data_4G6P # _entry.id 4G6P # _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 4G6P pdb_00004g6p 10.2210/pdb4g6p/pdb NDB NA1927 ? ? RCSB RCSB073806 ? ? WWPDB D_1000073806 ? ? # 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 2012-08-15 2 'Structure model' 1 1 2012-11-14 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' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_special_symmetry 5 3 'Structure model' struct_conn 6 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_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 4G6P _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-07-19 _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 4G6R . unspecified PDB 4G6S . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Liberman, J.A.' 1 'Jenkins, J.L.' 2 'Krucinska, J.' 3 'Wedekind, J.E.' 4 # _citation.id primary _citation.title 'A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 134 _citation.page_first 16933 _citation.page_last 16936 _citation.year 2012 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22989273 _citation.pdbx_database_id_DOI 10.1021/ja3070528 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Liberman, J.A.' 1 ? primary 'Guo, M.' 2 ? primary 'Jenkins, J.L.' 3 ? primary 'Krucinska, J.' 4 ? primary 'Chen, Y.' 5 ? primary 'Carey, P.R.' 6 ? primary 'Wedekind, J.E.' 7 ? # 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 'Loop A Substrate strand' 4066.497 1 ? ? ? ? 2 polymer syn 'Loop A and Loop B Ribozyme strand' 9762.989 1 ? ? ? ? 3 polymer syn 'Loop B of the Ribozyme Strand' 5976.554 1 ? ? ? ? 4 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 5 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 6 water nat water 18.015 3 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes 'UCCC(A2M)GUCCACCG' UCCCAGUCCACCG A ? 2 polyribonucleotide no yes 'CGGUGAGAAGGG(S9L)GGCAGAGAAACACACGA' CGGUGAGAAGGGXGGCAGAGAAACACACGA B ? 3 polyribonucleotide no yes 'UCGUGGU(P5P)CAUUACCUGCC' UCGUGGUACAUUACCUGCC C ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'SULFATE ION' SO4 5 'COBALT HEXAMMINE(III)' NCO 6 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 C n 1 3 C n 1 4 C n 1 5 A2M n 1 6 G n 1 7 U n 1 8 C n 1 9 C n 1 10 A n 1 11 C n 1 12 C n 1 13 G n 2 1 C n 2 2 G n 2 3 G n 2 4 U n 2 5 G n 2 6 A n 2 7 G n 2 8 A n 2 9 A n 2 10 G n 2 11 G n 2 12 G n 2 13 S9L n 2 14 G n 2 15 G n 2 16 C n 2 17 A n 2 18 G n 2 19 A n 2 20 G n 2 21 A n 2 22 A n 2 23 A n 2 24 C n 2 25 A n 2 26 C n 2 27 A n 2 28 C n 2 29 G n 2 30 A n 3 1 U n 3 2 C n 3 3 G n 3 4 U n 3 5 G n 3 6 G n 3 7 U n 3 8 P5P n 3 9 C n 3 10 A n 3 11 U n 3 12 U n 3 13 A n 3 14 C n 3 15 C n 3 16 U n 3 17 G n 3 18 C n 3 19 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 A2M 'RNA linking' n ;2'-O-methyladenosine 5'-(dihydrogen phosphate) ; ? 'C11 H16 N5 O7 P' 361.248 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 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 P5P 'RNA linking' n ;PURINE RIBOSIDE-5'-MONOPHOSPHATE ; ? 'C10 H13 N4 O7 P' 332.207 S9L non-polymer . '2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE' ? 'C6 H15 O7 P' 230.153 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 U 1 -5 -5 U U A . n A 1 2 C 2 -4 -4 C C A . n A 1 3 C 3 -3 -3 C C A . n A 1 4 C 4 -2 -2 C C A . n A 1 5 A2M 5 -1 -1 A2M A2M A . n A 1 6 G 6 1 1 G G A . n A 1 7 U 7 2 2 U U A . n A 1 8 C 8 3 3 C C A . n A 1 9 C 9 4 4 C C A . n A 1 10 A 10 5 5 A A A . n A 1 11 C 11 6 6 C C A . n A 1 12 C 12 7 7 C C A . n A 1 13 G 13 8 8 G G A . n B 2 1 C 1 2 2 C C B . n B 2 2 G 2 3 3 G G B . n B 2 3 G 3 4 4 G G B . n B 2 4 U 4 5 5 U U B . n B 2 5 G 5 6 6 G G B . n B 2 6 A 6 7 7 A A B . n B 2 7 G 7 8 8 G G B . n B 2 8 A 8 9 9 A A B . n B 2 9 A 9 10 10 A A B . n B 2 10 G 10 11 11 G G B . n B 2 11 G 11 12 12 G G B . n B 2 12 G 12 13 13 G G B . n B 2 13 S9L 13 14 14 S9L S9L B . n B 2 14 G 14 15 15 G G B . n B 2 15 G 15 16 16 G G B . n B 2 16 C 16 17 17 C C B . n B 2 17 A 17 18 18 A A B . n B 2 18 G 18 19 19 G G B . n B 2 19 A 19 20 20 A A B . n B 2 20 G 20 21 21 G G B . n B 2 21 A 21 22 22 A A B . n B 2 22 A 22 23 23 A A B . n B 2 23 A 23 24 24 A A B . n B 2 24 C 24 25 25 C C B . n B 2 25 A 25 26 26 A A B . n B 2 26 C 26 27 27 C C B . n B 2 27 A 27 28 28 A A B . n B 2 28 C 28 29 29 C C B . n B 2 29 G 29 30 30 G G B . n B 2 30 A 30 31 31 A A B . n C 3 1 U 1 31 31 U U C . n C 3 2 C 2 32 32 C C C . n C 3 3 G 3 33 33 G G C . n C 3 4 U 4 34 34 U U C . n C 3 5 G 5 35 35 G G C . n C 3 6 G 6 36 36 G G C . n C 3 7 U 7 37 37 U U C . n C 3 8 P5P 8 38 38 P5P P5P C . n C 3 9 C 9 39 39 C C C . n C 3 10 A 10 40 40 A A C . n C 3 11 U 11 41 41 U U C . n C 3 12 U 12 42 42 U U C . n C 3 13 A 13 43 43 A A C . n C 3 14 C 14 44 44 C C C . n C 3 15 C 15 45 45 C C C . n C 3 16 U 16 46 46 U U C . n C 3 17 G 17 47 47 G G C . n C 3 18 C 18 48 48 C C C . n C 3 19 C 19 49 49 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 4 SO4 1 201 201 SO4 SO4 A . E 5 NCO 1 101 102 NCO NCO B . F 5 NCO 1 101 101 NCO NCO C . G 6 HOH 1 201 101 HOH HOH B . H 6 HOH 1 201 102 HOH HOH C . H 6 HOH 2 202 103 HOH HOH C . