data_1XJR # _entry.id 1XJR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1XJR pdb_00001xjr 10.2210/pdb1xjr/pdb NDB UR0044 ? ? RCSB RCSB030433 ? ? WWPDB D_1000030433 ? ? # 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 2005-02-01 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.value' 16 4 'Structure model' '_struct_conn.pdbx_dist_value' 17 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 18 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 19 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 24 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 30 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 31 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 32 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1XJR _pdbx_database_status.recvd_initial_deposition_date 2004-09-24 _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_ _audit_author.name _audit_author.pdbx_ordinal 'Robertson, M.P.' 1 'Igel, H.' 2 'Baertsch, R.' 3 'Haussler, D.' 4 'Ares Jr., M.' 5 'Scott, W.G.' 6 # _citation.id primary _citation.title 'The structure of a rigorously conserved RNA element within the SARS virus genome' _citation.journal_abbrev 'Plos Biol.' _citation.journal_volume 3 _citation.page_first 86 _citation.page_last 94 _citation.year 2005 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1544-9173 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15630477 _citation.pdbx_database_id_DOI 10.1371/journal.pbio.0030005 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Robertson, M.P.' 1 ? primary 'Igel, H.' 2 ? primary 'Baertsch, R.' 3 ? primary 'Haussler, D.' 4 ? primary 'Ares Jr., M.' 5 ? primary 'Scott, W.G.' 6 ? # 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 's2m RNA' 15435.109 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 water nat water 18.015 11 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(GTP)GAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU' _entity_poly.pdbx_seq_one_letter_code_can GGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU _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 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GTP n 1 2 G n 1 3 A n 1 4 G n 1 5 U n 1 6 U n 1 7 C n 1 8 A n 1 9 C n 1 10 C n 1 11 G n 1 12 A n 1 13 G n 1 14 G n 1 15 C n 1 16 C n 1 17 A n 1 18 C n 1 19 G n 1 20 C n 1 21 G n 1 22 G n 1 23 A n 1 24 G n 1 25 U n 1 26 A n 1 27 C n 1 28 G n 1 29 A n 1 30 U n 1 31 C n 1 32 G n 1 33 A n 1 34 G n 1 35 G n 1 36 G n 1 37 U n 1 38 A n 1 39 C n 1 40 A n 1 41 G n 1 42 U n 1 43 G n 1 44 A n 1 45 A n 1 46 U n 1 47 U n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _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 'In vitro transcription from T7 RNA polymerase and DNA template' # 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 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 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 GTP 1 1 1 GTP GTP A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 U 5 5 5 U U A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 C 10 10 10 C C A . n A 1 11 G 11 11 11 G G A . n A 1 12 A 12 12 12 A A A . n A 1 13 G 13 13 13 G G A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 C 16 16 16 C C A . n A 1 17 A 17 17 17 A A A . n A 1 18 C 18 18 18 C C A . n A 1 19 G 19 19 19 G G A . n A 1 20 C 20 20 20 C C A . n A 1 21 G 21 21 21 G G A . n A 1 22 G 22 22 22 G G A . n A 1 23 A 23 23 23 A A A . n A 1 24 G 24 24 24 G G A . n A 1 25 U 25 25 25 U U A . n A 1 26 A 26 26 26 A A A . n A 1 27 C 27 27 27 C C A . n A 1 28 G 28 28 28 G G A . n A 1 29 A 29 29 29 A A A . n A 1 30 U 30 30 30 U U A . n A 1 31 C 31 31 31 C C A . n A 1 32 G 32 32 32 G G A . n A 1 33 A 33 33 33 A A A . n A 1 34 G 34 34 34 G G A . n A 1 35 G 35 35 35 G G A . n A 1 36 G 36 36 36 G G A . n A 1 37 U 37 37 37 