data_21LD # _entry.id 21LD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.417 _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 21LD pdb_000021ld 10.2210/pdb21ld/pdb WWPDB D_1300067420 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-11-04 _pdbx_audit_revision_history.part_number ? # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 21LD _pdbx_database_status.recvd_initial_deposition_date 2025-12-17 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBC _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 3 _pdbx_contact_author.email huanglin36@mail.sysu.edu.cn _pdbx_contact_author.name_first Lin _pdbx_contact_author.name_last Huang _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-2121-365X # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'He, Y.' 1 ? 'Huang, L.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Crystal structure of the ester-hydrolyzing ribozyme (EHR)' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'He, Y.' 1 ? primary 'Huang, L.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*CP*CP*AP*CP*UP*GP*CP*GP*AP*GP*UP*UP*UP*C)-3') ; 4399.643 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*GP*AP*AP*GP*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*CP*CP*CP*CP*CP*AP*GP*CP*C)-3') ; 7641.636 1 ? ? ? ? 3 polymer syn ;RNA (5'-R(*GP*CP*UP*GP*GP*GP*AP*CP*AP*AP*CP*UP*AP*GP*AP*CP*AP*UP*AP*CP*AP*GP*UP*G)-3') ; 7755.703 1 ? ? ? ? 4 non-polymer syn GUANINE 151.126 1 ? ? ? ? 5 water nat water 18.015 2 ? ? ? ? # 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 no CCACUGCGAGUUUC CCACUGCGAGUUUC B ? 2 polyribonucleotide no no GGAAGCUCUGACCGACCCCCAGCC GGAAGCUCUGACCGACCCCCAGCC C ? 3 polyribonucleotide no no GCUGGGACAACUAGACAUACAGUG GCUGGGACAACUAGACAUACAGUG D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 GUANINE GUN 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 C n 1 3 A n 1 4 C n 1 5 U n 1 6 G n 1 7 C n 1 8 G n 1 9 A n 1 10 G n 1 11 U n 1 12 U n 1 13 U n 1 14 C n 2 1 G n 2 2 G n 2 3 A n 2 4 A n 2 5 G n 2 6 C n 2 7 U n 2 8 C n 2 9 U n 2 10 G n 2 11 A n 2 12 C n 2 13 C n 2 14 G n 2 15 A n 2 16 C n 2 17 C n 2 18 C n 2 19 C n 2 20 C n 2 21 A n 2 22 G n 2 23 C n 2 24 C n 3 1 G n 3 2 C n 3 3 U n 3 4 G n 3 5 G n 3 6 G n 3 7 A n 3 8 C n 3 9 A n 3 10 A n 3 11 C n 3 12 U n 3 13 A n 3 14 G n 3 15 A n 3 16 C n 3 17 A n 3 18 U n 3 19 A n 3 20 C n 3 21 A n 3 22 G n 3 23 U n 3 24 G n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 14 'synthetic construct' ? 32630 ? 2 1 sample 1 24 'synthetic construct' ? 32630 ? 3 1 sample 1 24 'synthetic construct' ? 32630 ? # 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 GUN non-polymer . GUANINE ? 'C5 H5 N5 O' 151.126 HOH non-polymer . WATER ? 'H2 O' 18.015 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 C 1 1 1 C C B . n A 1 2 C 2 2 2 C C B . n A 1 3 A 3 3 3 A A B . n A 1 4 C 4 4 4 C C B . n A 1 5 U 5 5 5 U U B . n A 1 6 G 6 6 6 G G B . n A 1 7 C 7 7 7 C C B . n A 1 8 G 8 8 8 G G B . n A 1 9 A 9 9 9 A A B . n A 1 10 G 10 10 10 G G B . n A 1 11 U 11 11 11 U U B . n A 1 12 U 12 12 12 U U B . n A 1 13 U 13 13 13 U U B . n A 1 14 C 14 14 14 C C B . n B 2 1 G 1 1 1 G G C . n B 2 2 G 2 2 2 G G C . n B 2 3 A 3 3 3 A A C . n B 2 4 A 4 4 4 A A C . n B 2 5 G 5 5 5 G G C . n B 2 6 C 6 6 6 C C C . n B 2 7 U 7 7 7 U U C . n B 2 8 C 8 8 8 C C C . n B 2 9 U 9 9 9 U U C . n B 2 10 G 10 10 10 G G C . n B 2 11 A 11 11 11 A A C . n B 2 12 C 12 12 12 C C C . n B 2 13 C 13 13 13 