data_3NJ6 # _entry.id 3NJ6 # _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 3NJ6 pdb_00003nj6 10.2210/pdb3nj6/pdb NDB NA0608 ? ? RCSB RCSB059895 ? ? WWPDB D_1000059895 ? ? # 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 2010-08-25 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-08 4 'Structure model' 1 3 2024-02-21 5 'Structure model' 1 4 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' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' struct_site 6 5 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3NJ6 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-06-17 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3NJ7 _pdbx_database_related.details '1.9 A resolution X-ray structure of (GGCAGCAGCC)2' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kiliszek, A.' 1 'Kierzek, R.' 2 'Krzyzosiak, W.J.' 3 'Rypniewski, W.' 4 # _citation.id primary _citation.title ;Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 38 _citation.page_first 8370 _citation.page_last 8376 _citation.year 2010 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20702420 _citation.pdbx_database_id_DOI 10.1093/nar/gkq700 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kiliszek, A.' 1 ? primary 'Kierzek, R.' 2 ? primary 'Krzyzosiak, W.J.' 3 ? primary 'Rypniewski, W.' 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(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'" 3215.004 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 water nat water 18.015 76 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGCAGCAGCC _entity_poly.pdbx_seq_one_letter_code_can GGCAGCAGCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 A n 1 5 G n 1 6 C n 1 7 A n 1 8 G n 1 9 C n 1 10 C n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 A 4 4 4 A A A . n A 1 5 G 5 5 5 G G A . n A 1 6 C 6 6 6 C C A . n A 1 7 A 7 7 7 A A A . n A 1 8 G 8 8 8 G G A . n A 1 9 C 9 9 9 C C A . n A 1 10 C 10 10 10 C C A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SO4 1 11 11 SO4 SO4 A . C 3 HOH 1 12 12 HOH HOH A . C 3 HOH 2 13 13 HOH HOH A . C 3 HOH 3 14 14 HOH HOH A . C 3 HOH 4 15 15 HOH HOH A . C 3 HOH 5 16 16 HOH HOH A . C 3 HOH 6 17 17 HOH HOH A . C 3 HOH 7 18 18 HOH HOH A . C 3 HOH 8 19 19 HOH HOH A . C 3 HOH 9 20 20 HOH HOH A . C 3 HOH 10 21 21 HOH HOH A . C 3 HOH 11 22 22 HOH HOH A . C 3 HOH 12 23 23 HOH HOH A . C 3 HOH 13 24 24 HOH HOH A . C 3 HOH 14 25 25 HOH HOH A . C 3 HOH 15 26 26 HOH HOH A . C 3 HOH 16 27 27 HOH HOH A . C 3 HOH 17 28 28 HOH HOH A . C 3 HOH 18 29 29 HOH HOH A . C 3 HOH 19 30 30 HOH HOH A . C 3 HOH 20 31 31 HOH HOH A . C 3 HOH 21 32 32 HOH HOH A . C 3 HOH 22 33 33 HOH HOH A . C 3 HOH 23 34 34 HOH HOH A . C 3 HOH 24 35 35 HOH HOH A . C 3 HOH 25 36 36 HOH HOH A . C 3 HOH 26 37 37 HOH HOH A . C 3 HOH 27 38 38 HOH HOH A . C 3 HOH 28 39 39 HOH HOH A . C 3 HOH 29 40 40 HOH HOH A . C 3 HOH 30 41 41 HOH HOH A . C 3 HOH 31 42 42 HOH HOH A . C 3 HOH 32 43 43 HOH HOH A . C 3 HOH 33 44 44 HOH HOH A . C 3 HOH 34 45 45 HOH HOH A . C 3 HOH 35 46 46 HOH HOH A . C 3 HOH 36 47 47 HOH HOH A . C 3 HOH 37 48 48 HOH HOH A . C 3 HOH 38 49 49 HOH HOH A . C 3 HOH 39 50 50 HOH HOH A . C 3 HOH 40 51 51 HOH HOH A . C 3 HOH 41 52 52 HOH HOH A . C 3 HOH 42 53 53 HOH HOH A . C 3 HOH 43 54 54 HOH HOH A . C 3 HOH 44 55 55 HOH HOH A . C 3 HOH 45 56 56 HOH HOH A . C 3 HOH 46 57 57 HOH HOH A . C 3 HOH 47 58 58 HOH HOH A . C 3 HOH 48 59 59 HOH HOH