data_2NPZ # _entry.id 2NPZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 2NPZ pdb_00002npz 10.2210/pdb2npz/pdb NDB UR0107 ? ? RCSB RCSB040160 ? ? WWPDB D_1000040160 ? ? # 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 2007-08-14 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-12-27 4 'Structure model' 1 3 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_conn 5 3 'Structure model' struct_site 6 4 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_dist_value' 4 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 6 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 19 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 20 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 21 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2NPZ _pdbx_database_status.recvd_initial_deposition_date 2006-10-30 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1ZFR '2.05 Angstrom crystal structure of junctionless hairpin ribozyme' unspecified PDB 2NPY ;Crystal structure of junctioned hairpin ribozyme incorporating 9 atom linker at A14 and 2'-deoxy 2'-amino U at A-1 ; unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'MacElrevey, C.' 1 'Krucinska, J.' 2 'Wedekind, J.E.' 3 # _citation.id primary _citation.title 'A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 63 _citation.page_first 812 _citation.page_last 825 _citation.year 2007 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17582172 _citation.pdbx_database_id_DOI 10.1107/S090744490702464X # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'MacElrevey, C.' 1 ? primary 'Spitale, R.C.' 2 ? primary 'Krucinska, J.' 3 ? primary 'Wedekind, J.E.' 4 ? # 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 "5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3'" 4052.470 1 ? ? ? 'RIBOZYME SUBSTRATE STRAND' 2 polymer syn "5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'" 3970.448 1 ? ? ? 'RIBOZYME DOMAIN LINKING STRAND' 3 polymer syn "5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'" 5535.445 1 ? U39C 'S-TURN STRAND' 'RIBOZYME DOMAIN LINKING STRAND' 4 polymer syn "5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'" 5991.568 1 ? ? ? 'RIBOZYME S-TURN STRAND' 5 non-polymer syn 'PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER' 156.074 1 ? ? ? ? 6 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 1 ? ? ? ? 7 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 no UCCCAGUCCACCG UCCCAGUCCACCG A ? 2 polyribonucleotide no no CGGUGAGAAGGG CGGUGAGAAGGG B ? 3 polyribonucleotide no no GGCAGAGAAACACACGA GGCAGAGAAACACACGA C ? 4 polyribonucleotide no no UCGUGGUACAUUACCUGCC UCGUGGUACAUUACCUGCC D ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 5 'PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER' PDI 6 'COBALT HEXAMMINE(III)' NCO 7 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 A 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 3 1 G n 3 2 G n 3 3 C n 3 4 A n 3 5 G n 3 6 A n 3 7 G n 3 8 A n 3 9 A n 3 10 A n 3 11 C n 3 12 A n 3 13 C n 3 14 A n 3 15 C n 3 16 G n 3 17 A n 4 1 U n 4 2 C n 4 3 G n 4 4 U n 4 5 G n 4 6 G n 4 7 U n 4 8 A n 4 9 C n 4 10 A n 4 11 U n 4 12 U n 4 13 A n 4 14 C n 4 15 C n 4 16 U n 4 17 G n 4 18 C n 4 19 C 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 ? ? ? ? ? 'Chemically synthesized, occurs naturally in satellite RNA tobacco ringspot virus' 2 1 sample ? ? ? ? ? 'Chemically synthesized, occurs naturally in satellite RNA tobacco ringspot virus' 3 1 sample ? ? ? ? ? 