C C C . n B 2 14 G 14 14 14 G G C . n B 2 15 A 15 15 15 A A C . n B 2 16 C 16 16 16 C C C . n B 2 17 C 17 17 17 C C C . n B 2 18 C 18 18 18 C C C . n B 2 19 C 19 19 19 C C C . n B 2 20 C 20 20 20 C C C . n B 2 21 A 21 21 21 A A C . n B 2 22 G 22 22 22 G G C . n B 2 23 C 23 23 23 C C C . n B 2 24 C 24 24 24 C C C . n C 3 1 G 1 25 25 G G D . n C 3 2 C 2 26 26 C C D . n C 3 3 U 3 27 27 U U D . n C 3 4 G 4 28 28 G G D . n C 3 5 G 5 29 29 G G D . n C 3 6 G 6 30 30 G G D . n C 3 7 A 7 31 31 A A D . n C 3 8 C 8 32 32 C C D . n C 3 9 A 9 33 33 A A D . n C 3 10 A 10 34 34 A A D . n C 3 11 C 11 35 35 C C D . n C 3 12 U 12 36 36 U U D . n C 3 13 A 13 37 37 A A D . n C 3 14 G 14 38 38 G G D . n C 3 15 A 15 39 39 A A D . n C 3 16 C 16 40 40 C C D . n C 3 17 A 17 41 41 A A D . n C 3 18 U 18 42 42 U U D . n C 3 19 A 19 43 43 A A D . n C 3 20 C 20 44 44 C C D . n C 3 21 A 21 45 45 A A D . n C 3 22 G 22 46 46 G G D . n C 3 23 U 23 47 47 U U D . n C 3 24 G 24 48 48 G G D . n # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id GUN _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id GUN _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # 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 GUN 1 101 101 GUN GUN D . E 5 HOH 1 101 2 HOH HOH C . E 5 HOH 2 102 1 HOH HOH C . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_reference_DOI _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 ? 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 ? 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . ? 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? autoPROC ? ? ? . ? 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . ? 5 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 21LD _cell.details ? _cell.formula_units_Z ? _cell.length_a 71.880 _cell.length_a_esd ? _cell.length_b 71.880 _cell.length_b_esd ? _cell.length_c 82.581 _cell.length_c_esd ? _cell.volume 426674.093 _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 21LD _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 21LD _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.69 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 54.34 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.2 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;0.2 M Ammonium Acetate 0.1 M Sodium cacodylate trihydrate pH 6.2 34% MPD 10mM TCEP Hydrochloride ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 291 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER2 X 4M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2025-12-06 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.979183 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'SSRF BEAMLINE BL02U1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.979183 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL02U1 _diffrn_source.pdbx_synchrotron_site SSRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 21LD _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.69 _reflns.d_resolution_low 54.22 _reflns.