A . C 3 HOH 49 60 60 HOH HOH A . C 3 HOH 50 61 61 HOH HOH A . C 3 HOH 51 62 62 HOH HOH A . C 3 HOH 52 63 63 HOH HOH A . C 3 HOH 53 64 64 HOH HOH A . C 3 HOH 54 65 65 HOH HOH A . C 3 HOH 55 66 66 HOH HOH A . C 3 HOH 56 67 67 HOH HOH A . C 3 HOH 57 68 68 HOH HOH A . C 3 HOH 58 69 69 HOH HOH A . C 3 HOH 59 70 70 HOH HOH A . C 3 HOH 60 71 71 HOH HOH A . C 3 HOH 61 72 72 HOH HOH A . C 3 HOH 62 73 73 HOH HOH A . C 3 HOH 63 74 74 HOH HOH A . C 3 HOH 64 75 75 HOH HOH A . C 3 HOH 65 76 76 HOH HOH A . C 3 HOH 66 77 77 HOH HOH A . C 3 HOH 67 78 78 HOH HOH A . C 3 HOH 68 79 79 HOH HOH A . C 3 HOH 69 80 80 HOH HOH A . C 3 HOH 70 81 81 HOH HOH A . C 3 HOH 71 82 82 HOH HOH A . C 3 HOH 72 83 83 HOH HOH A . C 3 HOH 73 84 84 HOH HOH A . C 3 HOH 74 87 87 HOH HOH A . C 3 HOH 75 88 88 HOH HOH A . C 3 HOH 76 89 89 HOH HOH A . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 PHASER 2.1.1 'Thu Nov 22 16:35:27 2007' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 4 PHENIX 1.5_2 ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 5 PDB_EXTRACT 3.100 'Jan. 22, 2010' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 7 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? # _cell.entry_id 3NJ6 _cell.length_a 46.427 _cell.length_b 46.427 _cell.length_c 82.678 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3NJ6 _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3NJ6 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.67 _exptl_crystal.density_percent_sol 53.88 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'MgSO4, (NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2009-06-06 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator SI _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'BESSY BEAMLINE 14.1' _diffrn_source.pdbx_synchrotron_site BESSY _diffrn_source.pdbx_synchrotron_beamline 14.1 _diffrn_source.pdbx_wavelength 0.8000 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 3NJ6 _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 23.213 _reflns.d_resolution_high 0.95 _reflns.number_obs 21756 _reflns.number_all ? _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.03600 _reflns.pdbx_netI_over_sigmaI 74.1000 _reflns.B_iso_Wilson_estimate 6.80 _reflns.pdbx_redundancy 15.300 _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 0.95 _reflns_shell.d_res_low 0.97 _reflns_shell.percent_possible_all 98.0 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.29100 _reflns_shell.meanI_over_sigI_obs 7.700 _reflns_shell.pdbx_redundancy 11.00 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3NJ6 _refine.ls_number_reflns_obs 21748 _refine.ls_number_reflns_all 21748 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.340 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 23.21 _refine.ls_d_res_high 0.95 _refine.ls_percent_reflns_obs 99.7 _refine.ls_R_factor_obs 0.106 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.106 _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 100.000 _refine.ls_number_reflns_R_free 0 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 0.15 _refine.occupancy_max 1.00 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 11.44 _refine.aniso_B[1][1] 0.00000 _refine.aniso_B[2][2] 0.00000 _refine.aniso_B[3][3] 0.00000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.41 _refine.solvent_model_param_bsol 44.58 _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'A-RNA