'Chemically synthesized, occurs naturally in satellite RNA tobacco ringspot virus' 4 1 sample ? ? ? ? ? 'Chemically synthesized, occurs naturally in satellite RNA tobacco ringspot virus' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 PDI non-polymer . 'PHOSPHORIC ACID MONO-(3-HYDROXY-PROPYL) ESTER' ? 'C3 H9 O5 P' 156.074 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 1 1 U U A . n A 1 2 C 2 2 2 C C A . n A 1 3 C 3 3 3 C C A . n A 1 4 C 4 4 4 C C A . n A 1 5 A 5 5 5 A A A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 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 C 3 1 G 1 15 15 G G C . n C 3 2 G 2 16 16 G G C . n C 3 3 C 3 17 17 C C C . n C 3 4 A 4 18 18 A A C . n C 3 5 G 5 19 19 G G C . n C 3 6 A 6 20 20 A A C . n C 3 7 G 7 21 21 G G C . n C 3 8 A 8 22 22 A A C . n C 3 9 A 9 23 23 A A C . n C 3 10 A 10 24 24 A A C . n C 3 11 C 11 25 25 C C C . n C 3 12 A 12 26 26 A A C . n C 3 13 C 13 27 27 C C C . n C 3 14 A 14 28 28 A A C . n C 3 15 C 15 29 29 C C C . n C 3 16 G 16 30 30 G G C . n C 3 17 A 17 31 31 A A C . n D 4 1 U 1 31 31 U U D . n D 4 2 C 2 32 32 C C D . n D 4 3 G 3 33 33 G G D . n D 4 4 U 4 34 34 U U D . n D 4 5 G 5 35 35 G G D . n D 4 6 G 6 36 36 G G D . n D 4 7 U 7 37 37 U U D . n D 4 8 A 8 38 38 A A D . n D 4 9 C 9 39 39 C C D . n D 4 10 A 10 40 40 A A D . n D 4 11 U 11 41 41 U U D . n D 4 12 U 12 42 42 U U D . n D 4 13 A 13 43 43 A A D . n D 4 14 C 14 44 44 C C D . n D 4 15 C 15 45 45 C C D . n D 4 16 U 16 46 46 U U D . n D 4 17 G 17 47 47 G G D . n D 4 18 C 18 48 48 C C D . n D 4 19 C 19 49 49 C C D . 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 E 5 PDI 1 14 14 PDI C3P B . F 6 NCO 1 4 4 NCO NCO C . G 7 HOH 1 1 1 HOH HOH B . H 7 HOH 1 2 2 HOH HOH C . I 7 HOH 1 3 3 HOH HOH D . # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag Y _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id A _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 5 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id "O2'" _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id A _pdbx_unobs_or_zero_occ_atoms.label_comp_id A _pdbx_unobs_or_zero_occ_atoms.label_seq_id 5 _pdbx_unobs_or_zero_occ_atoms.label_atom_id "O2'" # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 CrystalClear 'data collection' . ? 2 CrystalClear 'data reduction' . ? 3 CrystalClear 'data scaling' . ? 4 CNS phasing . ? 5 # _cell.entry_id 2NPZ _cell.length_a 91.130 _cell.length_b 91.130 _cell.length_c 144.960 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2NPZ _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2NPZ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 4.4 _exptl_crystal.density_percent_sol 81.1 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;PEG 2000 MME, lithium sulfate, cacodylate, spermidine, cobalt hexaamine, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.0 ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'PEG 2000 MME' ? ? ? 1 2 1 'lithium sulfate' ? ? ? 1 3 1 cacodylate ? ? ? 1 4 1 spermidine ? ? ? 1 5 1 'cobalt hexaamine' ? ? ? 1 6 2 'PEG 2000 MME' ? ? ? 1 7 2 'cobalt hexaamine' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV' _diffrn_detector.pdbx_collection_date 2005-05-25 _diffrn_detector.details 'Osmic confocal blue' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Osmic confocal blue' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 2NPZ _reflns.observed_criterion_sigma_I -5.