data_2H1M # _entry.id 2H1M # _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 2H1M pdb_00002h1m 10.2210/pdb2h1m/pdb NDB AR0070 ? ? RCSB RCSB037816 ? ? WWPDB D_1000037816 ? ? # 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 2006-07-18 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 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' Advisory 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 4 'Structure model' 'Derived calculations' 7 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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_conn 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_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2H1M _pdbx_database_status.recvd_initial_deposition_date 2006-05-16 _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 ? # _audit_author.name 'Serganov, A.A.' _audit_author.pdbx_ordinal 1 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Synthesis, Oxidation Behavior, Crystallization and Structure of 2'-Methylseleno Guanosine Containing RNAs. ; J.Am.Chem.Soc. 128 9909 9918 2006 JACSAT US 0002-7863 0004 ? 16866550 10.1021/ja0621400 1 ;Syntheses of RNAs with up to 100 nucleotides containing site-specific 2'-methylseleno labels for use in X-ray crystallography. ; J.Am.Chem.Soc. 127 12035 12045 2005 JACSAT US 0002-7863 0004 ? ? ? 2 'Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.' Nat.Struct.Mol.Biol. 12 218 224 2005 ? US 1545-9993 ? ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Moroder, H.' 1 ? primary 'Kreutz, C.' 2 ? primary 'Lang, K.' 3 ? primary 'Serganov, A.' 4 ? primary 'Micura, R.' 5 ? 1 'Hobartner, C.' 6 ? 1 'Rieder, R.' 7 ? 1 'Kreutz, C.' 8 ? 1 'Puffer, B.' 9 ? 1 'Lang, K.' 10 ? 1 'Polonskaia, A.' 11 ? 1 'Serganov, A.A.' 12 ? 1 'Micura, R.' 13 ? 2 'Serganov, A.A.' 14 ? 2 'Keiper, S.' 15 ? 2 'Malinina, L.' 16 ? 2 'Tereshko, V.' 17 ? 2 'Skripkin, E.' 18 ? 2 'Hobartner, C.' 19 ? 2 'Polonskaia, A.' 20 ? 2 'Phan, A.T.' 21 ? 2 'Wombacher, R.' 22 ? 2 'Micura, R.' 23 ? 2 'Dauter, Z.' 24 ? 2 'Jaschke, A.' 25 ? 2 'Patel, D.J.' 26 ? # 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*CP*AP*(XUG)P*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3'" 5199.090 2 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 3 ? ? ? ? # _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 'GCA(XUG)AGUUAAAUCUGC' _entity_poly.pdbx_seq_one_letter_code_can GCAGAGUUAAAUCUGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'SULFATE ION' _pdbx_entity_nonpoly.comp_id SO4 # 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 C n 1 3 A n 1 4 XUG n 1 5 A n 1 6 G n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 A n 1 12 U n 1 13 C n 1 14 U n 1 15 G n 1 16 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 XUG 'DNA linking' n ;2'-SE-METHYL-2'-SELENOGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) ; "(D)-2'-METHYLSELENYL-2'-DEOXYGUANOSINE-5'-PHOSPHATE" 'C11 H16 N5 O7 P Se' 440.208 # 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 C 2 2 2 C C A . n A 1 3 A 3 3 3 A A A . n A 1 4 XUG 4 4 4 XUG XUG A . n A 1 5 A 5 5 5 A A A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 A 11 11 11 A A A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 C 16 16 16 C C A . n B 1 1 G 1 17 17 G G B . n B 1 2 C 2 18 18 C C B . n B 1 3 A 3 19 19 A A B . n B 1 4 XUG 4 20 20 XUG XUG B . n B 1 5 A 5 21 21 A A B . n B 1 6 G 6 22 22 G G B . n B 1 7 U 7 23 23 U U B . n B 1 8 U 8 24 24 U U B . n B 1 9 A 9 25 25 A A B . n B 1 10 A 10 26 26 A A B . n B 1 11 A 11 27 27 A A B . n B 1 12 U 12 28 28 U U B . n B 1 13 C 13 29 29 C C B . n B 1 14 U 14 30 30 U U B . n B 1 15 G 15 31 31 G G B . n B 1 16 C 16 32 32 C C B . 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 C 2 SO4 1 17 1 SO4 SO4 A . D 2 SO4 1 18 3 SO4 SO4 A . E 2 SO4 1 2 2 SO4 SO4 B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0005 ? 1 CBASS 'data collection' . ? 2 HKL-2000 'data scaling' . ? 3 MOLREP phasing . ? 4 # _cell.entry_id 2H1M _cell.length_a 46.314 _cell.length_b 46.314 _cell.length_c 128.348 _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 2H1M _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2H1M _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.55 _exptl_crystal.density_percent_sol 51.72 _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 5.6 _exptl_crystal_grow.pdbx_details '1.0 M Li2SO4, 0.1 M Na-citrate pH 5.6, 0.5 M ((NH4))2SO4, 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 Li2SO4 ? ? ? 