U U A . n A 1 38 A 38 38 38 A A A . n A 1 39 C 39 39 39 C C A . n A 1 40 A 40 40 40 A A A . n A 1 41 G 41 41 41 G G A . n A 1 42 U 42 42 42 U U A . n A 1 43 G 43 43 43 G G A . n A 1 44 A 44 44 44 A A A . n A 1 45 A 45 45 45 A A A . n A 1 46 U 46 46 46 U U A . n A 1 47 U 47 47 47 U U 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 MG 1 101 101 MG MO5 A . C 2 MG 1 201 201 MG MO5 A . D 3 HOH 1 202 100 HOH HOH A . D 3 HOH 2 203 101 HOH MO5 A . D 3 HOH 3 204 101 HOH MO5 A . D 3 HOH 4 205 101 HOH MO5 A . D 3 HOH 5 206 101 HOH MO5 A . D 3 HOH 6 207 101 HOH MO5 A . D 3 HOH 7 208 201 HOH MO5 A . D 3 HOH 8 209 201 HOH MO5 A . D 3 HOH 9 210 201 HOH MO5 A . D 3 HOH 10 211 201 HOH MO5 A . D 3 HOH 11 212 201 HOH MO5 A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0003 ? 1 MOSFLM 'data reduction' . ? 2 CCP4 'data scaling' '(SCALA)' ? 3 CNS phasing . ? 4 # _cell.entry_id 1XJR _cell.length_a 93.218 _cell.length_b 93.218 _cell.length_c 128.109 _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 1XJR _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1XJR _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 5.20 _exptl_crystal.density_percent_sol 73 _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 7 _exptl_crystal_grow.pdbx_details ;4.5 mg/ml s2m RNA in 30 mM Tris, pH 7.6, 100 mM NaCl and 60 mM MgCl2 and 50 mM MES, pH 5.6, 100 mM Mg(OAc)-2 and 20% MPD , VAPOR DIFFUSION, HANGING DROP, temperature 293K ; _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 Tris ? ? ? 1 2 1 NaCl ? ? ? 1 3 1 MgCl2 ? ? ? 1 4 1 MES ? ? ? 1 5 1 'Mg(OAc)-2' ? ? ? 1 6 1 MPD ? ? ? 1 7 2 NaCl ? ? ? 1 8 2 MgCl2 ? ? ? 1 9 2 MES ? ? ? 1 10 2 MPD ? ? ? # _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 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2004-05-05 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.98 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL9-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL9-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.98 # _reflns.entry_id 1XJR _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I -999. _reflns.d_resolution_high 2.7 _reflns.d_resolution_low 80.85 _reflns.number_all 9554 _reflns.number_obs 9497 _reflns.percent_possible_obs 99.4 _reflns.pdbx_Rmerge_I_obs 0.056 _reflns.pdbx_Rsym_value 0.052 _reflns.pdbx_netI_over_sigmaI 31.3 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 13.4 _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 2.7 _reflns_shell.d_res_low 2.85 _reflns_shell.percent_possible_all 99.7 _reflns_shell.Rmerge_I_obs 0.465 _reflns_shell.pdbx_Rsym_value 0.434 _reflns_shell.meanI_over_sigI_obs 6.5 _reflns_shell.pdbx_redundancy 13.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1352 _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 1XJR _refine.ls_number_reflns_obs 8516 _refine.ls_number_reflns_all 8516 _refine.pdbx_ls_sigma_I 0.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 80.85 _refine.ls_d_res_high 2.70 _refine.ls_percent_reflns_obs 98.97 _refine.ls_R_factor_obs 0.2325 _refine.ls_R_factor_all 0.2325 _refine.ls_R_factor_R_work 0.23136 _refine.ls_R_factor_R_free 0.24326 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 943 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.913 _refine.correlation_coeff_Fo_to_Fc_free 0.911 _refine.B_iso_mean 75.177 _refine.aniso_B[1][1] 0.06 _refine.aniso_B[2][2] 0.06 _refine.aniso_B[3][3] -0.10 _refine.aniso_B[1][2] 0.03 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.316 _refine.pdbx_overall_ESU_R_Free 0.238 _refine.overall_SU_ML 0.155 _refine.overall_SU_B 16.978 _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 1XJR _refine_analyze.Luzzati_coordinate_error_obs 0.316 _refine_analyze.Luzzati_sigma_a_obs 0.155 _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.238 _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_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 1024 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 1037 _refine_hist.d_res_high 2.70 _refine_hist.d_res_low 80.85 # 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 r_bond_refined_d 0.010 0.021 ? 