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.number_all ? _reflns.number_obs 6189 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 96.5 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 12.5 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 13.900 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all 0.024 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.078 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 2.69 _reflns_shell.d_res_low 2.84 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.200 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 906 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 13.3 _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all 2.047 _reflns_shell.pdbx_Rpim_I_all 0.558 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.570 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 1.968 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 94.53 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 21LD _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.69 _refine.ls_d_res_low 35.94 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 6147 _refine.ls_number_reflns_R_free 293 _refine.ls_number_reflns_R_work 5854 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.32 _refine.ls_percent_reflns_R_free 4.77 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1794 _refine.ls_R_factor_R_free 0.1981 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1784 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.correlation_coeff_I_to_Fcsqd_work ? _refine.correlation_coeff_I_to_Fcsqd_free ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 20.7906 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.3182 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 2.69 _refine_hist.d_res_low 35.94 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 1322 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1309 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_Zscore _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0018 ? 1473 ? f_bond_d ? ? ? 'X-RAY DIFFRACTION' ? 0.9365 ? 2288 ? f_angle_d ? ? ? 'X-RAY DIFFRACTION' ? 0.1223 ? 307 ? f_chiral_restr ? ? ? 'X-RAY DIFFRACTION' ? 0.0024 ? 63 ? f_plane_restr ? ? ? 'X-RAY DIFFRACTION' ? 11.1117 ? 732 ? f_dihedral_angle_d ? ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.correlation_coeff_Fo_to_Fc _refine_ls_shell.correlation_coeff_Fo_to_Fc_free _refine_ls_shell.correlation_coeff_I_to_Fcsqd_work _refine_ls_shell.correlation_coeff_I_to_Fcsqd_free _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 2.69 3.39 . . 151 2955 99.94 . . . . 0.3079 . . . . . . . . . . . . . . . 0.3120 'X-RAY DIFFRACTION' 3.39 35.94 . . 142 2899 92.88 . . . . 0.1497 . . . . . . . . . . . . . . . 0.1710 # _struct.entry_id 21LD _struct.title 'Crystal structure of the ester-hydrolyzing ribozyme (EHR)' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 21LD _struct_keywords.text 'Ribozyme, Ester hydrolysis, RNA, Guanine' _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 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 21LD 21LD ? 1 ? 1 2 PDB 21LD 21LD ? 2 ? 1 3 PDB 21LD 21LD ? 3 ? 1 # 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 21LD B 1 ? 14 ? 21LD 1 ? 14 ? 1 14 2 2 21LD C 1 ? 24 ? 21LD 1 ? 24 ? 1 24 3 3 21LD D 1 ? 24 ? 21LD 25 ? 48 ? 25 48 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _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 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 C G 24 N1 ? ? B C 2 D G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 C G 24 O6 ? ? B C 2 D G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 C G 24 N2 ? ? B C 2 D G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 3 N1 ? ? ? 1_555 C U 23 N3 ? ? B A 3 D U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 3 N6 ? ? ? 1_555 C U 23 O4 ? ? B A 3 D U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 N3 ? ? ? 