A A 15 ? A 2 ? 19 1 1 A C 16 1_555 A G 1 2_756 0.424 -0.134 0.267 -1.450 -8.509 0.544 32 A_C16:G1_A A 16 ? A 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 B G 1 1_555 C C 16 1_555 B C 2 1_555 C G 15 1_555 -0.137 -1.216 3.246 1.584 0.443 38.191 -1.911 0.406 3.224 0.677 -2.420 38.225 1 BB_G1C2:G15C16_CC B 1 ? C 16 ? B 2 ? C 15 ? 1 B C 2 1_555 C G 15 1_555 B A 3 1_555 C U 14 1_555 0.176 -1.574 3.204 1.033 9.852 31.668 -4.270 -0.150 2.614 17.525 -1.837 33.144 2 BB_C2A3:U14G15_CC B 2 ? C 15 ? B 3 ? C 14 ? 1 B A 3 1_555 C U 14 1_555 B G 4 1_555 C C 13 1_555 -0.151 -1.786 3.104 -1.450 9.250 26.730 -5.501 0.020 2.370 19.272 3.022 28.294 3 BB_A3G4:C13U14_CC B 3 ? C 14 ? B 4 ? C 13 ? 1 B G 4 1_555 C C 13 1_555 B A 5 1_555 C U 12 1_555 -0.089 -1.775 3.356 -1.709 8.276 33.494 -4.227 -0.105 2.850 14.083 2.909 34.514 4 BB_G4A5:U12C13_CC B 4 ? C 13 ? B 5 ? C 12 ? 1 B A 5 1_555 C U 12 1_555 B C 6 1_555 C G 11 1_555 -0.030 -1.682 3.247 2.617 11.220 32.959 -4.361 0.413 2.546 19.064 -4.448 34.862 5 BB_A5C6:G11U12_CC B 5 ? C 12 ? B 6 ? C 11 ? 1 B C 6 1_555 C G 11 1_555 B U 7 1_555 C A 10 1_555 0.387 -1.755 3.241 2.598 13.206 28.782 -5.361 -0.286 2.264 24.918 -4.903 31.713 6 BB_C6U7:A10G11_CC B 6 ? C 11 ? B 7 ? C 10 ? 1 B U 7 1_555 C A 10 1_555 B U 8 1_555 C A 9 1_555 0.130 -1.536 3.263 -0.252 4.861 31.512 -3.648 -0.281 2.997 8.884 0.460 31.877 7 BB_U7U8:A9A10_CC B 7 ? C 10 ? B 8 ? C 9 ? 1 B U 8 1_555 C A 9 1_555 B A 9 1_555 C U 8 1_555 -0.041 -1.352 3.122 -0.262 8.793 30.295 -3.962 0.032 2.635 16.396 0.488 31.517 8 BB_U8A9:U8A9_CC B 8 ? C 9 ? B 9 ? C 8 ? 1 B A 9 1_555 C U 8 1_555 B A 10 1_555 C U 7 1_555 -0.114 -1.530 3.271 0.125 4.920 30.910 -3.733 0.234 2.997 9.158 -0.232 31.289 9 BB_A9A10:U7U8_CC B 9 ? C 8 ? B 10 ? C 7 ? 1 B A 10 1_555 C U 7 1_555 B G 11 1_555 C C 6 1_555 -0.390 -1.749 3.217 -2.476 12.838 29.039 -5.266 0.313 2.284 24.120 4.651 31.789 10 BB_A10G11:C6U7_CC B 10 ? C 7 ? B 11 ? C 6 ? 1 B G 11 1_555 C C 6 1_555 B U 12 1_555 C A 5 1_555 -0.026 -1.696 3.260 -2.707 11.139 32.627 -4.437 -0.340 2.555 19.106 4.643 34.530 11 BB_G11U12:A5C6_CC B 11 ? C 6 ? B 12 ? C 5 ? 1 B U 12 1_555 C A 5 1_555 B C 13 1_555 C G 4 1_555 0.090 -1.789 3.359 1.171 8.437 33.622 -4.252 0.021 2.841 14.302 -1.985 34.654 12 BB_U12C13:G4A5_CC B 12 ? C 5 ? B 13 ? C 4 ? 1 B C 13 1_555 C G 4 1_555 B U 14 1_555 C A 3 1_555 0.188 -1.779 3.150 1.494 9.117 27.314 -5.368 -0.084 2.447 18.642 -3.056 28.806 13 BB_C13U14:A3G4_CC B 13 ? C 4 ? B 14 ? C 3 ? 1 B U 14 1_555 C A 3 1_555 B G 15 1_555 C C 2 1_555 -0.256 -1.623 3.164 -0.332 10.291 31.716 -4.363 0.397 2.531 18.239 0.588 33.305 14 BB_U14G15:C2A3_CC B 14 ? C 3 ? B 15 ? C 2 ? 1 B G 15 1_555 C C 2 1_555 B C 16 1_555 C G 1 1_555 0.105 -1.235 3.215 -1.922 0.556 37.896 -1.969 -0.401 3.188 0.856 2.957 37.947 15 BB_G15C16:G1C2_CC B 15 ? C 2 ? B 16 ? C 1 ? 