1157 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.924 3.000 ? 1806 'X-RAY DIFFRACTION' ? r_chiral_restr 0.078 0.200 ? 234 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.008 0.020 ? 498 'X-RAY DIFFRACTION' ? r_nbd_refined 0.169 0.200 ? 393 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.277 0.200 ? 683 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.150 0.200 ? 40 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.019 0.200 ? 1 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.136 0.200 ? 7 'X-RAY DIFFRACTION' ? r_scbond_it 1.075 3.000 ? 1672 'X-RAY DIFFRACTION' ? r_scangle_it 1.757 4.500 ? 1802 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.701 _refine_ls_shell.d_res_low 2.771 _refine_ls_shell.number_reflns_R_work 614 _refine_ls_shell.R_factor_R_work 0.41 _refine_ls_shell.percent_reflns_obs 99.42 _refine_ls_shell.R_factor_R_free 0.449 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 72 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1XJR _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 1XJR _struct.title 'The Structure of a Rigorously Conserved RNA Element Within the SARS Virus Genome' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1XJR _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, GNRA, 530-like loop, s2m, stem-loop, purine bulge, SARS' # 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 2 ? D N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1XJR _struct_ref.pdbx_db_accession 1XJR _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1XJR _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 47 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1XJR _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 47 _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 47 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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 # _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 covale1 covale both ? A GTP 1 "O3'" ? ? ? 1_555 A G 2 P ? ? A GTP 1 A G 2 1_555 ? ? ? ? ? ? ? 1.593 ? ? metalc1 metalc ? ? A A 12 OP1 ? ? ? 1_555 B MG . MG ? ? A A 12 A MG 101 1_555 ? ? ? ? ? ? ? 2.205 ? ? metalc2 metalc ? ? A A 12 OP2 ? ? ? 1_555 C MG . MG ? ? A A 12 A MG 201 1_555 ? ? ? ? ? ? ? 1.971 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 203 1_555 ? ? ? ? ? ? ? 2.101 ? ? metalc4 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 204 1_555 ? ? ? ? ? ? ? 2.116 ? ? metalc5 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 205 1_555 ? ? ? ? ? ? ? 2.103 ? ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 206 1_555 ? ? ? ? ? ? ? 2.068 ? ? metalc7 metalc ? ? B MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 207 1_555 ? ? ? ? ? ? ? 2.094 ? ? metalc8 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 201 A HOH 208 1_555 ? ? ? ? ? ? ? 2.084 ? ? metalc9 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 201 A HOH 209 1_555 ? ? ? ? ? ? ? 2.100 ? ? metalc10 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 201 A HOH 210 1_555 ? ? ? ? ? ? ? 2.073 ? ? metalc11 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 201 A HOH 211 1_555 ? ? ? ? ? ? ? 2.088 ? ? metalc12 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 201 A HOH 212 1_555 ? ? ? ? ? ? ? 2.072 ? ? hydrog1 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 47 N3 ? ? A A 3 A U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 47 O4 ? ? A A 3 A U 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 4 N1 ? ? ? 