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 34.66 _reflns.d_resolution_high 3.35 _reflns.number_obs 5453 _reflns.number_all 5532 _reflns.percent_possible_obs 98.6 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.106 _reflns.pdbx_netI_over_sigmaI 16.2 _reflns.B_iso_Wilson_estimate 63.3 _reflns.pdbx_redundancy 11.3 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 3.35 _reflns_shell.d_res_low 3.47 _reflns_shell.percent_possible_all 99.1 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.51 _reflns_shell.meanI_over_sigI_obs 4.7 _reflns_shell.pdbx_redundancy 12.4 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 522 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2NPZ _refine.ls_number_reflns_obs 5450 _refine.ls_number_reflns_all 5532 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F -3.0 _refine.pdbx_data_cutoff_high_absF 9836511.61 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.66 _refine.ls_d_res_high 3.35 _refine.ls_percent_reflns_obs 98.5 _refine.ls_R_factor_obs 0.268 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.261 _refine.ls_R_factor_R_free 0.277 _refine.ls_R_factor_R_free_error 0.012 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.5 _refine.ls_number_reflns_R_free 570 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 94.3 _refine.aniso_B[1][1] -1.68 _refine.aniso_B[2][2] -1.68 _refine.aniso_B[3][3] 3.37 _refine.aniso_B[1][2] -19.21 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.3 _refine.solvent_model_param_bsol 800 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model '2.05 angstrom junctionless ribozyme' _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 2NPZ _refine_analyze.Luzzati_coordinate_error_obs 0.53 _refine_analyze.Luzzati_sigma_a_obs 0.48 _refine_analyze.Luzzati_d_res_low_obs 34.74 _refine_analyze.Luzzati_coordinate_error_free 0.61 _refine_analyze.Luzzati_sigma_a_free 0.67 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1313 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 1331 _refine_hist.d_res_high 3.35 _refine_hist.d_res_low 34.66 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.4 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 17.1 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.70 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 4 _refine_ls_shell.d_res_high 3.35 _refine_ls_shell.d_res_low 3.69 _refine_ls_shell.number_reflns_R_work 1167 _refine_ls_shell.R_factor_R_work 0.334 _refine_ls_shell.percent_reflns_obs 99.5 _refine_ls_shell.R_factor_R_free 0.345 _refine_ls_shell.R_factor_R_free_error 0.028 _refine_ls_shell.percent_reflns_R_free 11.2 _refine_ls_shell.number_reflns_R_free 147 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 1167 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 water_rep.param dna-rnas9.top 'X-RAY DIFFRACTION' 2 dna-rnacm_rep.param water.top 'X-RAY DIFFRACTION' 3 cobalt.par cobalt.top 'X-RAY DIFFRACTION' 4 &_1_PARAMETER_INFILE_4 &_1_TOPOLOGY_INFILE_4 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 2NPZ _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 2NPZ _struct.title 'Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2NPZ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, RIBOZYME, HAIRPIN, E LOOP, S TURN, PROPYL' # 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 6 ? G N N 7 ? H N N 7 ? I N N 7 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 2NPZ 2NPZ ? ? ? 