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 PHENIX 1.6.2_432 ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 3 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 Blu-Ice . ? ? ? ? 'data collection' ? ? ? 5 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 6 PHENIX . ? ? ? ? phasing ? ? ? # _cell.length_a 93.664 _cell.length_b 93.664 _cell.length_c 134.270 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 4G6P _cell.pdbx_unique_axis ? _cell.Z_PDB 12 _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.space_group_name_H-M 'P 61 2 2' _symmetry.entry_id 4G6P _symmetry.Int_Tables_number 178 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 4G6P _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 4.29 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 71.34 _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.pH 7.0 _exptl_crystal_grow.temp 295 _exptl_crystal_grow.pdbx_details ;22% (w/v) PEG 2000 MME, 0.1M HEPES pH=7.0, 0.25 M Lithium Sulfate, 1mM Cobalt Hexamine, 2mM spermadine, vapor diffusion, Hanging Drop, temperature 295K ; _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 325 mm CCD' _diffrn_detector.pdbx_collection_date 2010-02-05 _diffrn_detector.details 'Rh coated flat mirror' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97885 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength_list 0.97885 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL11-1 # _reflns.entry_id 4G6P _reflns.d_resolution_high 2.640 _reflns.d_resolution_low 50.000 _reflns.number_obs 10642 _reflns.pdbx_Rmerge_I_obs 0.043 _reflns.pdbx_netI_over_sigmaI 20.600 _reflns.pdbx_chi_squared 1.270 _reflns.pdbx_redundancy 6.900 _reflns.percent_possible_obs 98.600 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_Rsym_value ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.640 2.730 ? ? ? 0.812 ? ? 0.669 6.600 ? 992 94.800 1 1 2.730 2.840 ? ? ? 0.468 ? ? 0.656 7.000 ? 1042 99.300 2 1 2.840 2.970 ? ? ? 0.276 ? ? 0.703 7.100 ? 1037 100.000 3 1 2.970 3.130 ? ? ? 0.119 ? ? 0.854 7.100 ? 1064 100.000 4 1 3.130 3.330 ? ? ? 0.064 ? ? 1.023 7.100 ? 1047 99.800 5 1 3.330 3.580 ? ? ? 0.056 ? ? 1.354 7.000 ? 1070 100.000 6 1 3.580 3.940 ? ? ? 0.045 ? ? 1.706 7.000 ? 1072 100.000 7 1 3.940 4.510 ? ? ? 0.039 ? ? 1.895 6.900 ? 1076 99.600 8 1 4.510 5.690 ? ? ? 0.032 ? ? 2.000 6.700 ? 1103 99.400 9 1 5.690 50.000 ? ? ? 0.027 ? ? 1.796 6.200 ? 1139 93.400 10 1 # _refine.entry_id 4G6P _refine.ls_d_res_high 2.6410 _refine.ls_d_res_low 31.0170 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 93.9000 _refine.ls_number_reflns_obs 10098 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_obs 0.1860 _refine.ls_R_factor_R_work 0.1854 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.1971 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.9800 _refine.ls_number_reflns_R_free 503 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 77.9394 _refine.solvent_model_param_bsol 46.5270 _refine.solvent_model_param_ksol 0.2950 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -11.6562 _refine.aniso_B[2][2] -11.6562 _refine.aniso_B[3][3] 23.3125 _refine.aniso_B[1][2] -0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] -0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.4000 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.0000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.7200 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 135.540 _refine.B_iso_min 56.400 _refine.pdbx_overall_phase_error 25.9000 _refine.occupancy_max 1.000 _refine.occupancy_min 0.370 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_R_factor_all ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1310 _refine_hist.pdbx_number_atoms_ligand 19 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 1332 _refine_hist.d_res_high 2.6410 _refine_hist.d_res_low 31.0170 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 1504 0.006 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 2343 0.960 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 307 0.069 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 62 0.008 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 784 16.957 ? ? ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 2.641 2.9067 4 83.0000 2055 . 0.4623 0.5461 . 107 . 2162 . . 