1_555 A U 46 O2 ? ? A G 4 A U 46 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog4 hydrog ? ? A G 4 O6 ? ? ? 1_555 A U 46 N3 ? ? A G 4 A U 46 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A U 5 N3 ? ? ? 1_555 A A 45 N1 ? ? A U 5 A A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 5 O4 ? ? ? 1_555 A A 45 N6 ? ? A U 5 A A 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 44 N1 ? ? A U 6 A A 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 6 O4 ? ? ? 1_555 A A 44 N6 ? ? A U 6 A A 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 43 N1 ? ? A C 7 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 43 O6 ? ? A C 7 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 43 N2 ? ? A C 7 A G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 8 N1 ? ? ? 1_555 A U 42 N3 ? ? A A 8 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 8 N6 ? ? ? 1_555 A U 42 O4 ? ? A A 8 A U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 41 N1 ? ? A C 9 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 41 O6 ? ? A C 9 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 41 N2 ? ? A C 9 A G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A C 10 O2 ? ? ? 1_555 A A 40 N6 ? ? A C 10 A A 40 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog18 hydrog ? ? A G 11 N2 ? ? ? 1_555 A A 33 N1 ? ? A G 11 A A 33 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog19 hydrog ? ? A G 13 N1 ? ? ? 1_555 A C 39 N3 ? ? A G 13 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 39 O2 ? ? A G 13 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 13 O6 ? ? ? 1_555 A C 39 N4 ? ? A G 13 A C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 14 N1 ? ? ? 1_555 A U 37 O2 ? ? A G 14 A U 37 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog23 hydrog ? ? A G 14 O6 ? ? ? 1_555 A U 37 N3 ? ? A G 14 A U 37 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog24 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 36 N1 ? ? A C 15 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 36 O6 ? ? A C 15 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 36 N2 ? ? A C 15 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 35 N1 ? ? A C 16 A G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 35 O6 ? ? A C 16 A G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 35 N2 ? ? A C 16 A G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 17 N1 ? ? ? 1_555 A G 34 N1 ? ? A A 17 A G 34 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog31 hydrog ? ? A A 17 N6 ? ? ? 1_555 A G 34 O6 ? ? A A 17 A G 34 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog32 hydrog ? ? A C 18 N3 ? ? ? 1_555 A G 32 N1 ? ? A C 18 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 18 N4 ? ? ? 1_555 A G 32 O6 ? ? A C 18 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 18 O2 ? ? ? 1_555 A G 32 N2 ? ? A C 18 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 18 O2 ? ? ? 1_555 A G 34 N2 ? ? A C 18 A G 34 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog36 hydrog ? ? A G 19 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 19 A C 20 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog37 hydrog ? ? A G 19 N1 ? ? ? 1_555 A C 31 N3 ? ? A G 19 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 19 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 19 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 19 O6 ? ? ? 1_555 A C 31 N4 ? ? A G 19 A C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 20 N3 ? ? ? 1_555 A G 28 N1 ? ? A C 20 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 20 N4 ? ? ? 1_555 A G 28 O6 ? ? A C 20 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 20 O2 ? ? ? 1_555 A G 28 N2 ? ? A C 20 A G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 21 N1 ? ? ? 