2 2 PDB 2NPZ 2NPZ ? ? ? 3 3 PDB 2NPZ 2NPZ ? ? ? 4 4 PDB 2NPZ 2NPZ ? ? ? # 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 2NPZ A 1 ? 13 ? 2NPZ 1 ? 13 ? 1 13 2 2 2NPZ B 1 ? 12 ? 2NPZ 2 ? 13 ? 2 13 3 3 2NPZ C 1 ? 17 ? 2NPZ 15 ? 31 ? 15 31 4 4 2NPZ D 1 ? 19 ? 2NPZ 31 ? 49 ? 31 49 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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,I # _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 one ? B G 12 "O3'" ? ? ? 1_555 E PDI . P ? ? B G 13 B PDI 14 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale2 covale one ? E PDI . OG ? ? ? 1_555 C G 1 P ? ? B PDI 14 C G 15 1_555 ? ? ? ? ? ? ? 1.601 ? ? hydrog1 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 2 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 2 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 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 4 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 6 N1 ? ? ? 1_555 C C 11 N3 ? ? A G 6 C C 25 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog11 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 10 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 10 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 11 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 12 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 13 B C 2 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog20 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 19 O2 ? ? C G 15 D C 49 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog21 hydrog ? ? C G 2 N1 ? ? ? 1_555 D C 18 N3 ? ? C G 16 D C 48 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog22 hydrog ? ? C C 3 N3 ? ? ? 1_555 D G 17 N1 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C C 3 N4 ? ? ? 1_555 D G 17 O6 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C C 3 O2 ? ? ? 1_555 D G 17 N2 ? ? C C 17 D G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C A 4 N1 ? ? ? 1_555 D U 16 N3 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C A 4 N6 ? ? ? 1_555 D U 16 O4 ? ? C A 18 D U 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C G 5 N1 ? ? ? 1_555 D C 15 N3 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C G 5 N2 ? ? ? 1_555 D C 15 O2 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C G 5 O6 ? ? ? 1_555 D C 15 N4 ? ? C G 19 D C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C A 6 N1 ? ? ? 1_555 D C 14 N4 ? ? C A 20 D C 44 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog31 hydrog ? ? C G 7 N2 ? ? ? 1_555 D A 13 N7 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog32 hydrog ? ? C G 7 N3 ? ? ? 1_555 D A 13 N6 ? ? C G 21 D A 43 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog33 hydrog ? ? C A 9 N6 ? ? ? 1_555 D A 10 N1 ? ? C A 23 D A 40 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog34 hydrog ? ? C A 12 N1 ? ? ? 1_555 D G 6 N1 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog35 hydrog ? ? C A 12 N6 ? ? ? 1_555 D G 6 O6 ? ? C A 26 D G 36 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog36 hydrog ? ? C C 13 N4 ? ? ? 1_555 D G 5 O6 ? ? C C 27 D G 35 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog37 hydrog ? ? C A 14 N1 ? ? ? 1_555 D U 4 N3 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C A 14 N6 ? ? ? 1_555 D U 4 O4 ? ? C A 28 D U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C C 15 N4 ? ? ? 