'X-RAY DIFFRACTION' 2.9067 3.3269 4 96.0000 2385 . 0.2661 0.3038 . 124 . 2509 . . 'X-RAY DIFFRACTION' 3.3269 4.1899 4 99.0000 2515 . 0.1865 0.1783 . 133 . 2648 . . 'X-RAY DIFFRACTION' 4.1899 31.017 4 98.0000 2640 . 0.1395 0.1516 . 139 . 2779 . . 'X-RAY DIFFRACTION' # _struct.entry_id 4G6P _struct.title 'Minimal Hairpin Ribozyme in the Precatalytic State with A38P Variation' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4G6P _struct_keywords.text 'RNA, Structure-activity relationship, Nucleic Acid Conformation' _struct_keywords.pdbx_keywords 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 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 5 ? G N N 6 ? H N N 6 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 PDB 4G6P 4G6P 1 UCCCAGUCCACCG ? ? 2 PDB 4G6P 4G6P 2 CGGUGAGAAGGGXGGCAGAGAAACACACGA ? ? 3 PDB 4G6P 4G6P 3 UCGUGGUACAUUACCUGCC ? ? # 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 4G6P A 1 ? 13 ? 4G6P -5 ? 8 ? -5 8 2 2 4G6P B 1 ? 30 ? 4G6P 2 ? 31 ? 2 31 3 3 4G6P C 1 ? 19 ? 4G6P 31 ? 49 ? 31 49 # _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 # 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)' 6570 ? 1 MORE -25 ? 1 'SSA (A^2)' 9380 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A C 4 "O3'" ? ? ? 1_555 A A2M 5 P ? ? A C -2 A A2M -1 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale2 covale both ? B G 12 "O3'" ? ? ? 1_555 B S9L 13 P ? ? B G 13 B S9L 14 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale3 covale both ? B S9L 13 "O3'" ? ? ? 1_555 B G 14 P ? ? B S9L 14 B G 15 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale4 covale both ? C U 7 "O3'" ? ? ? 1_555 C P5P 8 P ? ? C U 37 C P5P 38 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale5 covale both ? C P5P 8 "O3'" ? ? ? 1_555 C C 9 P ? ? C P5P 38 C C 39 1_555 ? ? ? ? ? ? ? 1.616 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 12 N1 ? ? A C -4 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 12 O6 ? ? A C -4 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 12 N2 ? ? A C -4 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 11 N1 ? ? A C -3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 11 O6 ? ? A C -3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 11 N2 ? ? A C -3 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 10 N1 ? ? A C -2 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 10 O6 ? ? A C -2 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 10 N2 ? ? A C -2 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A2M 5 N3 ? ? ? 1_555 B A 8 N6 ? ? A A2M -1 B A 9 1_555 ? ? ? ? ? ? 'A2M-A MISPAIR' ? ? ? hydrog11 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 24 N3 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 24 O2 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 24 N4 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 7 O4 ? ? ? 1_555 B G 7 N2 ? ? A U 2 B G 8 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog15 hydrog ? ? A C 8 N4 ? ? ? 1_555 B A 6 N1 ? ? A C 3 B A 7 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog16 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 4 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 4 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 4 B G 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 5 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 5 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 6 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 6 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 6 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 7 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 7 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 7 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 8 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 8 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 8 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B G 14 N1 ? ? ? 1_555 C C 19 N3 ? ? B G 15 C C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B G 14 N2 ? ? ? 1_555 C C 19 O2 ? ? B G 15 C C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B G 14 O6 ? ? ? 1_555 C C 19 N4 ? ? B G 15 C C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B G 15 N1 ? ? ? 1_555 C C 18 N3 ? ? B G 16 C C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B G 15 N2 ? ? ? 1_555 C C 18 O2 ? ? B G 16 C C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 15 O6 ? ? ? 1_555 C C 18 N4 ? ? B G 16 C C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B C 16 N3 ? ? ? 1_555 C G 17 N1 ? ? B C 17 C G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B C 16 N4 ? ? ? 1_555 C G 17 O6 ? ? B C 17 C G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B C 16 O2 ? ? ? 