1 2 1 Na-citrate ? ? ? 1 3 1 '(NH4))2SO4' ? ? ? 1 4 1 H2O ? ? ? 1 5 2 Li2SO4 ? ? ? 1 6 2 Na-citrate ? ? ? 1 7 2 H2O ? ? ? # _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 315' _diffrn_detector.pdbx_collection_date 2005-10-11 _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 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.978948 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X25' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X25 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.978948 # _reflns.entry_id 2H1M _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 2.9 _reflns.d_resolution_low 20 _reflns.number_all 2227 _reflns.number_obs 2227 _reflns.percent_possible_obs 97.2 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.112 _reflns.pdbx_netI_over_sigmaI 12.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.9 _reflns_shell.d_res_low 3.0 _reflns_shell.percent_possible_all 99.5 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.32 _reflns_shell.meanI_over_sigI_obs 6.5 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 221 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 2H1M _refine.ls_number_reflns_obs 2118 _refine.ls_number_reflns_all 2227 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 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 20.00 _refine.ls_d_res_high 2.90 _refine.ls_percent_reflns_obs 97.24 _refine.ls_R_factor_obs 0.21352 _refine.ls_R_factor_all 0.21352 _refine.ls_R_factor_R_work 0.21225 _refine.ls_R_factor_R_free 0.2386 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 102 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.942 _refine.correlation_coeff_Fo_to_Fc_free 0.949 _refine.B_iso_mean 35.247 _refine.aniso_B[1][1] 0.86 _refine.aniso_B[2][2] 0.86 _refine.aniso_B[3][3] -1.29 _refine.aniso_B[1][2] 0.43 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model 'Similar RNA structure from the crystal grown in different conditions.' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free 0.406 _refine.overall_SU_ML 0.323 _refine.overall_SU_B 42.148 _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_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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_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 680 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 695 _refine_hist.d_res_high 2.90 _refine_hist.d_res_low 20.00 # 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 0.005 0.021 ? 772 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.125 3.000 ? 1198 'X-RAY DIFFRACTION' ? r_chiral_restr 0.047 0.200 ? 156 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.001 0.020 ? 332 'X-RAY DIFFRACTION' ? r_nbd_refined 0.154 0.200 ? 292 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.269 0.200 ? 496 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.134 0.200 ? 9 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.108 0.200 ? 34 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.081 0.200 ? 2 'X-RAY DIFFRACTION' ? r_scbond_it 0.471 3.000 ? 1088 'X-RAY DIFFRACTION' ? r_scangle_it 0.922 4.500 ? 1198 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.900 _refine_ls_shell.d_res_low 2.974 _refine_ls_shell.number_reflns_R_work 170 _refine_ls_shell.R_factor_R_work 0.343 _refine_ls_shell.percent_reflns_obs 99.44 _refine_ls_shell.R_factor_R_free 0.249 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 6 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 2H1M _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 2H1M _struct.title ;Synthesis, Oxidation Behavior, Crystallization and Structure of 2'-Methylseleno Guanosine Containing RNAs ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2H1M _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;A-RNA STRUCTURE, MISMATCH A RNA, RIBONUCLEIC ACID, Se 2'-methylSe, 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 1 ? C N N 2 ? D N N 2 ? E N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2H1M _struct_ref.pdbx_db_accession 2H1M _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2H1M A 1 ? 16 ? 2H1M 1 ? 16 ? 1 16 2 1 2H1M B 1 ? 16 ? 2H1M 17 ? 32 ? 17 32 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details 'The biological assembly is a duplex RNA.' _struct_biol.pdbx_parent_biol_id ? # 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 A 3 "O3'" ? ? ? 