1_555 A C 27 N3 ? ? A G 21 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 21 N2 ? ? ? 1_555 A C 27 O2 ? ? A G 21 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 21 O6 ? ? ? 1_555 A C 27 N4 ? ? A G 21 A C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 22 N2 ? ? ? 1_555 A A 26 N7 ? ? A G 22 A A 26 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog47 hydrog ? ? A G 22 N3 ? ? ? 1_555 A A 26 N6 ? ? A G 22 A A 26 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog48 hydrog ? ? A G 28 N2 ? ? ? 1_555 A C 31 O2 ? ? A G 28 A C 31 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog49 hydrog ? ? A A 38 N3 ? ? ? 1_555 A C 39 N4 ? ? A A 38 A C 39 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP1 ? A A 12 ? A A 12 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 203 ? 1_555 103.5 ? 2 OP1 ? A A 12 ? A A 12 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 82.7 ? 3 O ? D HOH . ? A HOH 203 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 173.6 ? 4 OP1 ? A A 12 ? A A 12 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 205 ? 1_555 92.7 ? 5 O ? D HOH . ? A HOH 203 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 205 ? 1_555 89.1 ? 6 O ? D HOH . ? A HOH 204 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 205 ? 1_555 89.2 ? 7 OP1 ? A A 12 ? A A 12 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 206 ? 1_555 87.8 ? 8 O ? D HOH . ? A HOH 203 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 206 ? 1_555 88.6 ? 9 O ? D HOH . ? A HOH 204 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 206 ? 1_555 93.0 ? 10 O ? D HOH . ? A HOH 205 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 206 ? 1_555 177.8 ? 11 OP1 ? A A 12 ? A A 12 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 207 ? 1_555 169.7 ? 12 O ? D HOH . ? A HOH 203 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 207 ? 1_555 85.9 ? 13 O ? D HOH . ? A HOH 204 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 207 ? 1_555 88.0 ? 14 O ? D HOH . ? A HOH 205 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 207 ? 1_555 91.5 ? 15 O ? D HOH . ? A HOH 206 ? 1_555 MG ? B MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 207 ? 1_555 88.3 ? 16 OP2 ? A A 12 ? A A 12 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 208 ? 1_555 81.2 ? 17 OP2 ? A A 12 ? A A 12 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 209 ? 1_555 98.5 ? 18 O ? D HOH . ? A HOH 208 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 209 ? 1_555 175.9 ? 19 OP2 ? A A 12 ? A A 12 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 210 ? 1_555 95.2 ? 20 O ? D HOH . ? A HOH 208 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 210 ? 1_555 90.0 ? 21 O ? D HOH . ? A HOH 209 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 210 ? 1_555 94.1 ? 22 OP2 ? A A 12 ? A A 12 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 211 ? 1_555 88.1 ? 23 O ? D HOH . ? A HOH 208 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 211 ? 1_555 89.5 ? 24 O ? D HOH . ? A HOH 209 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 211 ? 1_555 86.5 ? 25 O ? D HOH . ? A HOH 210 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 211 ? 1_555 176.5 ? 26 OP2 ? A A 12 ? A A 12 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 212 ? 1_555 172.0 ? 27 O ? D HOH . ? A HOH 208 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 212 ? 1_555 91.0 ? 28 O ? D HOH . ? A HOH 209 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 212 ? 1_555 89.4 ? 29 O ? D HOH . ? A HOH 210 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 212 ? 1_555 83.7 ? 30 O ? D HOH . ? A HOH 211 ? 1_555 MG ? C MG . ? A MG 201 ? 1_555 O ? D HOH . ? A HOH 212 ? 1_555 92.9 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A MG 101 ? 6 'BINDING SITE FOR RESIDUE MG A 101' AC2 Software A MG 201 ? 