1_555 C G 17 N2 ? ? B C 17 C G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B A 17 N1 ? ? ? 1_555 C U 16 N3 ? ? B A 18 C U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B A 17 N6 ? ? ? 1_555 C U 16 O4 ? ? B A 18 C U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B G 18 N1 ? ? ? 1_555 C C 15 N3 ? ? B G 19 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B G 18 N2 ? ? ? 1_555 C C 15 O2 ? ? B G 19 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B G 18 O6 ? ? ? 1_555 C C 15 N4 ? ? B G 19 C C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B A 19 N1 ? ? ? 1_555 C C 14 N4 ? ? B A 20 C C 44 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog45 hydrog ? ? B G 20 N2 ? ? ? 1_555 C A 13 N7 ? ? B G 21 C A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog46 hydrog ? ? B G 20 N3 ? ? ? 1_555 C A 13 N6 ? ? B G 21 C A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog47 hydrog ? ? B A 21 N6 ? ? ? 1_555 C U 11 O2 ? ? B A 22 C U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog48 hydrog ? ? B A 21 N7 ? ? ? 1_555 C U 11 N3 ? ? B A 22 C U 41 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog49 hydrog ? ? B A 22 N6 ? ? ? 1_555 C A 10 N1 ? ? B A 23 C A 40 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog50 hydrog ? ? B A 23 N6 ? ? ? 1_555 C P5P 8 N7 ? ? B A 24 C P5P 38 1_555 ? ? ? ? ? ? 'A-P5P MISPAIR' ? ? ? hydrog51 hydrog ? ? B A 25 N1 ? ? ? 1_555 C G 6 N1 ? ? B A 26 C G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog52 hydrog ? ? B A 25 N6 ? ? ? 1_555 C G 6 O6 ? ? B A 26 C G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog53 hydrog ? ? B C 26 N3 ? ? ? 1_555 C G 5 N1 ? ? B C 27 C G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? B C 26 N4 ? ? ? 1_555 C G 5 O6 ? ? B C 27 C G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B C 26 O2 ? ? ? 1_555 C G 5 N2 ? ? B C 27 C G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B A 27 N1 ? ? ? 1_555 C U 4 N3 ? ? B A 28 C U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B A 27 N6 ? ? ? 1_555 C U 4 O4 ? ? B A 28 C U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? B C 28 N3 ? ? ? 1_555 C G 3 N1 ? ? B C 29 C G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B C 28 N4 ? ? ? 1_555 C G 3 O6 ? ? B C 29 C G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? B C 28 O2 ? ? ? 1_555 C G 3 N2 ? ? B C 29 C G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B G 29 N1 ? ? ? 1_555 C C 2 N3 ? ? B G 30 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? B G 29 N2 ? ? ? 1_555 C C 2 O2 ? ? B G 30 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? B G 29 O6 ? ? ? 1_555 C C 2 N4 ? ? B G 30 C C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? B A 30 N1 ? ? ? 1_555 C U 1 N3 ? ? B A 31 C U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? B A 30 N6 ? ? ? 1_555 C U 1 O4 ? ? B A 31 C U 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 201 ? 3 'BINDING SITE FOR RESIDUE SO4 A 201' AC2 Software B NCO 101 ? 6 'BINDING SITE FOR RESIDUE NCO B 101' AC3 Software C NCO 101 ? 4 'BINDING SITE FOR RESIDUE NCO 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 3 U A 1 ? U A -5 . ? 1_555 ? 2 AC1 3 C A 2 ? C A -4 . ? 1_555 ? 3 AC1 3 NCO E . ? NCO B 101 . ? 1_555 ? 4 AC2 6 U A 1 ? U A -5 . ? 10_665 ? 5 AC2 6 C A 2 ? C A -4 . ? 1_555 ? 6 AC2 6 SO4 D . ? SO4 A 201 . ? 1_555 ? 7 AC2 6 G B 10 ? G B 11 . ? 1_555 ? 8 AC2 6 G B 11 ? G B 12 . ? 1_555 ? 9 AC2 6 G B 12 ? G B 13 . ? 1_555 ? 10 AC3 4 A B 19 ? A B 20 . ? 1_555 ? 11 AC3 4 G B 20 ? G B 21 . ? 1_555 ? 12 AC3 4 A C 10 ? A C 40 . ? 1_555 ? 13 AC3 4 U C 11 ? U C 41 . ? 1_555 ? # _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 A _pdbx_validate_rmsd_bond.auth_comp_id_1 A2M _pdbx_validate_rmsd_bond.auth_seq_id_1 -1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 A _pdbx_validate_rmsd_bond.auth_atom_id_2 P _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 1 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 A _pdbx_validate_rmsd_bond.bond_value 1.514 _pdbx_validate_rmsd_bond.bond_target_value 1.607 _pdbx_validate_rmsd_bond.bond_deviation -0.093 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.012 _pdbx_validate_rmsd_bond.linker_flag Y # 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 "O3'" A C -2 ? ? P A A2M -1 ? ? OP2 A A2M -1 ? ? 126.57 110.50 16.07 1.10 Y 2 1 "C3'" A A2M -1 ? ? "O3'" A A2M -1 ? A P A G 1 ? A 134.23 119.70 14.53 1.20 Y # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A A2M 5 A A2M -1 ? A ? 