1_555 D G 3 O6 ? ? C C 29 D G 33 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog40 hydrog ? ? C G 16 N1 ? ? ? 1_555 D C 2 N3 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C G 16 N2 ? ? ? 1_555 D C 2 O2 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C G 16 O6 ? ? ? 1_555 D C 2 N4 ? ? C G 30 D C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C A 17 N1 ? ? ? 1_555 D U 1 N3 ? ? C A 31 D U 31 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? # 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 C NCO 4 ? 4 'BINDING SITE FOR RESIDUE NCO C 4' AC2 Software B PDI 14 ? 3 'BINDING SITE FOR RESIDUE PDI B 14' # 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 4 A C 6 ? A C 20 . ? 1_555 ? 2 AC1 4 G C 7 ? G C 21 . ? 1_555 ? 3 AC1 4 A D 10 ? A D 40 . ? 1_555 ? 4 AC1 4 U D 11 ? U D 41 . ? 1_555 ? 5 AC2 3 U A 1 ? U A 1 . ? 10_665 ? 6 AC2 3 G B 12 ? G B 13 . ? 1_555 ? 7 AC2 3 G C 1 ? G C 15 . ? 1_555 ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 NCO CO CO N N 114 NCO N1 N N N 115 NCO N2 N N N 116 NCO N3 N N N 117 NCO N4 N N N 118 NCO N5 N N N 119 NCO N6 N N N 120 NCO HN11 H N N 121 NCO HN12 H N N 122 NCO HN13 H N N 123 NCO HN21 H N N 124 NCO HN22 H N N 125 NCO HN23 H N N 126 NCO HN31 H N N 127 NCO HN32 H N N 128 NCO HN33 H N N 129 NCO HN41 H N N 130 NCO HN42 H N N 131 NCO HN43 H N N 132 NCO HN51 H N N 133 NCO HN52 H N N 134 NCO HN53 H N N 135 NCO HN61 H N N 136 NCO HN62 H N N 137 NCO HN63 H N N 138 PDI O3P O N N 139 PDI P P N N 140 PDI O1P O N N 141 PDI O2P O N N 142 PDI OA O N N 143 PDI CA C N N 144 PDI CB C N N 145 PDI CG C N N 146 PDI OG O N N 147 PDI HOP3 H N N 148 PDI HOP2 H N N 149 PDI HA1 H N N 150 PDI HA2 H N N 151 PDI HB1 H N N 152 PDI HB2 H N N 153 PDI HG1 H N N 154 PDI HG2 H N N 155 PDI HGT H N N 156 U OP3 O N N 157 U P P N N 158 U OP1 O N N 159 U OP2 O N N 160 U "O5'" O N N 161 U "C5'" C N N 162 U "C4'" C N R 163 U "O4'" O N N 164 U "C3'" C N S 165 U "O3'" O N N 166 U "C2'" C N R 167 U "O2'" O N N 168 U "C1'" C N R 169 U N1 N N N 170 U C2 C N N 171 U O2 O N N 172 U N3 N N N 173 U C4 C N N 174 U O4 O N N 175 U C5 C N N 176 U C6 C N N 177 U HOP3 H N N 178 U HOP2 H N N 179 U "H5'" H N N 180 U "H5''" H N N 181 U "H4'" H N N 182 U "H3'" H N N 183 U "HO3'" H N N 184 U "H2'" H N N 185 U "HO2'" H N N 186 U "H1'" H N N 187 U H3 H N N 188 U H5 H N N 189 U H6 H N N 190 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 NCO CO N1 sing N N 118 NCO CO N2 sing N N 119 NCO CO N3 sing N N 120 NCO CO N4 sing N N 121 NCO CO N5 sing N N 122 NCO CO N6 sing N N 123 NCO N1 HN11 sing N N 124 NCO N1 HN12 sing N N 125 NCO N1 HN13 sing N N 126 NCO N2 HN21 sing N N 127 NCO N2 HN22 sing N N 128 NCO N2 HN23 sing N N 129 NCO N3 HN31 sing N N 130 NCO N3 HN32 sing N N 131 NCO N3 HN33 sing N N 132 NCO N4 HN41 sing N N 133 NCO N4 HN42 sing N N 134 NCO N4 HN43 sing N N 135 NCO N5 HN51 sing N N 136 NCO N5 HN52 sing N N 137 NCO N5 HN53 sing N N 138 NCO N6 HN61 sing N N 139 NCO N6 HN62 sing N N 140 NCO N6 HN63 sing N N 141 PDI O3P P sing N N 142 PDI O3P HOP3 sing N N 143 PDI P O1P doub N N 144 PDI P O2P sing N N 145 PDI P OA sing N N 146 PDI O2P HOP2 sing N N 147 PDI OA CA sing N N 148 PDI CA CB sing N N 149 PDI CA HA1 sing N N 150 PDI CA HA2 sing N N 151 PDI CB CG sing N N 152 PDI CB HB1 sing N N 153 PDI CB HB2 sing N N 154 PDI CG OG sing N N 155 PDI CG HG1 sing N N 156 PDI CG HG2 sing N N 157 PDI OG HGT sing N N 158 U OP3 P sing N N 159 U OP3 HOP3 sing N N 160 U P OP1 doub N N 161 U P OP2 sing N N 162 