6 'BINDING SITE FOR RESIDUE MG A 201' # 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 6 A A 12 ? A A 12 . ? 1_555 ? 2 AC1 6 HOH D . ? HOH A 203 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 204 . ? 1_555 ? 4 AC1 6 HOH D . ? HOH A 205 . ? 1_555 ? 5 AC1 6 HOH D . ? HOH A 206 . ? 1_555 ? 6 AC1 6 HOH D . ? HOH A 207 . ? 1_555 ? 7 AC2 6 A A 12 ? A A 12 . ? 1_555 ? 8 AC2 6 HOH D . ? HOH A 208 . ? 1_555 ? 9 AC2 6 HOH D . ? HOH A 209 . ? 1_555 ? 10 AC2 6 HOH D . ? HOH A 210 . ? 1_555 ? 11 AC2 6 HOH D . ? HOH A 211 . ? 1_555 ? 12 AC2 6 HOH D . ? HOH A 212 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O3'" A GTP 1 ? ? P A G 2 ? ? "O5'" A G 2 ? ? 91.12 104.00 -12.88 1.90 Y 2 1 "O3'" A GTP 1 ? ? P A G 2 ? ? OP2 A G 2 ? ? 126.11 110.50 15.61 1.10 Y 3 1 "O4'" A G 19 ? ? "C1'" A G 19 ? ? N9 A G 19 ? ? 115.82 108.50 7.32 0.70 N 4 1 "O4'" A G 21 ? ? "C1'" A G 21 ? ? N9 A G 21 ? ? 113.92 108.50 5.42 0.70 N 5 1 "O4'" A G 22 ? ? "C1'" A G 22 ? ? N9 A G 22 ? ? 115.63 108.50 7.13 0.70 N 6 1 "C1'" A U 25 ? ? "O4'" A U 25 ? ? "C4'" A U 25 ? ? 103.09 109.70 -6.61 0.70 N 7 1 "O4'" A U 25 ? ? "C1'" A U 25 ? ? N1 A U 25 ? ? 114.82 108.50 6.32 0.70 N 8 1 "O4'" A G 28 ? ? "C1'" A G 28 ? ? N9 A G 28 ? ? 115.03 108.50 6.53 0.70 N 9 1 "C1'" A A 29 ? ? "O4'" A A 29 ? ? "C4'" A A 29 ? ? 102.99 109.70 -6.71 0.70 N 10 1 "O4'" A A 29 ? ? "C1'" A A 29 ? ? N9 A A 29 ? ? 114.18 108.50 5.68 0.70 N 11 1 "C3'" A A 29 ? ? "O3'" A A 29 ? ? P A U 30 ? ? 127.64 119.70 7.94 1.20 Y 12 1 "O5'" A A 33 ? ? "C5'" A A 33 ? ? "C4'" A A 33 ? ? 104.29 109.40 -5.11 0.80 N 13 1 "O4'" A A 38 ? ? "C1'" A A 38 ? ? N9 A A 38 ? ? 113.47 108.50 4.97 0.70 N 14 1 "O4'" A A 44 ? ? "C1'" A A 44 ? ? N9 A A 44 ? ? 112.90 108.50 4.40 0.70 N 15 1 "O4'" A U 47 ? ? "C1'" A U 47 ? ? N1 A U 47 ? ? 114.97 108.50 6.47 0.70 N # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id GTP _pdbx_struct_mod_residue.label_seq_id 1 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id GTP _pdbx_struct_mod_residue.auth_seq_id 1 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id G _pdbx_struct_mod_residue.details "GUANOSINE-5'-TRIPHOSPHATE" # 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 GTP PG P N N 111 GTP O1G O N N 112 GTP O2G O N N 113 GTP O3G O N N 114 GTP O3B O N N 115 GTP PB P N N 116 GTP O1B O N N 117 GTP O2B O N N 118 GTP O3A O N N 119 GTP PA P N N 120 GTP O1A O N N 121 GTP O2A O N N 122 GTP "O5'" O N N 123 GTP "C5'" C N N 124 GTP "C4'" C N R 125 GTP "O4'" O N N 126 GTP "C3'" C N S 127 GTP "O3'" O N N 128 GTP "C2'" C N R 129 GTP "O2'" O N N 130 GTP "C1'" C N R 131 GTP N9 N Y N 132 GTP C8 C Y N 133 GTP N7 N Y N 134 GTP C5 C Y N 135 GTP C6 C N N 136 GTP O6 O N N 137 GTP N1 N N N 138 GTP C2 C N N 139 GTP N2 N N N 140 GTP N3 N N N 141 GTP C4 C Y N 142 GTP HOG2 H N N 143 GTP HOG3 H N N 144 GTP HOB2 H N N 145 GTP HOA2 H N N 146 GTP "H5'" H N N 147 GTP "H5''" H N N 148 GTP "H4'" H N N 149 GTP "H3'" H N N 150 GTP "HO3'" H N N 151 GTP "H2'" H N N 152 GTP "HO2'" H N N 153 GTP "H1'" H N N 154 GTP H8 H N N 155 GTP HN1 H N N 156 GTP HN21 H N N 157 GTP HN22 H N N 158 HOH O O N N 159 HOH H1 H N N 160 HOH H2 H N N 161 MG MG MG N N 162 U OP3 O N N 163 U P P N N 164 U OP1 O N N 165 U OP2 O N N 166 U "O5'" O N N 167 U "C5'" C N N 168 U "C4'" C N R 169 U "O4'" O N N 170 U "C3'" C N S 171 U "O3'" O N N 172 U "C2'" C N R 173 U "O2'" O N N 174 U "C1'" C N R 175 U N1 N N N 176 U C2 C N N 177 U O2 O N N 178 U N3 N N N 179 U C4 C N N 180 U O4 O N N 181 U C5 C N N 182 U C6 C N N 183 U HOP3 H N N 184 U HOP2 H N N 185 U "H5'" H N N 186 U "H5''" H N N 187 U "H4'" H N N 188 U "H3'" H N N 189 U "HO3'" H N N 190 U "H2'" H N N 191 U "HO2'" H N N 192 U "H1'" H N N 193 U H3 H N N 194 U H5 H N N 195 U H6 H N N 196 # 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 GTP PG O1G doub N N 116 