1_555 C G 22 N1 ? ? B C 4 D G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N4 ? ? ? 1_555 C G 22 O6 ? ? B C 4 D G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 O2 ? ? ? 1_555 C G 22 N2 ? ? B C 4 D G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 5 N3 ? ? ? 1_555 C A 21 N1 ? ? B U 5 D A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 O4 ? ? ? 1_555 C A 21 N6 ? ? B U 5 D A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 6 N1 ? ? ? 1_555 C C 20 N3 ? ? B G 6 D C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 6 N2 ? ? ? 1_555 C C 20 O2 ? ? B G 6 D C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 6 O6 ? ? ? 1_555 C C 20 N4 ? ? B G 6 D C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 8 N1 ? ? ? 1_555 B C 8 N3 ? ? B G 8 C C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 8 N2 ? ? ? 1_555 B C 8 O2 ? ? B G 8 C C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 O6 ? ? ? 1_555 B C 8 N4 ? ? B G 8 C C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 7 N3 ? ? B A 9 C U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 7 O4 ? ? B A 9 C U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 6 N3 ? ? B G 10 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 6 O2 ? ? B G 10 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 6 N4 ? ? B G 10 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 11 N3 ? ? ? 1_555 B G 5 O6 ? ? B U 11 C G 5 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A U 11 O2 ? ? ? 1_555 B G 5 N1 ? ? B U 11 C G 5 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 4 N1 ? ? B U 12 C A 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 4 N6 ? ? B U 12 C A 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 3 N1 ? ? B U 13 C A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 3 N6 ? ? B U 13 C A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 2 N1 ? ? B C 14 C G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 2 O6 ? ? B C 14 C G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 2 N2 ? ? B C 14 C G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B U 9 N3 ? ? ? 1_555 C A 10 N7 ? ? C U 9 D A 34 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog32 hydrog ? ? B U 9 O2 ? ? ? 1_555 C A 10 N6 ? ? C U 9 D A 34 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog33 hydrog ? ? B A 11 N6 ? ? ? 1_555 C A 19 N3 ? ? C A 11 D A 43 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog34 hydrog ? ? B C 13 N3 ? ? ? 1_555 C G 14 N1 ? ? C C 13 D G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B C 13 N4 ? ? ? 1_555 C G 14 O6 ? ? C C 13 D G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B C 13 O2 ? ? ? 1_555 C G 14 N2 ? ? C C 13 D G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B C 13 O2 ? ? ? 1_555 C A 17 N6 ? ? C C 13 D A 41 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog38 hydrog ? ? B G 14 N1 ? ? ? 1_555 C C 11 N3 ? ? C G 14 D C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B G 14 N2 ? ? ? 1_555 C C 11 O2 ? ? C G 14 D C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B G 14 O6 ? ? ? 1_555 C C 11 N4 ? ? C G 14 D C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B C 18 N3 ? ? ? 1_555 C G 6 N1 ? ? C C 18 D G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B C 18 N4 ? ? ? 1_555 C G 6 O6 ? ? C C 18 D G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B C 18 O2 ? ? ? 