HELIX' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model anisotropic _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.080 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _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_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? # _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 3NJ6 _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs 0.08 _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? # _refine_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 213 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 76 _refine_hist.number_atoms_total 294 _refine_hist.d_res_high 0.95 _refine_hist.d_res_low 23.21 # 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 f_bond_d 0.016 ? ? 242 'X-RAY DIFFRACTION' ? f_angle_d 1.996 ? ? 376 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 14.302 ? ? 96 'X-RAY DIFFRACTION' ? f_chiral_restr 0.098 ? ? 49 'X-RAY DIFFRACTION' ? f_plane_restr 0.031 ? ? 10 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 0.9520 0.9630 699 0.1110 94.00 0.1110 . . 699 . . . . 'X-RAY DIFFRACTION' . 0.9630 0.9740 690 0.1010 99.00 0.1010 . . 690 . . . . 'X-RAY DIFFRACTION' . 0.9740 0.9860 744 0.0940 100.00 0.0940 . . 744 . . . . 'X-RAY DIFFRACTION' . 0.9860 0.9980 687 0.0870 100.00 0.0870 . . 687 . . . . 'X-RAY DIFFRACTION' . 0.9980 1.0120 725 0.0820 100.00 0.0820 . . 725 . . . . 'X-RAY DIFFRACTION' . 1.0120 1.0250 709 0.0720 100.00 0.0720 . . 709 . . . . 'X-RAY DIFFRACTION' . 1.0250 1.0400 733 0.0750 100.00 0.0750 . . 733 . . . . 'X-RAY DIFFRACTION' . 1.0400 1.0560 719 0.0740 100.00 0.0740 . . 719 . . . . 'X-RAY DIFFRACTION' . 1.0560 1.0720 718 0.0680 100.00 0.0680 . . 718 . . . . 'X-RAY DIFFRACTION' . 1.0720 1.0900 704 0.0620 100.00 0.0620 . . 704 . . . . 'X-RAY DIFFRACTION' . 1.0900 1.1090 713 0.0650 100.00 0.0650 . . 713 . . . . 'X-RAY DIFFRACTION' . 1.1090 1.1290 727 0.0660 100.00 0.0660 . . 727 . . . . 'X-RAY DIFFRACTION' . 1.1290 1.1500 711 0.0640 100.00 0.0640 . . 711 . . . . 'X-RAY DIFFRACTION' . 1.1500 1.1740 718 0.0590 100.00 0.0590 . . 718 . . . . 'X-RAY DIFFRACTION' . 1.1740 1.1990 737 0.0660 100.00 0.0660 . . 737 . . . . 'X-RAY DIFFRACTION' . 1.1990 1.2270 727 0.0660 100.00 0.0660 . . 727 . . . . 'X-RAY DIFFRACTION' . 1.2270 1.2580 705 0.0710 100.00 0.0710 . . 705 . . . . 'X-RAY DIFFRACTION' . 1.2580 1.2920 731 0.0670 100.00 0.0670 . . 731 . . . . 'X-RAY DIFFRACTION' . 1.2920 1.3300 723 0.0710 100.00 0.0710 . . 723 . . . . 'X-RAY DIFFRACTION' . 1.3300 1.3730 728 0.0730 100.00 0.0730 . . 728 . . . . 'X-RAY DIFFRACTION' . 1.3730 1.4220 724 0.0800 100.00 0.0800 . . 724 . . . . 'X-RAY DIFFRACTION' . 1.4220 1.4790 732 0.0810 100.00 0.0810 . . 732 . . . . 'X-RAY DIFFRACTION' . 1.4790 1.5460 732 0.0910 100.00 0.0910 . . 732 . . . . 'X-RAY DIFFRACTION' . 1.5460 1.6280 716 0.0910 100.00 0.0910 . . 716 . . . . 'X-RAY DIFFRACTION' . 1.6280 1.7300 739 0.0910 100.00 0.0910 . . 739 . . . . 'X-RAY DIFFRACTION' . 1.7300 1.8630 724 0.1020 100.00 0.1020 . . 724 . . . . 'X-RAY DIFFRACTION' . 1.8630 2.0500 742 0.1210 100.00 0.1210 . . 742 . . . . 'X-RAY DIFFRACTION' . 2.0500 2.3470 740 0.1260 100.00 0.1260 . . 740 . . . . 'X-RAY DIFFRACTION' . 2.3470 2.9560 759 0.1410 100.00 0.1410 . . 759 . . . . 'X-RAY DIFFRACTION' . 2.9560 23.2200 792 0.1490 99.00 0.1490 . . 