U P "O5'" sing N N 163 U OP2 HOP2 sing N N 164 U "O5'" "C5'" sing N N 165 U "C5'" "C4'" sing N N 166 U "C5'" "H5'" sing N N 167 U "C5'" "H5''" sing N N 168 U "C4'" "O4'" sing N N 169 U "C4'" "C3'" sing N N 170 U "C4'" "H4'" sing N N 171 U "O4'" "C1'" sing N N 172 U "C3'" "O3'" sing N N 173 U "C3'" "C2'" sing N N 174 U "C3'" "H3'" sing N N 175 U "O3'" "HO3'" sing N N 176 U "C2'" "O2'" sing N N 177 U "C2'" "C1'" sing N N 178 U "C2'" "H2'" sing N N 179 U "O2'" "HO2'" sing N N 180 U "C1'" N1 sing N N 181 U "C1'" "H1'" sing N N 182 U N1 C2 sing N N 183 U N1 C6 sing N N 184 U C2 O2 doub N N 185 U C2 N3 sing N N 186 U N3 C4 sing N N 187 U N3 H3 sing N N 188 U C4 O4 doub N N 189 U C4 C5 sing N N 190 U C5 C6 doub N N 191 U C5 H5 sing N N 192 U C6 H6 sing N N 193 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2NPZ 'double helix' 2NPZ 'a-form double helix' 2NPZ '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 0.437 -0.363 -0.934 15.076 -24.638 1.663 1 A_C2:G13_B A 2 ? B 13 ? 19 1 1 A C 3 1_555 B G 11 1_555 -0.490 -0.020 0.323 -8.370 -1.904 3.624 2 A_C3:G12_B A 3 ? B 12 ? 19 1 1 A C 4 1_555 B G 10 1_555 -0.259 0.313 -0.009 7.927 8.283 6.307 3 A_C4:G11_B A 4 ? B 11 ? 19 1 1 C C 11 1_555 A G 6 1_555 0.963 -0.269 0.398 -1.319 -7.667 -15.960 4 C_C25:G6_A C 25 ? A 6 ? ? ? 1 C A 12 1_555 D G 6 1_555 -0.411 1.554 -0.250 -23.522 -27.428 -10.151 5 C_A26:G36_D C 26 ? D 36 ? 8 1 1 C C 13 1_555 D G 5 1_555 0.510 0.240 -0.117 -7.363 -26.119 -2.194 6 C_C27:G35_D C 27 ? D 35 ? ? ? 1 C A 14 1_555 D U 4 1_555 -0.235 -0.030 0.708 7.572 -11.115 4.466 7 C_A28:U34_D C 28 ? D 34 ? 20 1 1 C C 15 1_555 D G 3 1_555 0.241 0.252 -0.343 10.318 -17.711 -5.065 8 C_C29:G33_D C 29 ? D 33 ? ? ? 1 C G 16 1_555 D C 2 1_555 0.116 -0.162 -0.327 -10.529 -9.272 5.588 9 C_G30:C32_D C 30 ? D 32 ? 19 1 1 C A 17 1_555 D U 1 1_555 1.055 0.285 0.774 2.169 7.281 10.249 10 C_A31:U31_D C 31 ? D 31 ? ? ? 1 A A 10 1_555 B U 4 1_555 -0.082 0.332 0.260 5.711 -16.786 -5.465 11 A_A10:U5_B A 10 ? B 5 ? 20 1 1 A C 11 1_555 B G 3 1_555 -0.089 -0.145 0.269 7.529 -10.711 -2.224 12 A_C11:G4_B A 11 ? B 4 ? 19 1 1 A C 12 1_555 B G 2 1_555 -0.074 -0.027 0.269 11.528 1.086 4.236 13 A_C12:G3_B A 12 ? B 3 ? 19 1 1 A G 13 1_555 B C 1 1_555 0.599 0.164 -0.281 5.314 -13.087 -11.161 14 A_G13:C2_B A 13 ? B 2 ? ? ? 1 C G 1 1_555 D C 19 1_555 -1.137 -0.069 1.106 8.416 6.462 9.564 15 C_G15:C49_D C 15 ? D 49 ? ? 1 1 C G 2 1_555 D C 18 1_555 -0.653 0.138 -0.572 -4.236 -3.087 11.423 16 C_G16:C48_D C 16 ? D 48 ? ? 1 1 C C 3 1_555 D G 17 1_555 0.587 0.136 -0.001 -0.238 -1.305 6.730 17 C_C17:G47_D C 17 ? D 47 ? 19 1 1 C A 4 1_555 D U 16 1_555 -0.172 -0.033 -0.406 -6.893 0.536 2.300 18 C_A18:U46_D C 18 ? D 46 ? 20 1 1 C G 5 1_555 D C 15 1_555 0.267 -0.090 -0.716 -5.202 -4.733 -1.098 19 C_G19:C45_D C 19 ? D 45 ? 19 1 1 C A 6 1_555 D C 14 1_555 2.654 0.296 -0.647 -15.986 -2.706 6.327 20 C_A20:C44_D C 20 ? D 44 ? ? ? 1 C G 7 1_555 D A 13 1_555 7.058 -3.838 0.312 -9.942 -8.762 -11.856 21 C_G21:A43_D C 21 ? D 43 ? 11 10 1 D A 10 1_555 C A 9 1_555 4.481 1.476 -0.676 -4.683 -28.068 -89.048 22 D_A40:A23_C D 40 ? C 23 ? ? ? # 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 -0.210 -1.940 3.741 -11.263 19.344 28.323 -5.880 -1.253 2.007 33.672 19.605 35.958 1 AA_C2C3:G12G13_BB A 2 ? 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 0.332 -1.354 2.931 -1.638 9.131 31.390 -3.727 -0.827 2.432 16.433 2.948 32.699 2 AA_C3C4:G11G12_BB A 3 ? B 12 ? A 4 ? B 11 ? 