2 C P5P 8 C P5P 38 ? A ;PURINE RIBOSIDE-5'-MONOPHOSPHATE ; # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id U _pdbx_struct_special_symmetry.auth_seq_id -5 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id A _pdbx_struct_special_symmetry.label_comp_id U _pdbx_struct_special_symmetry.label_seq_id 1 # 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 A2M P P N N 38 A2M OP1 O N N 39 A2M OP3 O N N 40 A2M "O5'" O N N 41 A2M "C5'" C N N 42 A2M "C4'" C N R 43 A2M "O4'" O N N 44 A2M "C3'" C N R 45 A2M "O3'" O N N 46 A2M "C2'" C N R 47 A2M "O2'" O N N 48 A2M "C1'" C N R 49 A2M "CM'" C N N 50 A2M N9 N Y N 51 A2M C8 C Y N 52 A2M N7 N Y N 53 A2M C5 C Y N 54 A2M C6 C Y N 55 A2M N6 N N N 56 A2M N1 N Y N 57 A2M C2 C Y N 58 A2M N3 N Y N 59 A2M C4 C Y N 60 A2M HOP3 H N N 61 A2M "H5'" H N N 62 A2M "H5''" H N N 63 A2M "H4'" H N N 64 A2M "H3'" H N N 65 A2M "HO3'" H N N 66 A2M "H2'" H N N 67 A2M "H1'" H N N 68 A2M "HM'1" H N N 69 A2M "HM'2" H N N 70 A2M "HM'3" H N N 71 A2M H8 H N N 72 A2M H61 H N N 73 A2M H62 H N N 74 A2M H2 H N N 75 A2M OP2 O N N 76 A2M HOP2 H N N 77 C OP3 O N N 78 C P P N N 79 C OP1 O N N 80 C OP2 O N N 81 C "O5'" O N N 82 C "C5'" C N N 83 C "C4'" C N R 84 C "O4'" O N N 85 C "C3'" C N S 86 C "O3'" O N N 87 C "C2'" C N R 88 C "O2'" O N N 89 C "C1'" C N R 90 C N1 N N N 91 C C2 C N N 92 C O2 O N N 93 C N3 N N N 94 C C4 C N N 95 C N4 N N N 96 C C5 C N N 97 C C6 C N N 98 C HOP3 H N N 99 C HOP2 H N N 100 C "H5'" H N N 101 C "H5''" H N N 102 C "H4'" H N N 103 C "H3'" H N N 104 C "HO3'" H N N 105 C "H2'" H N N 106 C "HO2'" H N N 107 C "H1'" H N N 108 C H41 H N N 109 C H42 H N N 110 C H5 H N N 111 C H6 H N N 112 G OP3 O N N 113 G P P N N 114 G OP1 O N N 115 G OP2 O N N 116 G "O5'" O N N 117 G "C5'" C N N 118 G "C4'" C N R 119 G "O4'" O N N 120 G "C3'" C N S 121 G "O3'" O N N 122 G "C2'" C N R 123 G "O2'" O N N 124 G "C1'" C N R 125 G N9 N Y N 126 G C8 C Y N 127 G N7 N Y N 128 G C5 C Y N 129 G C6 C N N 130 G O6 O N N 131 G N1 N N N 132 G C2 C N N 133 G N2 N N N 134 G N3 N N N 135 G C4 C Y N 136 G HOP3 H N N 137 G HOP2 H N N 138 G "H5'" H N N 139 G "H5''" H N N 140 G "H4'" H N N 141 G "H3'" H N N 142 G "HO3'" H N N 143 G "H2'" H N N 144 G "HO2'" H N N 145 G "H1'" H N N 146 G H8 H N N 147 G H1 H N N 148 G H21 H N N 149 G H22 H N N 150 HOH O O N N 151 HOH H1 H N N 152 HOH H2 H N N 153 NCO CO CO N N 154 NCO N1 N N N 155 NCO N2 N N N 156 NCO N3 N N N 157 NCO N4 N N N 158 NCO N5 N N N 159 NCO N6 N N N 160 NCO HN11 H N N 161 NCO HN12 H N N 162 NCO HN13 H N N 163 NCO HN21 H N N 164 NCO HN22 H N N 165 NCO HN23 H N N 166 NCO HN31 H N N 167 NCO HN32 H N N 168 NCO HN33 H N N 169 NCO HN41 H N N 170 NCO HN42 H N N 171 NCO HN43 H N N 172 NCO HN51 H N N 173 NCO HN52 H N N 174 NCO HN53 H N N 175 NCO HN61 H N N 176 NCO HN62 H N N 177 NCO HN63 H N N 178 P5P N1 N Y N 179 P5P C2 C Y N 180 P5P N3 N Y N 181 P5P C4 C Y N 182 P5P C5 C Y N 183 P5P C6 C Y N 184 P5P N7 N Y N 185 P5P C8 C Y N 186 P5P N9 N Y N 187 P5P "C1'" C N R 188 P5P "C2'" C N R 189 P5P "O2'" O N N 190 P5P "C3'" C N S 191 P5P "O3'" O N N 192 P5P "C4'" C N R 193 P5P "O4'" O N N 194 P5P "C5'" C N N 195 P5P "O5'" O N N 196 P5P P P N N 197 P5P OP1 O N N 198 P5P OP2 O N N 199 P5P OP3 O N N 200 P5P H2 H N N 201 P5P H6 H N N 202 P5P H8 H N N 203 P5P "H1'" H N N 204 P5P "H2'" H N N 205 P5P "HO2'" H N N 206 P5P "H3'" H N N 207 P5P "HO3'" H N N 208 P5P "H4'" H N N 209 P5P "H5'1" H N N 210 P5P "H5'2" H N N 211 P5P HOP2 H N N 212 P5P HOP3 H N N 213 S9L O3P O N N 214 S9L P P N N 215 S9L O1P O N N 216 S9L O2P O N N 217 S9L "O5'" O N N 218 S9L C12 C N N 219 S9L C22 C N N 220 S9L OH3 O N N 221 S9L C13 C N N 222 S9L C23 C N N 223 S9L OH4 O N N 224 S9L C14 C N N 225 S9L C24 C N N 226 S9L "O3'" O N N 227 S9L HO3P H N N 228 S9L HO1P H N N 229 S9L H121 H N N 230 S9L H122 H N N 231 S9L H221 H N N 232 S9L H222 H N N 233 S9L H131 H N N 234 S9L H132 H N N 235 S9L H231 H N N 236 S9L H232 H N N 237 S9L H141 H N N 238 S9L H142 H N N 239 S9L H241 H N N 240 S9L H242 H N N 241 S9L "HO3'" H N N 242 SO4 S S N N 243 SO4 O1 O N N 244 SO4 O2 O N N 245 SO4 O3 O N N 246 SO4 O4 O N N 247 U OP3 O N N 248 U P P N N 249 U OP1 O N N 250 U OP2 O N N 251 U "O5'" O N N 252 U "C5'" C N N 253 U "C4'" C N R 254 U "O4'" O N N 255 U "C3'" C N S 256 U "O3'" O N N 257 U "C2'" C N R 258 U "O2'" O N N 259 U "C1'" C N R 260 U N1 N N N 261 U C2 C N N 262 U O2 O N N 263 U N3 N N N 264 U C4 C N N 265 U O4 O N N 266 U C5 C N N 267 U C6 C N N 268 U HOP3 H N N 269 U HOP2 H N N 270 U "H5'" H N N 271 U "H5''" H N N 272 U "H4'" H N N 273 U "H3'" H N N 274 U "HO3'" H N N 275 U "H2'" H N N 276 U "HO2'" H N N 277 U "H1'" H N N 278 U H3 H N N 279 U H5 H N N 280 U H6 H N N 281 # 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 A2M P OP1 doub N N 40 A2M P OP3 sing N N 41 A2M P "O5'" sing N N 42 A2M OP3 HOP3 sing N N 43 A2M "O5'" "C5'" sing N N 44 A2M "C5'" "C4'" sing N N 45 A2M "C5'" "H5'" sing