1_555 C G 6 N2 ? ? C C 18 D G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B C 19 N3 ? ? ? 1_555 C G 5 N1 ? ? C C 19 D G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? B C 19 N4 ? ? ? 1_555 C G 5 O6 ? ? C C 19 D G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? B C 19 O2 ? ? ? 1_555 C G 5 N2 ? ? C C 19 D G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? B C 20 N3 ? ? ? 1_555 C G 4 N1 ? ? C C 20 D G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? B C 20 N4 ? ? ? 1_555 C G 4 O6 ? ? C C 20 D G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? B C 20 O2 ? ? ? 1_555 C G 4 N2 ? ? C C 20 D G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? B A 21 N1 ? ? ? 1_555 C U 3 N3 ? ? C A 21 D U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? B A 21 N6 ? ? ? 1_555 C U 3 O4 ? ? C A 21 D U 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? B G 22 N1 ? ? ? 1_555 C C 2 N3 ? ? C G 22 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? B G 22 N2 ? ? ? 1_555 C C 2 O2 ? ? C G 22 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? B G 22 O6 ? ? ? 1_555 C C 2 N4 ? ? C G 22 D C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B C 23 N3 ? ? ? 1_555 C G 1 N1 ? ? C C 23 D G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? B C 23 N4 ? ? ? 1_555 C G 1 O6 ? ? C C 23 D G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? B C 23 O2 ? ? ? 1_555 C G 1 N2 ? ? C C 23 D G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_entry_details.entry_id 21LD _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O3'" D C 44 ? ? P D A 45 ? ? OP2 D A 45 ? ? 87.10 105.20 -18.10 2.20 Y 2 1 "O3'" D C 44 ? ? P D A 45 ? ? OP1 D A 45 ? ? 80.66 105.20 -24.54 2.20 Y 3 1 OP1 D A 45 ? ? P D A 45 ? ? OP2 D A 45 ? ? 129.01 119.60 9.41 1.50 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y+1/2,x+1/2,z+1/4 3 y+1/2,-x+1/2,z+3/4 4 x+1/2,-y+1/2,-z+3/4 5 -x+1/2,y+1/2,-z+1/4 6 -x,-y,z+1/2 7 y,x,-z 8 -y,-x,-z+1/2 # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_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[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined 15.5052705238 -18.3549118506 1.98893468918 0.958842249866 ? -0.132901200977 ? 0.0388803028613 ? 0.918993118296 ? -0.144873499197 ? 0.977974854818 ? 3.57011071497 ? -1.50843572253 ? -0.683681032264 ? 4.14260821827 ? 2.2440689159 ? 1.19072118267 ? 0.427521746754 ? -0.15350270889 ? 0.163945928919 ? -0.198428085063 ? -0.691372507279 ? 0.555178806353 ? -0.399454076324 ? -0.42531454153 ? 0.0220537037792 ? 2 'X-RAY DIFFRACTION' ? refined 21.3482671714 -12.3845423413 5.48575786531 0.794373245047 ? -0.104015340174 ? -0.0428275482112 ? 0.888401930199 ? -0.138761931667 ? 0.981297708209 ? 6.07820588565 ? -1.52812449356 ? -4.59116064221 ? 0.591195573345 ? 1.49956608022 ? 3.94327379939 ? 0.433718574638 ? -0.621714007108 ? 0.826465576638 ? 0.531996782779 ? -0.105853363371 ? -0.24580754617 ? 0.0753657006794 ? 0.267673702077 ? -0.349462253738 ? 3 'X-RAY DIFFRACTION' ? refined 42.5613366728 0.718874225793 -0.122484378963 0.929422321208 ? -0.0649660900094 ? 0.094838518187 ? 0.775322138999 ? 0.0412668904723 ? 0.722037090901 ? 8.44212667471 ? -4.512442422 ? 3.70331843391 ? 8.09878333526 ? -1.11941971396 ? 3.03356353458 ? 0.308121359592 ? 1.15240200384 ? 0.461760253338 ? -0.624478703133 ? -0.163849352966 ? -0.298546881142 ? -0.733244771527 ? 0.736767475214 ? 0.0943290733097 ? 4 'X-RAY DIFFRACTION' ? refined 36.4932064234 -6.71750995413 1.36558759608 0.613044861445 ? 