1 C C 11 1_555 A G 6 1_555 C A 12 1_555 D G 6 1_555 0.539 -2.738 3.661 5.615 1.403 37.551 -4.407 -0.028 3.601 2.164 -8.659 37.979 3 CC_C25A26:G36G6_DA C 25 ? A 6 ? C 26 ? D 36 ? 1 C A 12 1_555 D G 6 1_555 C C 13 1_555 D G 5 1_555 0.529 -0.296 3.131 -4.272 -3.480 35.242 -0.003 -1.455 3.062 -5.705 7.003 35.656 4 CC_A26C27:G35G36_DD C 26 ? D 36 ? C 27 ? D 35 ? 1 C C 13 1_555 D G 5 1_555 C A 14 1_555 D U 4 1_555 0.483 -1.729 2.548 -6.312 11.849 33.903 -3.894 -1.373 1.751 19.401 10.335 36.392 5 CC_C27A28:U34G35_DD C 27 ? D 35 ? C 28 ? D 34 ? 1 C A 14 1_555 D U 4 1_555 C C 15 1_555 D G 3 1_555 0.142 -1.146 3.079 10.573 -1.957 33.644 -1.613 1.270 3.044 -3.279 -17.713 35.273 6 CC_A28C29:G33U34_DD C 28 ? D 34 ? C 29 ? D 33 ? 1 C C 15 1_555 D G 3 1_555 C G 16 1_555 D C 2 1_555 0.914 -1.566 3.172 3.249 18.430 30.316 -4.884 -1.091 2.008 31.729 -5.594 35.511 7 CC_C29G30:C32G33_DD C 29 ? D 33 ? C 30 ? D 32 ? 1 C G 16 1_555 D C 2 1_555 C A 17 1_555 D U 1 1_555 0.267 -1.710 2.497 -8.451 4.523 38.170 -2.932 -1.126 2.182 6.787 12.681 39.311 8 CC_G30A31:U31C32_DD C 30 ? D 32 ? C 31 ? D 31 ? 1 A A 10 1_555 B U 4 1_555 A C 11 1_555 B G 3 1_555 -0.566 -2.060 2.946 -3.669 5.453 30.593 -4.705 0.454 2.597 10.188 6.854 31.275 9 AA_A10C11:G4U5_BB A 10 ? B 5 ? A 11 ? B 4 ? 1 A C 11 1_555 B G 3 1_555 A C 12 1_555 B G 2 1_555 0.062 -1.892 2.970 -3.938 7.962 30.184 -4.738 -0.730 2.379 14.888 7.364 31.435 10 AA_C11C12:G3G4_BB A 11 ? B 4 ? A 12 ? B 3 ? 1 A C 12 1_555 B G 2 1_555 A G 13 1_555 B C 1 1_555 -0.725 -1.715 3.726 1.055 3.854 32.469 -3.781 1.488 3.480 6.860 -1.878 32.707 11 AA_C12G13:C2G3_BB A 12 ? B 3 ? A 13 ? B 2 ? 1 C G 1 1_555 D C 19 1_555 C G 2 1_555 D C 18 1_555 -0.322 -2.007 3.200 8.273 11.496 38.716 -3.962 1.254 2.418 16.676 -12.001 41.132 12 CC_G15G16:C48C49_DD C 15 ? D 49 ? C 16 ? D 48 ? 1 C G 2 1_555 D C 18 1_555 C C 3 1_555 D G 17 1_555 -0.859 -1.417 2.883 -7.422 8.369 33.837 -3.367 0.476 2.595 13.915 12.340 35.586 13 CC_G16C17:G47C48_DD C 16 ? D 48 ? C 17 ? D 47 ? 1 C C 3 1_555 D G 17 1_555 C A 4 1_555 D U 16 1_555 -0.527 -1.546 3.179 -1.007 13.866 31.261 -4.568 0.757 2.321 24.284 1.763 34.142 14 CC_C17A18:U46G47_DD C 17 ? D 47 ? C 18 ? D 46 ? 1 C A 4 1_555 D U 16 1_555 C G 5 1_555 D C 15 1_555 -0.510 -1.922 3.299 -1.656 6.128 32.594 -4.351 0.627 2.921 10.791 2.916 33.190 15 CC_A18G19:C45U46_DD C 18 ? D 46 ? C 19 ? D 45 ? 1 C G 5 1_555 D C 15 1_555 C A 6 1_555 D C 14 1_555 0.708 -1.348 3.740 0.939 1.801 41.294 -2.129 -0.888 3.695 2.552 -1.330 41.341 16 CC_G19A20:C44C45_DD C 19 ? D 45 ? C 20 ? D 44 ? 1 C A 6 1_555 D C 14 1_555 C G 7 1_555 D A 13 1_555 -0.138 -1.192 3.097 8.053 9.936 53.241 -1.847 0.595 2.804 10.910 -8.843 54.646 17 CC_A20G21:A43C44_DD C 20 ? D 44 ? C 21 ? D 43 ? 1 C G 7 1_555 D A 13 1_555 D A 10 1_555 C A 9 1_555 -4.582 5.153 2.833 137.415 81.304 -30.871 -3.568 -0.713 2.035 -44.438 75.106 -160.407 18 CD_G21A40:A23A43_CD C 21 ? D 43 ? D 40 ? C 23 ? # _pdbx_initial_refinement_model.accession_code ? _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 Other _pdbx_initial_refinement_model.details '2.05 angstrom junctionless ribozyme' # _atom_sites.entry_id 2NPZ _atom_sites.fract_transf_matrix[1][1] 0.010973 _atom_sites.fract_transf_matrix[1][2] 0.006335 _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] 0.012671 _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] 0.006898 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C CO N O P # loop_