N N 46 A2M "C5'" "H5''" sing N N 47 A2M "C4'" "O4'" sing N N 48 A2M "C4'" "C3'" sing N N 49 A2M "C4'" "H4'" sing N N 50 A2M "O4'" "C1'" sing N N 51 A2M "C3'" "O3'" sing N N 52 A2M "C3'" "C2'" sing N N 53 A2M "C3'" "H3'" sing N N 54 A2M "O3'" "HO3'" sing N N 55 A2M "C2'" "O2'" sing N N 56 A2M "C2'" "C1'" sing N N 57 A2M "C2'" "H2'" sing N N 58 A2M "O2'" "CM'" sing N N 59 A2M "C1'" N9 sing N N 60 A2M "C1'" "H1'" sing N N 61 A2M "CM'" "HM'1" sing N N 62 A2M "CM'" "HM'2" sing N N 63 A2M "CM'" "HM'3" sing N N 64 A2M N9 C8 sing Y N 65 A2M N9 C4 sing Y N 66 A2M C8 N7 doub Y N 67 A2M C8 H8 sing N N 68 A2M N7 C5 sing Y N 69 A2M C5 C6 sing Y N 70 A2M C5 C4 doub Y N 71 A2M C6 N6 sing N N 72 A2M C6 N1 doub Y N 73 A2M N6 H61 sing N N 74 A2M N6 H62 sing N N 75 A2M N1 C2 sing Y N 76 A2M C2 N3 doub Y N 77 A2M C2 H2 sing N N 78 A2M N3 C4 sing Y N 79 A2M P OP2 sing N N 80 A2M OP2 HOP2 sing N N 81 C OP3 P sing N N 82 C OP3 HOP3 sing N N 83 C P OP1 doub N N 84 C P OP2 sing N N 85 C P "O5'" sing N N 86 C OP2 HOP2 sing N N 87 C "O5'" "C5'" sing N N 88 C "C5'" "C4'" sing N N 89 C "C5'" "H5'" sing N N 90 C "C5'" "H5''" sing N N 91 C "C4'" "O4'" sing N N 92 C "C4'" "C3'" sing N N 93 C "C4'" "H4'" sing N N 94 C "O4'" "C1'" sing N N 95 C "C3'" "O3'" sing N N 96 C "C3'" "C2'" sing N N 97 C "C3'" "H3'" sing N N 98 C "O3'" "HO3'" sing N N 99 C "C2'" "O2'" sing N N 100 C "C2'" "C1'" sing N N 101 C "C2'" "H2'" sing N N 102 C "O2'" "HO2'" sing N N 103 C "C1'" N1 sing N N 104 C "C1'" "H1'" sing N N 105 C N1 C2 sing N N 106 C N1 C6 sing N N 107 C C2 O2 doub N N 108 C C2 N3 sing N N 109 C N3 C4 doub N N 110 C C4 N4 sing N N 111 C C4 C5 sing N N 112 C N4 H41 sing N N 113 C N4 H42 sing N N 114 C C5 C6 doub N N 115 C C5 H5 sing N N 116 C C6 H6 sing N N 117 G OP3 P sing N N 118 G OP3 HOP3 sing N N 119 G P OP1 doub N N 120 G P OP2 sing N N 121 G P "O5'" sing N N 122 G OP2 HOP2 sing N N 123 G "O5'" "C5'" sing N N 124 G "C5'" "C4'" sing N N 125 G "C5'" "H5'" sing N N 126 G "C5'" "H5''" sing N N 127 G "C4'" "O4'" sing N N 128 G "C4'" "C3'" sing N N 129 G "C4'" "H4'" sing N N 130 G "O4'" "C1'" sing N N 131 G "C3'" "O3'" sing N N 132 G "C3'" "C2'" sing N N 133 G "C3'" "H3'" sing N N 134 G "O3'" "HO3'" sing N N 135 G "C2'" "O2'" sing N N 136 G "C2'" "C1'" sing N N 137 G "C2'" "H2'" sing N N 138 G "O2'" "HO2'" sing N N 139 G "C1'" N9 sing N N 140 G "C1'" "H1'" sing N N 141 G N9 C8 sing Y N 142 G N9 C4 sing Y N 143 G C8 N7 doub Y N 144 G C8 H8 sing N N 145 G N7 C5 sing Y N 146 G C5 C6 sing N N 147 G C5 C4 doub Y N 148 G C6 O6 doub N N 149 G C6 N1 sing N N 150 G N1 C2 sing N N 151 G N1 H1 sing N N 152 G C2 N2 sing N N 153 G C2 N3 doub N N 154 G N2 H21 sing N N 155 G N2 H22 sing N N 156 G N3 C4 sing N N 157 HOH O H1 sing N N 158 HOH O H2 sing N N 159 NCO CO N1 sing N N 160 NCO CO N2 sing N N 161 NCO CO N3 sing N N 162 NCO CO N4 sing N N 163 NCO CO N5 sing N N 164 NCO CO N6 sing N N 165 NCO N1 HN11 sing N N 166 NCO N1 HN12 sing N N 167 NCO N1 HN13 sing N N 168 NCO N2 HN21 sing N N 169 NCO N2 HN22 sing N N 170 NCO N2 HN23 sing N N 171 NCO N3 HN31 sing N N 172 NCO N3 HN32 sing N N 173 NCO N3 HN33 sing N N 174 NCO N4 HN41 sing N N 175 NCO N4 HN42 sing N N 176 NCO N4 HN43 sing N N 177 NCO N5 HN51 sing N N 178 NCO N5 HN52 sing N N 179 NCO N5 HN53 sing N N 180 NCO N6 HN61 sing N N 181 NCO N6 HN62 sing N N 182 NCO N6 HN63 sing N N 183 P5P N1 C2 sing Y N 184 P5P N1 C6 doub Y N 185 P5P C2 N3 doub Y N 186 P5P C2 H2 sing N N 187 P5P N3 C4 sing Y N 188 P5P C4 C5 doub Y N 189 P5P C4 N9 sing Y N 190 P5P C5 C6 sing Y N 191 P5P C5 N7 sing Y N 192 P5P C6 H6 sing N N 193 P5P N7 C8 doub Y N 194 P5P C8 N9 sing Y N 195 P5P C8 H8 sing N N 196 P5P N9 "C1'" sing N N 197 P5P "C1'" "C2'" sing N N 198 P5P "C1'" "O4'" sing N N 199 P5P "C1'" "H1'" sing N N 200 P5P "C2'" "O2'" sing N N 201 P5P "C2'" "C3'" sing N N 202 P5P "C2'" "H2'" sing N N 203 P5P "O2'" "HO2'" sing N N 204 P5P "C3'" "O3'" sing N N 205 P5P "C3'" "C4'" sing N N 206 P5P "C3'" "H3'" sing N N 207 P5P "O3'" "HO3'" sing N N 208 P5P "C4'" "O4'" sing N N 209 P5P "C4'" "C5'" sing N N 210 P5P "C4'" "H4'" sing N N 211 P5P "C5'" "O5'" sing N N 212 P5P "C5'" "H5'1" sing N N 213 P5P "C5'" "H5'2" sing N N 214 P5P "O5'" P sing N N 215 P5P P OP1 doub N N 216 P5P P OP2 sing N N 217 P5P P OP3 sing N N 218 P5P OP2 HOP2 sing N N 219 P5P OP3 HOP3 sing N N 220 S9L O3P P sing N N 221 S9L O3P HO3P sing N N 222 S9L P O2P doub N N 223 S9L P O1P sing N N 224 S9L P "O5'" sing N N 225 S9L O1P HO1P sing N N 226 S9L "O5'" C12 sing N N 227 S9L C12 C22 sing N N 228 S9L C12 H121 sing N N 229 S9L C12 H122 sing N N 230 S9L C22 OH3 sing N N 231 S9L C22 H221 sing N N 232 S9L C22 H222 sing N N 233 S9L OH3 C23 sing N N 234 S9L C13 C23 sing