0.051892361608 ? 0.0343958659703 ? 0.578109902304 ? 0.0614245057136 ? 0.676011952232 ? 9.70945507523 ? 4.38188949995 ? 3.61338665053 ? 4.76884495786 ? 4.00808146502 ? 4.73669007868 ? -0.126087219085 ? 0.251372280232 ? 0.275051757524 ? 0.162525282478 ? -0.0440759276209 ? 0.442077980645 ? 0.407959446622 ? -0.231248834539 ? 0.19851175302 ? 5 'X-RAY DIFFRACTION' ? refined 24.3165371696 -24.6407344201 -5.39622707588 0.958097763149 ? -0.0467629871309 ? -0.0634607721622 ? 0.832814309466 ? -0.02769440613 ? 0.939514331639 ? 7.34595635036 ? 6.11786892227 ? 1.22483915122 ? 8.08077911904 ? 0.185078488244 ? 0.811407386213 ? -0.398497840868 ? 0.216432638774 ? -0.523827471248 ? -0.320894241649 ? 0.134449044116 ? -0.570254289461 ? 0.123934449259 ? -0.0494362712667 ? 0.269906470578 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_PDB_ins_code _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 A ? B 1 ? A ? B 14 ? ? ;chain 'B' and (resid 1 through 14 ) ; 2 'X-RAY DIFFRACTION' 2 B ? C 1 ? B ? C 15 ? ? ;chain 'C' and (resid 1 through 15 ) ; 3 'X-RAY DIFFRACTION' 3 B ? C 16 ? B ? C 24 ? ? ;chain 'C' and (resid 16 through 24 ) ; 4 'X-RAY DIFFRACTION' 4 C ? D 25 ? C ? D 34 ? ? ;chain 'D' and (resid 25 through 34 ) ; 5 'X-RAY DIFFRACTION' 5 C ? D 35 ? C ? D 48 ? ? ;chain 'D' and (resid 35 through 48 ) ; # 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 GUN N9 N Y N 111 GUN C8 C Y N 112 GUN N7 N Y N 113 GUN C5 C Y N 114 GUN C6 C N N 115 GUN O6 O N N 116 GUN N1 N N N 117 GUN C2 C N N 118 GUN N2 N N N 119 GUN N3 N N N 120 GUN C4 C Y N 121 GUN HN9 H N N 122 GUN H8 H N N 123 GUN HN1 H N N 124 GUN HN21 H N N 125 GUN HN22 H N N 126 HOH O O N N 127 HOH H1 H N N 128 HOH H2 H N N 129 U OP3 O N N 130 U P P N N 131 U OP1 O N N 132 U OP2 O N N 133 U "O5'" O N N 134 U "C5'" C N N 135 U "C4'" C N R 136 U "O4'" O N N 137 U "C3'" C N S 138 U "O3'" O N N 139 U "C2'" C N R 140 U "O2'" O N N 141 U "C1'" C N R 142 U N1 N N N 143 U C2 C N N 144 U O2 O N N 145 U N3 N N N 146 U C4 C N N 147 U O4 O N N 148 U C5 C N N 149 U C6 C N N 150 U HOP3 H N N 151 U HOP2 H N N 152 U "H5'" H N N 153 U "H5''" H N N 154 U "H4'" H N N 155 U "H3'" H N N 156 U "HO3'" H N N 157 U "H2'" H N N 158 U "HO2'" H N N 159 U "H1'" H N N 160 U H3 H N N 161 U H5 H N N 162 U H6 H N N 163 # 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 GUN N9 C8 sing Y N 116 GUN N9 C4 sing Y N 117 GUN N9 HN9 sing N N 118 GUN C8 N7 doub Y N 119 GUN C8 H8 sing N N 120 GUN N7 C5 sing Y N 121 GUN C5 C6 sing N N 122 GUN C5 C4 doub Y N 123 GUN C6 O6 doub N N 124 GUN C6 N1 sing N N 125 GUN N1 C2 sing N N 126 GUN N1 HN1 sing N N 127 GUN C2 N2 sing N N 128 GUN C2 N3 doub N N 129 GUN N2 HN21 sing N N 130 GUN N2 HN22 sing N N 131 GUN N3 C4 sing N N 132 HOH O H1 sing N N 133 HOH O H2 sing N N 134 U OP3 P sing N N 135 U OP3 HOP3 sing N N 136 U P OP1 doub N N 137 U P OP2 sing N N 138 U P "O5'" sing N N 139 U OP2 HOP2 sing N N 140 U "O5'" "C5'" sing N N 141 U "C5'" "C4'" sing N N 142 U "C5'" "H5'" sing N N 143 U "C5'" "H5''" sing N N 144 U "C4'" "O4'" sing N N 145 U "C4'" "C3'" sing N N 146 U "C4'" "H4'" sing N N 147 U "O4'" "C1'" sing N N 148 U "C3'" "O3'" sing N N 149 U "C3'" "C2'" sing N N 150 U "C3'" "H3'" sing N N 151 U "O3'" "HO3'" sing N N 152 U "C2'" "O2'" sing N N 153 U "C2'" "C1'" sing N N 154 U "C2'" "H2'" sing N N 155 U "O2'" "HO2'" sing N N 156 U "C1'" N1 sing N N 157 U "C1'" "H1'" sing N N 158 U N1 C2 sing N N 159 U N1 C6 sing N N 160 U C2 O2 doub N N 161 U C2 N3 sing N N 162 U N3 C4 sing N N 163 U N3 H3 sing N N 164 U C4 O4 doub N N 165 U C4 C5 sing N N 166 U C5 C6 doub N N 167 U C5 H5 sing N N 168 U C6 H6 sing N N 169 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 21LD 'double helix' 21LD '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 A C 2 1_555 C G 24 1_555 -0.158 -0.020 0.227 4.485 -4.409 4.051 1 B_C2:G48_D B 2 ? D 48 ? 