792 . . . . # _struct.entry_id 3NJ6 _struct.title '0.95 A resolution X-ray structure of (GGCAGCAGCC)2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3NJ6 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'CAG repeats, polyQ diseases, 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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3NJ6 _struct_ref.pdbx_db_accession 3NJ6 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GGCAGCAGCC _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3NJ6 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3NJ6 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 970 ? 1 MORE -4 ? 1 'SSA (A^2)' 3900 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 10 N3 ? ? A G 1 A C 10 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 10 O2 ? ? A G 1 A C 10 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 10 N4 ? ? A G 1 A C 10 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 9 N3 ? ? A G 2 A C 9 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 9 O2 ? ? A G 2 A C 9 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 9 N4 ? ? A G 2 A C 9 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 8 N1 ? ? A C 3 A G 8 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 8 O6 ? ? A C 3 A G 8 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 8 N2 ? ? A C 3 A G 8 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 6 N3 ? ? A G 5 A C 6 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 6 O2 ? ? A G 5 A C 6 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 6 N4 ? ? A G 5 A C 6 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 5 N1 ? ? A C 6 A G 5 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 5 O6 ? ? A C 6 A G 5 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 5 N2 ? ? A C 6 A G 5 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 3 N3 ? ? A G 8 A C 3 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 3 O2 ? ? A G 8 A C 3 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 3 N4 ? ? A G 8 A C 3 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 2 N1 ? ? A C 9 A G 2 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 2 O6 ? ? A C 9 A G 2 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 2 N2 ? ? A C 9 A G 2 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 1 N1 ? ? A C 10 A G 1 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 1 O6 ? ? A C 10 A G 1 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 1 N2 ? ? A C 10 A G 1 6_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id SO4 _struct_site.pdbx_auth_seq_id 11 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'BINDING SITE FOR RESIDUE SO4 A 11' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 A A 4 ? A A 4 . ? 6_555 ? 2 AC1 9 A A 7 ? A A 7 . ? 1_555 ? 3 AC1 9 HOH C . ? HOH A 17 . ? 1_555 ? 4 AC1 9 HOH C . ? HOH A 22 . ? 1_555 ? 5 AC1 9 HOH C . ? HOH A 29 . ? 1_555 ? 6 AC1 9 HOH C . ? HOH A 35 . ? 6_555 ? 7 AC1 9 HOH C . ? HOH A 59 . ? 1_555 ? 8 AC1 9 HOH C . ? HOH A 77 . ? 1_555 ? 9 AC1 9 HOH C . ? HOH A 89 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 C4 _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 C _pdbx_validate_rmsd_angle.auth_seq_id_1 9 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 C5 _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 C _pdbx_validate_rmsd_angle.auth_seq_id_2 9 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 C6 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 C _pdbx_validate_rmsd_angle.auth_seq_id_3 9 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 114.36 _pdbx_validate_rmsd_angle.angle_target_value 117.40 _pdbx_validate_rmsd_angle.angle_deviation -3.04 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id G _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 2 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.056 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 12 ? C HOH . 