GTP PG O2G sing N N 117 GTP PG O3G sing N N 118 GTP PG O3B sing N N 119 GTP O2G HOG2 sing N N 120 GTP O3G HOG3 sing N N 121 GTP O3B PB sing N N 122 GTP PB O1B doub N N 123 GTP PB O2B sing N N 124 GTP PB O3A sing N N 125 GTP O2B HOB2 sing N N 126 GTP O3A PA sing N N 127 GTP PA O1A doub N N 128 GTP PA O2A sing N N 129 GTP PA "O5'" sing N N 130 GTP O2A HOA2 sing N N 131 GTP "O5'" "C5'" sing N N 132 GTP "C5'" "C4'" sing N N 133 GTP "C5'" "H5'" sing N N 134 GTP "C5'" "H5''" sing N N 135 GTP "C4'" "O4'" sing N N 136 GTP "C4'" "C3'" sing N N 137 GTP "C4'" "H4'" sing N N 138 GTP "O4'" "C1'" sing N N 139 GTP "C3'" "O3'" sing N N 140 GTP "C3'" "C2'" sing N N 141 GTP "C3'" "H3'" sing N N 142 GTP "O3'" "HO3'" sing N N 143 GTP "C2'" "O2'" sing N N 144 GTP "C2'" "C1'" sing N N 145 GTP "C2'" "H2'" sing N N 146 GTP "O2'" "HO2'" sing N N 147 GTP "C1'" N9 sing N N 148 GTP "C1'" "H1'" sing N N 149 GTP N9 C8 sing Y N 150 GTP N9 C4 sing Y N 151 GTP C8 N7 doub Y N 152 GTP C8 H8 sing N N 153 GTP N7 C5 sing Y N 154 GTP C5 C6 sing N N 155 GTP C5 C4 doub Y N 156 GTP C6 O6 doub N N 157 GTP C6 N1 sing N N 158 GTP N1 C2 sing N N 159 GTP N1 HN1 sing N N 160 GTP C2 N2 sing N N 161 GTP C2 N3 doub N N 162 GTP N2 HN21 sing N N 163 GTP N2 HN22 sing N N 164 GTP N3 C4 sing N N 165 HOH O H1 sing N N 166 HOH O H2 sing N N 167 U OP3 P sing N N 168 U OP3 HOP3 sing N N 169 U P OP1 doub N N 170 U P OP2 sing N N 171 U P "O5'" sing N N 172 U OP2 HOP2 sing N N 173 U "O5'" "C5'" sing N N 174 U "C5'" "C4'" sing N N 175 U "C5'" "H5'" sing N N 176 U "C5'" "H5''" sing N N 177 U "C4'" "O4'" sing N N 178 U "C4'" "C3'" sing N N 179 U "C4'" "H4'" sing N N 180 U "O4'" "C1'" sing N N 181 U "C3'" "O3'" sing N N 182 U "C3'" "C2'" sing N N 183 U "C3'" "H3'" sing N N 184 U "O3'" "HO3'" sing N N 185 U "C2'" "O2'" sing N N 186 U "C2'" "C1'" sing N N 187 U "C2'" "H2'" sing N N 188 U "O2'" "HO2'" sing N N 189 U "C1'" N1 sing N N 190 U "C1'" "H1'" sing N N 191 U N1 C2 sing N N 192 U N1 C6 sing N N 193 U C2 O2 doub N N 194 U C2 N3 sing N N 195 U N3 C4 sing N N 196 U N3 H3 sing N N 197 U C4 O4 doub N N 198 U C4 C5 sing N N 199 U C5 C6 doub N N 200 U C5 H5 sing N N 201 U C6 H6 sing N N 202 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1XJR 'double helix' 1XJR 'a-form double helix' 1XJR 'hairpin loop' 1XJR 'bulge loop' 1XJR 'mismatched base pair' 1XJR 'quadruple 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 A 3 1_555 A U 47 1_555 -0.505 -0.201 0.058 -2.675 -10.687 2.422 1 A_A3:U47_A A 3 ? A 47 ? 20 1 1 A G 4 1_555 A U 46 1_555 -2.603 -0.584 0.210 1.158 -12.753 4.087 2 A_G4:U46_A A 4 ? A 46 ? 28 ? 1 A U 5 1_555 A A 45 1_555 -0.322 -0.153 0.209 4.678 -21.656 0.869 3 A_U5:A45_A A 5 ? A 45 ? 20 1 1 A U 6 1_555 A A 44 1_555 0.166 -0.153 0.053 3.622 -15.625 0.506 4 A_U6:A44_A A 6 ? A 44 ? 20 1 1 A C 7 1_555 A G 43 1_555 0.426 -0.221 -0.100 4.886 -14.700 0.083 5 A_C7:G43_A A 7 ? A 43 ? 19 1 1 A A 8 1_555 A U 42 1_555 0.017 -0.206 0.355 1.845 -14.870 1.165 6 A_A8:U42_A A 8 ? A 42 ? 20 1 1 A C 9 1_555 A G 41 1_555 0.417 -0.159 0.111 -3.970 -12.604 -0.585 7 A_C9:G41_A A 9 ? A 41 ? 19 1 1 A C 10 1_555 A A 40 1_555 5.078 -1.340 -0.244 -6.548 -7.942 -6.700 8 A_C10:A40_A A 10 ? A 40 ? ? ? 1 A G 13 1_555 A C 39 1_555 -0.081 -0.182 -0.124 6.613 2.163 -1.014 9 A_G13:C39_A A 13 ? A 39 ? 19 1 1 A G 14 1_555 A U 37 1_555 -2.372 -0.719 0.402 13.990 -11.822 -3.479 10 A_G14:U37_A A 14 ? A 37 ? 28 ? 1 A C 15 1_555 A G 36 1_555 -0.052 -0.229 0.075 11.982 -19.856 2.116 11 A_C15:G36_A A 15 ? A 36 ? 19 1 1 A C 16 1_555 A G 35 1_555 0.348 -0.384 0.277 0.088 -13.513 -0.886 12 A_C16:G35_A A 16 ? A 35 ? 19 1 1 A A 17 1_555 A G 34 1_555 0.017 1.269 -0.751 -23.752 -20.340 -4.317 13 A_A17:G34_A A 17 ? A 34 ? 8 1 1 A C 18 1_555 A G 32 1_555 0.279 -0.036 -0.119 0.277 -15.591 0.789 14 A_C18:G32_A A 18 ? A 32 ? 