19 1 1 A A 3 1_555 C U 23 1_555 -0.532 -0.202 0.332 4.304 -15.498 4.985 2 B_A3:U47_D B 3 ? D 47 ? 20 1 1 A C 4 1_555 C G 22 1_555 0.043 -0.135 0.155 4.323 -14.697 0.344 3 B_C4:G46_D B 4 ? D 46 ? 19 1 1 A U 5 1_555 C A 21 1_555 0.236 -0.163 0.122 -4.062 -17.329 5.588 4 B_U5:A45_D B 5 ? D 45 ? 20 1 1 A G 6 1_555 C C 20 1_555 -0.167 -0.098 -0.010 -14.509 -17.433 -3.322 5 B_G6:C44_D B 6 ? D 44 ? 19 1 1 B A 11 1_555 C A 19 1_555 -6.909 -0.530 -0.616 15.588 16.107 63.243 6 C_A11:A43_D C 11 ? D 43 ? ? 5 1 B C 13 1_555 C G 14 1_555 -0.076 -0.139 -0.127 -3.682 -5.980 -2.624 7 C_C13:G38_D C 13 ? D 38 ? 19 1 1 B G 14 1_555 C C 11 1_555 -0.130 -0.057 -0.111 -7.710 -3.530 -3.175 8 C_G14:C35_D C 14 ? D 35 ? 19 1 1 B G 2 1_555 A C 14 1_555 0.668 0.171 -0.187 -9.690 -8.502 -2.800 9 C_G2:C14_B C 2 ? B 14 ? 19 1 1 B A 3 1_555 A U 13 1_555 0.139 -0.213 -0.094 -0.935 -20.243 6.643 10 C_A3:U13_B C 3 ? B 13 ? 20 1 1 B A 4 1_555 A U 12 1_555 -0.080 -0.174 0.398 5.951 -20.317 10.717 11 C_A4:U12_B C 4 ? B 12 ? 20 1 1 B G 5 1_555 A U 11 1_555 -1.521 -0.192 -0.031 -4.320 -17.405 0.275 12 C_G5:U11_B C 5 ? B 11 ? 28 1 1 B C 6 1_555 A G 10 1_555 -0.300 -0.089 0.225 -3.168 -15.633 4.544 13 C_C6:G10_B C 6 ? B 10 ? 19 1 1 B U 7 1_555 A A 9 1_555 0.444 -0.140 0.134 -4.532 -11.522 -2.816 14 C_U7:A9_B C 7 ? B 9 ? 20 1 1 B C 8 1_555 A G 8 1_555 0.045 -0.076 0.203 -1.102 -11.267 2.737 15 C_C8:G8_B C 8 ? B 8 ? 19 1 1 B U 9 1_555 C A 10 1_555 4.574 -2.727 -0.029 -9.559 1.566 -95.610 16 C_U9:A34_D C 9 ? D 34 ? 24 4 1 B C 18 1_555 C G 6 1_555 0.524 -0.098 -0.677 17.776 -14.887 6.876 17 C_C18:G30_D C 18 ? D 30 ? 19 1 1 B C 19 1_555 C G 5 1_555 0.163 -0.126 -0.297 5.502 -8.717 3.242 18 C_C19:G29_D C 19 ? D 29 ? 19 1 1 B C 20 1_555 C G 4 1_555 0.011 -0.203 -0.159 1.822 -1.810 -0.090 19 C_C20:G28_D C 20 ? D 28 ? 19 1 1 B A 21 1_555 C U 3 1_555 0.258 -0.059 0.310 -0.121 -6.384 -3.193 20 C_A21:U27_D C 21 ? D 27 ? 20 1 1 B G 22 1_555 C C 2 1_555 0.275 -0.251 -0.065 3.264 -19.974 1.232 21 C_G22:C26_D C 22 ? D 26 ? 19 1 1 B C 23 1_555 C G 1 1_555 -0.438 -0.106 0.172 8.991 -14.806 0.610 22 C_C23:G25_D C 23 ? D 25 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A C 2 1_555 C G 24 1_555 A A 3 1_555 C U 23 1_555 -0.357 -1.621 3.011 -1.233 11.528 29.447 -4.758 0.466 2.246 21.650 2.315 31.600 1 BB_C2A3:U47G48_DD B 2 ? D 48 ? B 3 ? D 47 ? 1 A A 3 1_555 C U 23 1_555 A C 4 1_555 C G 22 1_555 -0.289 -1.232 3.204 0.239 7.298 33.854 -3.129 0.521 2.882 12.354 -0.405 34.609 2 BB_A3C4:G46U47_DD B 3 ? D 47 ? B 4 ? D 46 ? 1 A C 4 1_555 C G 22 1_555 A U 5 1_555 C A 21 1_555 0.596 -1.611 3.405 2.155 7.652 32.965 -3.986 -0.678 2.998 13.245 -3.730 33.885 3 BB_C4U5:A45G46_DD B 4 ? D 46 ? B 5 ? D 45 ? 1 A U 5 1_555 C A 21 1_555 A G 6 1_555 C C 20 1_555 -0.416 -1.656 3.355 1.708 11.419 29.646 -4.978 1.052 2.533 21.326 -3.189 31.768 4 BB_U5G6:C44A45_DD B 5 ? D 45 ? B 6 ? D 44 ? 1 A G 6 1_555 C C 20 1_555 B A 11 1_555 C A 19 1_555 -3.087 -4.083 2.977 9.860 18.258 57.953 -4.588 3.343 1.266 18.216 -9.838 61.251 5 BC_G6A11:A43C44_DD B 6 ? D 44 ? C 11 ? D 43 ? 