2 1 A HOH 18 ? C HOH . 3 1 A HOH 25 ? C HOH . 4 1 A HOH 39 ? C HOH . 5 1 A HOH 56 ? C HOH . 6 1 A HOH 62 ? C HOH . # _pdbx_phasing_MR.entry_id 3NJ6 _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor 61.160 _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 2.500 _pdbx_phasing_MR.d_res_low_rotation 23.210 _pdbx_phasing_MR.d_res_high_translation 2.500 _pdbx_phasing_MR.d_res_low_translation 23.210 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 SO4 S S N N 114 SO4 O1 O N N 115 SO4 O2 O N N 116 SO4 O3 O N N 117 SO4 O4 O N N 118 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 SO4 S O1 doub N N 118 SO4 S O2 doub N N 119 SO4 S O3 sing N N 120 SO4 S O4 sing N N 121 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3NJ6 'a-form double helix' 3NJ6 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 10 6_555 -0.242 -0.085 -0.119 -7.436 -1.423 -0.536 1 A_G1:C10_A A 1 ? A 10 ? 19 1 1 A G 2 1_555 A C 9 6_555 -0.311 -0.157 -0.191 -4.930 -10.209 -1.405 2 A_G2:C9_A A 2 ? A 9 ? 19 1 1 A C 3 1_555 A G 8 6_555 0.236 -0.167 -0.020 -4.638 -10.973 -1.226 3 A_C3:G8_A A 3 ? A 8 ? 19 1 1 A G 1 1_555 A C 10 1_555 -0.242 -0.085 -0.119 -7.436 -1.423 -0.536 4 A_G1:C10_A A 1 ? A 10 ? 19 1 1 A G 2 1_555 A C 9 1_555 -0.311 -0.157 -0.191 -4.931 -10.209 -1.405 5 A_G2:C9_A A 2 ? A 9 ? 19 1 1 A C 3 1_555 A G 8 1_555 0.236 -0.167 -0.020 -4.638 -10.973 -1.226 6 A_C3:G8_A A 3 ? A 8 ? 19 1 1 A G 5 1_555 A C 6 6_555 -0.179 -0.091 -0.010 1.899 -5.431 -0.084 7 A_G5:C6_A A 5 ? A 6 ? 19 1 1 A C 6 1_555 A G 5 6_555 0.179 -0.091 -0.010 -1.899 -5.431 -0.084 8 A_C6:G5_A A 6 ? A 5 ? 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 G 1 1_555 A C 10 6_555 A G 2 1_555 A C 9 6_555 -0.580 -2.208 3.267 -0.921 5.345 29.280 -5.352 0.948 2.845 10.461 1.802 29.767 1 AA_G1G2:C9C10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A G 2 1_555 A C 9 6_555 A C 3 1_555 A G 8 6_555 -0.251 -1.576 3.308 -1.103 4.900 33.023 -3.536 0.258 3.056 8.558 1.927 33.392 2 AA_G2C3:G8C9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A G 1 1_555 A C 10 1_555 A G 2 1_555 A C 9 1_555 -0.580 -2.208 3.267 -0.921 5.345 29.280 -5.352 0.948 2.845 10.461 1.802 29.767 3 AA_G1G2:C9C10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A G 2 1_555 A C 9 1_555 A C 3 1_555 A G 8 1_555 -0.251 -1.576 3.308 -1.103 4.900 33.023 -3.536 0.258 3.056 8.558 1.927 33.392 4 AA_G2C3:G8C9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A G 5 1_555 A C 6 6_555 A C 6 1_555 A G 5 6_555 0.000 -2.169 3.426 0.000 2.957 35.008 -4.045 0.000 3.238 4.905 0.000 35.129 5 AA_G5C6:G5C6_AA A 5 ? A 6 ? A 6 ? A 5 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'A-form RNA helix' # _atom_sites.entry_id 3NJ6 _atom_sites.fract_transf_matrix[1][1] 0.021539 _atom_sites.fract_transf_matrix[1][2] 0.012436 _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] 0.024871 _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] 0.012095 _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 H N O P S # loop_