19 1 1 A G 19 1_555 A C 31 1_555 -0.072 -0.037 0.536 18.277 -5.094 -4.568 15 A_G19:C31_A A 19 ? A 31 ? 19 1 1 A G 11 1_555 A A 33 1_555 -2.984 4.208 -1.746 -45.628 -16.586 -122.943 16 A_G11:A33_A A 11 ? A 33 ? ? 5 1 A C 20 1_555 A G 28 1_555 0.155 -0.009 0.040 -25.095 5.886 -2.920 17 A_C20:G28_A A 20 ? A 28 ? 19 1 1 A G 21 1_555 A C 27 1_555 -0.072 -0.098 0.003 11.984 1.440 -0.563 18 A_G21:C27_A A 21 ? A 27 ? 19 1 1 A G 22 1_555 A A 26 1_555 6.956 -4.454 0.851 23.049 1.052 3.332 19 A_G22:A26_A A 22 ? A 26 ? 11 9 # 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 A 3 1_555 A U 47 1_555 A G 4 1_555 A U 46 1_555 0.192 -1.900 2.866 -4.941 10.881 25.146 -5.931 -1.297 1.831 23.381 10.618 27.800 1 AA_A3G4:U46U47_AA A 3 ? A 47 ? A 4 ? A 46 ? 1 A G 4 1_555 A U 46 1_555 A U 5 1_555 A A 45 1_555 -0.360 -1.373 3.157 -1.642 6.046 39.501 -2.659 0.350 2.936 8.878 2.412 39.975 2 AA_G4U5:A45U46_AA A 4 ? A 46 ? A 5 ? A 45 ? 1 A U 5 1_555 A A 45 1_555 A U 6 1_555 A A 44 1_555 -0.182 -1.300 3.207 -2.246 5.046 36.465 -2.710 -0.003 3.012 8.007 3.564 36.866 3 AA_U5U6:A44A45_AA A 5 ? A 45 ? A 6 ? A 44 ? 1 A U 6 1_555 A A 44 1_555 A C 7 1_555 A G 43 1_555 -0.260 -1.065 3.189 0.041 6.806 33.809 -2.796 0.444 2.925 11.558 -0.070 34.467 4 AA_U6C7:G43A44_AA A 6 ? A 44 ? A 7 ? A 43 ? 1 A C 7 1_555 A G 43 1_555 A A 8 1_555 A U 42 1_555 0.276 -1.714 3.162 -1.180 9.895 27.543 -5.274 -0.772 2.401 19.972 2.381 29.257 5 AA_C7A8:U42G43_AA A 7 ? A 43 ? A 8 ? A 42 ? 1 A A 8 1_555 A U 42 1_555 A C 9 1_555 A G 41 1_555 0.254 -1.835 3.350 4.195 4.962 34.732 -3.751 0.197 3.076 8.223 -6.953 35.316 6 AA_A8C9:G41U42_AA A 8 ? A 42 ? A 9 ? A 41 ? 1 A C 9 1_555 A G 41 1_555 A C 10 1_555 A A 40 1_555 -0.180 -1.240 3.432 7.886 6.250 49.806 -1.897 0.778 3.203 7.335 -9.255 50.748 7 AA_C9C10:A40G41_AA A 9 ? A 41 ? A 10 ? A 40 ? 1 A C 10 1_555 A A 40 1_555 A G 13 1_555 A C 39 1_555 -4.367 0.082 3.131 5.514 4.661 54.253 -0.162 5.050 2.707 5.086 -6.016 54.695 8 AA_C10G13:C39A40_AA A 10 ? A 40 ? A 13 ? A 39 ? 1 A G 13 1_555 A C 39 1_555 A G 14 1_555 A U 37 1_555 1.682 -2.313 2.997 -12.539 1.391 43.388 -3.120 -3.137 2.376 1.836 16.548 45.099 9 AA_G13G14:U37C39_AA A 13 ? A 39 ? A 14 ? A 37 ? 1 A G 14 1_555 A U 37 1_555 A C 15 1_555 A G 36 1_555 0.135 -1.140 3.284 -1.456 1.515 45.275 -1.614 -0.305 3.241 1.967 1.890 45.321 10 AA_G14C15:G36U37_AA A 14 ? A 37 ? A 15 ? A 36 ? 1 A C 15 1_555 A G 36 1_555 A C 16 1_555 A G 35 1_555 -0.685 -1.763 3.435 -5.237 6.490 34.848 -3.819 0.347 3.134 10.649 8.592 35.802 11 AA_C15C16:G35G36_AA A 15 ? A 36 ? A 16 ? A 35 ? 1 A C 16 1_555 A G 35 1_555 A A 17 1_555 A G 34 1_555 -0.062 -1.938 3.655 9.695 14.428 34.467 -4.747 1.307 2.566 22.654 -15.223 38.483 12 AA_C16A17:G34G35_AA A 16 ? A 35 ? A 17 ? A 34 ? 1 A A 17 1_555 A G 34 1_555 A C 18 1_555 A G 32 1_555 1.105 0.165 2.832 -6.271 8.650 37.778 -0.629 -2.282 2.598 13.043 9.456 39.206 13 AA_A17C18:G32G34_AA A 17 ? A 34 ? A 18 ? A 32 ? 1 A C 18 1_555 A G 32 1_555 A G 19 1_555 A C 31 1_555 0.125 0.019 2.959 -3.744 16.165 25.999 -2.842 -0.903 2.504 32.103 7.436 30.766 14 AA_C18G19:C31G32_AA A 18 ? A 32 ? A 19 ? A 31 ? 1 A C 20 1_555 A G 28 1_555 A G 21 1_555 A C 27 1_555 0.329 -0.678 2.424 0.959 11.230 23.693 -3.619 -0.544 1.921 25.578 -2.184 26.202 15 AA_C20G21:C27G28_AA A 20 ? A 28 ? A 21 ? A 27 ? 1 A G 21 1_555 A C 27 1_555 A G 22 1_555 A A 26 1_555 1.309 -0.619 3.242 0.345 11.527 59.174 -1.172 -1.289 3.092 11.553 -0.346 60.187 16 AA_G21G22:A26C27_AA A 21 ? A 27 ? A 22 ? A 26 ? # _atom_sites.entry_id 1XJR _atom_sites.fract_transf_matrix[1][1] 0.010728 _atom_sites.fract_transf_matrix[1][2] 0.006194 _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] 0.012387 _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] 0.007806 _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 MG N O P # loop_