1 A G 1 1_555 A C 16 2_756 A C 2 1_555 A G 15 2_756 -0.117 -1.238 3.242 1.560 0.721 38.090 -1.986 0.374 3.211 1.103 -2.388 38.128 16 AA_G1C2:G15C16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A C 2 1_555 A G 15 2_756 A A 3 1_555 A U 14 2_756 0.255 -1.625 3.161 0.901 9.559 31.777 -4.290 -0.311 2.584 16.979 -1.601 33.160 17 AA_C2A3:U14G15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A A 3 1_555 A U 14 2_756 A G 4 1_555 A C 13 2_756 -0.165 -1.819 3.149 -1.448 9.091 26.345 -5.672 0.041 2.404 19.215 3.060 27.880 18 AA_A3G4:C13U14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A C 13 2_756 A A 5 1_555 A U 12 2_756 -0.155 -1.793 3.317 -1.843 8.019 33.902 -4.155 -0.008 2.837 13.506 3.104 34.858 19 AA_G4A5:U12C13_AA A 4 ? A 13 ? A 5 ? A 12 ? 1 A A 5 1_555 A U 12 2_756 A C 6 1_555 A G 11 2_756 -0.012 -1.718 3.261 2.903 11.347 33.103 -4.411 0.419 2.543 19.183 -4.908 35.059 20 AA_A5C6:G11U12_AA A 5 ? A 12 ? A 6 ? A 11 ? 1 A C 6 1_555 A G 11 2_756 A U 7 1_555 A A 10 2_756 0.405 -1.772 3.266 2.847 13.167 28.954 -5.369 -0.275 2.293 24.717 -5.345 31.874 21 AA_C6U7:A10G11_AA A 6 ? A 11 ? A 7 ? A 10 ? 1 A U 7 1_555 A A 10 2_756 A U 8 1_555 A A 9 2_756 0.116 -1.514 3.236 -0.002 4.661 31.186 -3.616 -0.214 2.984 8.610 0.004 31.524 22 AA_U7U8:A9A10_AA A 7 ? A 10 ? A 8 ? A 9 ? 1 A U 8 1_555 A A 9 2_756 A A 9 1_555 A U 8 2_756 0.000 -1.329 3.131 0.000 9.130 29.859 -4.034 0.000 2.620 17.220 0.000 31.193 23 AA_U8A9:U8A9_AA A 8 ? A 9 ? A 9 ? A 8 ? 1 A A 9 1_555 A U 8 2_756 A A 10 1_555 A U 7 2_756 -0.116 -1.514 3.236 0.002 4.661 31.186 -3.616 0.214 2.984 8.610 -0.004 31.524 24 AA_A9A10:U7U8_AA A 9 ? A 8 ? A 10 ? A 7 ? 1 A A 10 1_555 A U 7 2_756 A G 11 1_555 A C 6 2_756 -0.405 -1.772 3.266 -2.847 13.167 28.954 -5.369 0.275 2.293 24.717 5.345 31.874 25 AA_A10G11:C6U7_AA A 10 ? A 7 ? A 11 ? A 6 ? 1 A G 11 1_555 A C 6 2_756 A U 12 1_555 A A 5 2_756 0.012 -1.718 3.261 -2.903 11.347 33.103 -4.411 -0.419 2.543 19.183 4.908 35.059 26 AA_G11U12:A5C6_AA A 11 ? A 6 ? A 12 ? A 5 ? 1 A U 12 1_555 A A 5 2_756 A C 13 1_555 A G 4 2_756 0.155 -1.793 3.317 1.843 8.019 33.902 -4.155 0.008 2.837 13.506 -3.104 34.858 27 AA_U12C13:G4A5_AA A 12 ? A 5 ? A 13 ? A 4 ? 1 A C 13 1_555 A G 4 2_756 A U 14 1_555 A A 3 2_756 0.165 -1.819 3.149 1.448 9.091 26.345 -5.672 -0.041 2.404 19.215 -3.060 27.880 28 AA_C13U14:A3G4_AA A 13 ? A 4 ? A 14 ? A 3 ? 1 A U 14 1_555 A A 3 2_756 A G 15 1_555 A C 2 2_756 -0.255 -1.625 3.161 -0.901 9.559 31.777 -4.290 0.311 2.584 16.979 1.601 33.160 29 AA_U14G15:C2A3_AA A 14 ? A 3 ? A 15 ? A 2 ? 1 A G 15 1_555 A C 2 2_756 A C 16 1_555 A G 1 2_756 0.117 -1.238 3.242 -1.560 0.721 38.090 -1.986 -0.374 3.211 1.104 2.388 38.128 30 AA_G15C16:G1C2_AA A 15 ? A 2 ? A 16 ? A 1 ? # _atom_sites.entry_id 4NFO _atom_sites.fract_transf_matrix[1][1] 0.013337 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.008008 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023213 _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] 0.023922 _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_