1 B A 11 1_555 C A 19 1_555 B C 13 1_555 C G 14 1_555 1.961 -1.263 6.858 -9.634 6.174 125.067 -0.817 -1.270 6.728 3.476 5.424 125.364 6 CC_A11C13:G38A43_DD C 11 ? D 43 ? C 13 ? D 38 ? 1 B C 13 1_555 C G 14 1_555 B G 14 1_555 C C 11 1_555 -0.252 -1.819 3.384 0.674 7.192 24.451 -6.092 0.756 2.738 16.527 -1.548 25.480 7 CC_C13G14:C35G38_DD C 13 ? D 38 ? C 14 ? D 35 ? 1 B G 2 1_555 A C 14 1_555 B A 3 1_555 A U 13 1_555 -0.066 -0.973 2.979 -0.675 9.763 27.932 -3.695 0.005 2.504 19.484 1.348 29.564 8 CC_G2A3:U13C14_BB C 2 ? B 14 ? C 3 ? B 13 ? 1 B A 3 1_555 A U 13 1_555 B A 4 1_555 A U 12 1_555 0.269 -0.582 2.997 -2.898 10.509 29.573 -2.810 -0.975 2.606 19.762 5.450 31.477 9 CC_A3A4:U12U13_BB C 3 ? B 13 ? C 4 ? B 12 ? 1 B A 4 1_555 A U 12 1_555 B G 5 1_555 A U 11 1_555 0.483 -1.844 3.181 1.762 16.872 27.581 -5.790 -0.610 1.808 31.858 -3.326 32.294 10 CC_A4G5:U11U12_BB C 4 ? B 12 ? C 5 ? B 11 ? 1 B G 5 1_555 A U 11 1_555 B C 6 1_555 A G 10 1_555 -0.241 -1.522 3.124 -3.396 4.605 37.393 -2.901 -0.035 2.932 7.132 5.260 37.813 11 CC_G5C6:G10U11_BB C 5 ? B 11 ? C 6 ? B 10 ? 1 B C 6 1_555 A G 10 1_555 B U 7 1_555 A A 9 1_555 -0.847 -1.384 3.259 0.564 5.700 35.255 -3.049 1.460 2.992 9.335 -0.923 35.703 12 CC_C6U7:A9G10_BB C 6 ? B 10 ? C 7 ? B 9 ? 1 B U 7 1_555 A A 9 1_555 B C 8 1_555 A G 8 1_555 0.556 -1.735 2.972 1.709 10.140 26.461 -5.459 -0.811 2.201 21.163 -3.567 28.355 13 CC_U7C8:G8A9_BB C 7 ? B 9 ? C 8 ? B 8 ? 1 B C 8 1_555 A G 8 1_555 B U 9 1_555 C A 10 1_555 -2.671 -2.034 3.349 4.786 0.188 81.422 -1.562 2.167 3.211 0.144 -3.666 81.538 14 CC_C8U9:A34G8_DB C 8 ? B 8 ? C 9 ? D 34 ? 1 B C 18 1_555 C G 6 1_555 B C 19 1_555 C G 5 1_555 -0.147 -1.784 3.564 -2.204 10.029 30.814 -4.972 -0.128 2.862 18.249 4.010 32.441 15 CC_C18C19:G29G30_DD C 18 ? D 30 ? C 19 ? D 29 ? 1 B C 19 1_555 C G 5 1_555 B C 20 1_555 C G 4 1_555 -0.756 -1.975 3.321 -0.565 8.511 30.624 -5.074 1.285 2.701 15.734 1.044 31.762 16 CC_C19C20:G28G29_DD C 19 ? D 29 ? C 20 ? D 28 ? 1 B C 20 1_555 C G 4 1_555 B A 21 1_555 C U 3 1_555 -0.196 -1.584 3.237 -0.314 9.541 29.728 -4.612 0.310 2.617 18.020 0.593 31.190 17 CC_C20A21:U27G28_DD C 20 ? D 28 ? C 21 ? D 27 ? 1 B A 21 1_555 C U 3 1_555 B G 22 1_555 C C 2 1_555 0.224 -1.285 3.188 4.767 9.962 31.319 -3.796 0.346 2.670 17.775 -8.505 33.163 18 CC_A21G22:C26U27_DD C 21 ? D 27 ? C 22 ? D 26 ? 1 B G 22 1_555 C C 2 1_555 B C 23 1_555 C G 1 1_555 0.719 -1.497 2.972 -0.103 3.588 31.197 -3.360 -1.345 2.784 6.644 0.191 31.397 19 CC_G22C23:G25C26_DD C 22 ? D 26 ? C 23 ? D 25 ? # _pdbx_audit_support.funding_organization 'National Natural Science Foundation of China (NSFC)' _pdbx_audit_support.country China _pdbx_audit_support.grant_number 32171191 _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 7Q7X _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'P 41 21 2' _space_group.name_Hall 'P 4abw 2nw' _space_group.IT_number 92 _space_group.crystal_system tetragonal _space_group.id 1 # _atom_sites.entry_id 21LD _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.013912 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.013912 _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] 0.012109 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.51345 0.48472 ? ? 24.73122 6.32584 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 7.96527 ? ? ? 9.05267 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_ # loop_ #