N N 235 S9L C13 OH4 sing N N 236 S9L C13 H131 sing N N 237 S9L C13 H132 sing N N 238 S9L C23 H231 sing N N 239 S9L C23 H232 sing N N 240 S9L OH4 C24 sing N N 241 S9L C14 C24 sing N N 242 S9L C14 "O3'" sing N N 243 S9L C14 H141 sing N N 244 S9L C14 H142 sing N N 245 S9L C24 H241 sing N N 246 S9L C24 H242 sing N N 247 S9L "O3'" "HO3'" sing N N 248 SO4 S O1 doub N N 249 SO4 S O2 doub N N 250 SO4 S O3 sing N N 251 SO4 S O4 sing N N 252 U OP3 P sing N N 253 U OP3 HOP3 sing N N 254 U P OP1 doub N N 255 U P OP2 sing N N 256 U P "O5'" sing N N 257 U OP2 HOP2 sing N N 258 U "O5'" "C5'" sing N N 259 U "C5'" "C4'" sing N N 260 U "C5'" "H5'" sing N N 261 U "C5'" "H5''" sing N N 262 U "C4'" "O4'" sing N N 263 U "C4'" "C3'" sing N N 264 U "C4'" "H4'" sing N N 265 U "O4'" "C1'" sing N N 266 U "C3'" "O3'" sing N N 267 U "C3'" "C2'" sing N N 268 U "C3'" "H3'" sing N N 269 U "O3'" "HO3'" sing N N 270 U "C2'" "O2'" sing N N 271 U "C2'" "C1'" sing N N 272 U "C2'" "H2'" sing N N 273 U "O2'" "HO2'" sing N N 274 U "C1'" N1 sing N N 275 U "C1'" "H1'" sing N N 276 U N1 C2 sing N N 277 U N1 C6 sing N N 278 U C2 O2 doub N N 279 U C2 N3 sing N N 280 U N3 C4 sing N N 281 U N3 H3 sing N N 282 U C4 O4 doub N N 283 U C4 C5 sing N N 284 U C5 C6 doub N N 285 U C5 H5 sing N N 286 U C6 H6 sing N N 287 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4G6P 'double helix' 4G6P 'a-form double helix' 4G6P 'bulge loop' 4G6P 'mismatched base pair' 4G6P 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 2 1_555 B G 12 1_555 0.310 -0.154 -0.120 6.892 -19.624 3.350 1 A_C-4:G13_B A -4 ? B 13 ? 19 1 1 A C 3 1_555 B G 11 1_555 0.112 -0.148 -0.103 -1.997 -7.365 -0.342 2 A_C-3:G12_B A -3 ? B 12 ? 19 1 1 A C 4 1_555 B G 10 1_555 0.151 -0.036 0.009 3.455 2.925 3.210 3 A_C-2:G11_B A -2 ? B 11 ? 19 1 1 A A2M 5 1_555 B A 8 1_555 6.653 -3.696 -0.140 15.193 7.295 -27.920 4 A_A2M-1:A9_B A -1 ? B 9 ? ? ? 1 A U 7 1_555 B G 7 1_555 -8.088 -3.377 -0.448 13.650 2.496 -1.830 5 A_U2:G8_B A 2 ? B 8 ? ? ? 1 A C 8 1_555 B A 6 1_555 -1.964 0.733 -1.299 24.789 -17.102 5.213 6 A_C3:A7_B A 3 ? B 7 ? ? ? 1 A C 9 1_555 B G 5 1_555 -0.186 0.127 -0.250 10.723 -11.982 0.265 7 A_C4:G6_B A 4 ? B 6 ? 19 1 1 A A 10 1_555 B U 4 1_555 0.086 0.035 0.398 4.247 -12.138 1.908 8 A_A5:U5_B A 5 ? B 5 ? 20 1 1 A C 11 1_555 B G 3 1_555 0.260 0.175 0.131 6.636 -12.814 3.980 9 A_C6:G4_B A 6 ? B 4 ? 19 1 1 A C 12 1_555 B G 2 1_555 0.154 -0.151 0.541 -0.626 -10.305 1.229 10 A_C7:G3_B A 7 ? B 3 ? 19 1 1 A G 13 1_555 B C 1 1_555 -0.388 -0.015 0.240 -0.455 -10.262 5.465 11 A_G8:C2_B A 8 ? B 2 ? 19 1 1 B G 14 1_555 C C 19 1_555 -0.422 0.055 0.713 7.609 -9.190 1.954 12 B_G15:C49_C B 15 ? C 49 ? 19 1 1 B G 15 1_555 C C 18 1_555 -0.291 -0.039 0.287 8.804 -12.446 -0.331 13 B_G16:C48_C B 16 ? C 48 ? 19 1 1 B C 16 1_555 C G 17 1_555 -0.014 0.093 0.080 5.191 -13.167 3.168 14 B_C17:G47_C B 17 ? C 47 ? 19 1 1 B A 17 1_555 C U 16 1_555 -0.450 0.007 0.093 -0.682 -9.119 2.042 15 B_A18:U46_C B 18 ? C 46 ? 20 1 1 B G 18 1_555 C C 15 1_555 -0.194 -0.215 -0.409 -10.107 -7.855 0.498 16 B_G19:C45_C B 19 ? C 45 ? 19 1 1 B A 19 1_555 C C 14 1_555 2.044 0.350 -0.199 -12.609 -6.205 17.725 17 B_A20:C44_C B 20 ? C 44 ? ? 1 1 B G 20 1_555 C A 13 1_555 7.055 -4.631 0.004 -8.801 -0.621 -8.124 18 B_G21:A43_C B 21 ? C 43 ? 11 10 1 B A 21 1_555 C U 11 1_555 -4.357 -1.811 -0.293 -1.385 -8.848 -98.156 19 B_A22:U41_C B 22 ? C 41 ? 24 4 1 B A 22 1_555 C A 10 1_555 -4.201 1.287 -0.368 2.366 -15.705 -96.450 20 B_A23:A40_C B 23 ? C 40 ? ? ? 1 B A 23 1_555 C P5P 8 1_555 5.149 2.853 -0.649 -4.034 -15.782 -145.668 21 B_A24:P5P38_C B 24 ? C 38 ? ? ? 1 B C 24 1_555 A G 6 1_555 0.133 -0.054 0.084 20.063 -12.200 0.061 22 B_C25:G1_A B 25 ? A 1 ? 19 1 1 B A 25 1_555 C G 6 1_555 -0.031 1.461 -0.472 -10.951 -17.335 -15.605 23 B_A26:G36_C B 26 ? C 36 ? 8 1 1 B C 26 1_555 C G 5 1_555 -0.144 -0.194 0.277 6.353 -20.838 -0.521 24 B_C27:G35_C B 27 ? C 35 ? 19 1 1 B A 27 1_555 C U 4 1_555 0.203 -0.163 0.413 4.305 -19.355 -0.851 25 B_A28:U34_C B 28 ? C 34 ? 20 1 1 B C 28 1_555 C G 3 1_555 0.057 -0.084 0.241 4.773 -11.762 3.110 26 B_C29:G33_C B 29 ? C 33 ? 19 1 1 B G 29 1_555 C C 2 1_555 -0.351 -0.056 0.236 -5.830 -14.945 -0.276 27 B_G30:C32_C B 30 ? C 32 ? 19 1 1 B A 30 1_555 C U 1 1_555 0.338 0.008 0.316 -3.296 -9.387 3.403 28 B_A31:U31_C B 31 ? C 31 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 2 1_555 B G 12 1_555 A C 3 1_555 B G 11 1_555 -0.737 -1.859 3.549 -0.924 9.606 31.173 -4.995 1.152 2.884 17.361 1.670 32.597 1 AA_C-4C-3:G12G13_BB A -4 ? B 13 ? A -3 ? B 12 ? 1 A C 3 1_555 B G 11 1_555 A C 4 1_555 B G 10 1_555 0.677 -1.650 3.278 0.494 9.378 26.318 -5.476 -1.295 2.561 19.811 -1.044 27.916 2 AA_C-3C-2:G11G12_BB A -3 ? B 12 ? A -2 ? B 11 ? 1 A C 4 1_555 B G 10 1_555 A A2M 5 1_555 B A 8 1_555 -0.081 -0.849 5.290 -3.590 29.970 74.857 -1.944 -0.091 4.740 23.757 2.846 79.879 3 AA_C-2A2M-1:A9G11_BB A -2 ? B 11 ? A -1 ? B 9 ? 1 A A2M 5 1_555 B A 8 1_555 A U 7 1_555 B G 7 1_555 -1.104 -0.228 3.365 2.411 3.543 4.338 -18.707 21.650 1.826 36.932 -25.129 6.097 4 AA_A2M-1U2:G8A9_BB A -1 ? B 9 ? A 2 ? B 8 ? 1 A U 7 1_555 B G 7 1_555 A C 8 1_555 B A 6 1_555 0.133 -0.850 3.143 -0.613 7.124 57.762 -1.230 -0.168 3.027 7.343 0.631 58.165 5 AA_U2C3:A7G8_BB A 2 ? B 8 ? A 3 ? B 7 ? 1 A C 8 1_555 B A 6 1_555 A C 9 1_555 B G 5 1_555 -0.144 -1.362 3.847 -7.456 9.324 37.205 -3.317 -0.805 3.388 14.174 11.335 39.009 6 AA_C3C4:G6A7_BB A 3 ? B 7 ? A 4 ? B 6 ? 1 A C 9 1_555 B G 5 1_555 A A 10 1_555 B U 4 1_555 -0.252 -1.676 3.271 -4.817 12.019 33.205 -4.358 -0.234 2.542 20.106 8.059 35.574 7 AA_C4A5:U5G6_BB A 4 ? B 6 ? A 5 ? B 5 ? 1 A A 10 1_555 B U 4 1_555 A C 11 1_555 B G 3 1_555 -0.279 -1.569 3.233 1.051 2.384 29.423 -3.568 0.763 3.087 4.682 -2.064 29.536 8 AA_A5C6:G4U5_BB A 5 ? B 5 ? A 6 ? B 4 ? 1 A C 11 1_555 B G 3 1_555 A C 12 1_555 B G 2 1_555 -0.039 -2.006 3.288 -3.640 7.651 32.295 -4.685 -0.499 2.742 13.468 6.408 33.359 9 AA_C6C7:G3G4_BB A 6 ? B 4 ? A 7 ? B 3 ? 1 A C 12 1_555 B G 2 1_555 A G 13 1_555 B C 1 1_555 0.347 -1.960 3.018 4.046 7.705 29.580 -4.977 0.022 2.466 14.695 -7.717 30.806 10 AA_C7G8:C2G3_BB A 7 ? B 3 ? A 8 ? B 2 ? 1 B G 14 1_555 C C 19 1_555 B G 15 1_555 C C 18 1_555 -0.842 -1.102 3.123 -0.912 8.194 34.153 -2.956 1.271 2.813 13.705 1.525 35.106 11 BB_G15G16:C48C49_CC B 15 ? C 49 ? B 16 ? C 48 ? 1 B G 15 1_555 C C 18 1_555 B C 16 1_555 C G 17 1_555 0.277 -1.343 3.395 1.004 7.054 33.968 -3.333 -0.311 3.070 11.912 -1.696 34.686 12 BB_G16C17:G47C48_CC B 16 ? C 48 ? B 17 ? C 47 ? 1 B C 16 1_555 C G 17 1_555 B A 17 1_555 C U 16 1_555 0.348 -1.893 3.250 -2.052 11.477 30.067 -5.232 -0.952 2.359 21.150 3.781 32.199 13 BB_C17A18:U46G47_CC B 17 ? C 47 ? B 18 ? C 46 ? 1 B A 17 1_555 C U 16 1_555 B G 18 1_555 C C 15 1_555 0.116 -2.080 3.584 2.391 7.519 32.058 -4.974 0.213 3.032 13.363 -4.249 32.990 14 BB_A18G19:C45U46_CC B 18 ? C 46 ? B 19 ? C 45 ? 1 B G 18 1_555 C C 15 1_555 B A 19 1_555 C C 14 1_555 1.149 -1.402 3.355 0.895 6.694 36.685 -3.074 -1.679 3.087 10.525 -1.407 37.281 15 BB_G19A20:C44C45_CC B 19 ? C 45 ? B 20 ? C 44 ? 1 B A 19 1_555 C C 14 1_555 B G 20 1_555 C A 13 1_555 -0.772 -1.045 3.237 6.969 5.867 59.716 -1.316 1.097 3.033 5.855 -6.955 60.343 16 BB_A20G21:A43C44_CC B 20 ? C 44 ? B 21 ? C 43 ? 1 B G 20 1_555 C A 13 1_555 B A 21 1_555 C U 11 1_555 -2.290 -0.433 3.330 3.040 0.576 11.272 -2.855 15.084 2.597 2.864 -15.106 11.688 17 BB_G21A22:U41A43_CC B 21 ? C 43 ? B 22 ? C 41 ? 1 B A 21 1_555 C U 11 1_555 B A 22 1_555 C A 10 1_555 -0.116 -2.271 3.486 -10.159 4.440 46.522 -3.174 -0.700 3.225 5.529 12.651 47.754 18 BB_A22A23:A40U41_CC B 22 ? C 41 ? B 23 ? C 40 ? 1 B A 22 1_555 C A 10 1_555 B A 23 1_555 C P5P 8 1_555 -3.172 -2.803 3.690 -5.288 0.882 72.627 -2.395 2.474 3.852 0.744 4.459 72.798 19 BB_A23A24:P5P38A40_CC B 23 ? C 40 ? B 24 ? C 38 ? 1 B A 23 1_555 C P5P 8 1_555 B C 24 1_555 A G 6 1_555 2.284 -0.242 2.872 -1.081 3.484 -32.040 -0.118 3.940 2.955 -6.286 -1.951 -32.242 20 BB_A24C25:G1P5P38_AC B 24 ? C 38 ? B 25 ? A 1 ? 1 B C 24 1_555 A G 6 1_555 B A 25 1_555 C G 6 1_555 0.303 -1.946 3.860 6.496 6.269 47.548 -2.937 0.211 3.601 7.694 -7.973 48.348 21 BB_C25A26:G36G1_CA B 25 ? A 1 ? B 26 ? C 36 ? 1 B A 25 1_555 C G 6 1_555 B C 26 1_555 C G 5 1_555 1.101 -0.643 2.906 -6.287 3.863 28.964 -1.922 -3.235 2.512 7.569 12.319 29.870 22 BB_A26C27:G35G36_CC B 26 ? C 36 ? B 27 ? C 35 ? 1 B C 26 1_555 C G 5 1_555 B A 27 1_555 C U 4 1_555 0.158 -1.115 3.214 -0.143 6.327 38.120 -2.432 -0.256 2.997 9.605 0.217 38.623 23 BB_C27A28:U34G35_CC B 27 ? C 35 ? B 28 ? C 34 ? 1 B A 27 1_555 C U 4 1_555 B C 28 1_555 C G 3 1_555 0.542 -1.264 3.238 2.402 1.237 30.777 -2.611 -0.557 3.218 2.325 -4.514 30.892 24 BB_A28C29:G33U34_CC B 28 ? C 34 ? B 29 ? C 33 ? 1 B C 28 1_555 C G 3 1_555 B G 29 1_555 C C 2 1_555 0.287 -1.493 3.337 2.880 9.281 34.146 -3.767 -0.063 2.860 15.422 -4.785 35.462 25 BB_C29G30:C32G33_CC B 29 ? C 33 ? B 30 ? C 32 ? 1 B G 29 1_555 C C 2 1_555 B A 30 1_555 C U 1 1_555 0.877 -1.523 3.090 4.166 4.850 32.998 -3.372 -0.884 2.929 8.440 -7.251 33.595 26 BB_G30A31:U31C32_CC B 30 ? C 32 ? B 31 ? C 31 ? # _atom_sites.entry_id 4G6P _atom_sites.fract_transf_matrix[1][1] 0.010676 _atom_sites.fract_transf_matrix[1][2] 0.006164 _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] 0.012328 _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] 0.007448 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C CO N O P S # loop_