1_555 A XUG 4 P ? ? A A 3 A XUG 4 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale2 covale both ? A XUG 4 "O3'" ? ? ? 1_555 A A 5 P ? ? A XUG 4 A A 5 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale3 covale both ? B A 3 "O3'" ? ? ? 1_555 B XUG 4 P ? ? B A 19 B XUG 20 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale4 covale both ? B XUG 4 "O3'" ? ? ? 1_555 B A 5 P ? ? B XUG 20 B A 21 1_555 ? ? ? ? ? ? ? 1.598 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 16 N3 ? ? A G 1 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 16 O2 ? ? A G 1 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 16 N4 ? ? A G 1 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 2 B G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 2 B G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 2 B G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 14 N3 ? ? A A 3 B U 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 14 O4 ? ? A A 3 B U 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A XUG 4 N1 ? ? ? 1_555 B C 13 N3 ? ? A XUG 4 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A XUG 4 N2 ? ? ? 1_555 B C 13 O2 ? ? A XUG 4 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A XUG 4 O6 ? ? ? 1_555 B C 13 N4 ? ? A XUG 4 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 12 N3 ? ? A A 5 B U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 12 O4 ? ? A A 5 B U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 B A 11 N6 ? ? A G 6 B A 27 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog15 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 7 B A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 7 B A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 8 B A 25 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog18 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 9 B U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 9 B U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 10 B U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 10 B U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 12 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 12 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 13 N3 ? ? ? 1_555 B XUG 4 N1 ? ? A C 13 B XUG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 13 N4 ? ? ? 1_555 B XUG 4 O6 ? ? A C 13 B XUG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 O2 ? ? ? 1_555 B XUG 4 N2 ? ? A C 13 B XUG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 14 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 14 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 14 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 14 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 15 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 15 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 15 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 16 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 16 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 16 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 16 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 16 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 17 ? 2 'BINDING SITE FOR RESIDUE SO4 A 17' AC2 Software B SO4 2 ? 2 'BINDING SITE FOR RESIDUE SO4 B 2' AC3 Software A SO4 18 ? 2 'BINDING SITE FOR RESIDUE SO4 A 18' # 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 2 C A 2 ? C A 2 . ? 1_555 ? 2 AC1 2 C B 13 ? C B 29 . ? 1_555 ? 3 AC2 2 C B 2 ? C B 18 . ? 1_555 ? 4 AC2 2 A B 3 ? A B 19 . ? 1_555 ? 5 AC3 2 G A 1 ? G A 1 . ? 5_565 ? 6 AC3 2 C A 16 ? C A 16 . ? 1_555 ? # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A XUG 4 A XUG 4 ? DG ? 2 B XUG 4 B XUG 20 ? DG ? # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x -17.4451 _pdbx_refine_tls.origin_y 30.2251 _pdbx_refine_tls.origin_z 0.2219 _pdbx_refine_tls.T[1][1] 0.3097 _pdbx_refine_tls.T[2][2] 0.1852 _pdbx_refine_tls.T[3][3] 0.1447 _pdbx_refine_tls.T[1][2] 0.1043 _pdbx_refine_tls.T[1][3] 0.0045 _pdbx_refine_tls.T[2][3] -0.0046 _pdbx_refine_tls.L[1][1] 0.3148 _pdbx_refine_tls.L[2][2] 0.1581 _pdbx_refine_tls.L[3][3] 6.3136 _pdbx_refine_tls.L[1][2] 0.2230 _pdbx_refine_tls.L[1][3] -0.1367 _pdbx_refine_tls.L[2][3] -0.1174 _pdbx_refine_tls.S[1][1] 0.0344 _pdbx_refine_tls.S[1][2] 0.0583 _pdbx_refine_tls.S[1][3] 0.0380 _pdbx_refine_tls.S[2][1] 0.1622 _pdbx_refine_tls.S[2][2] -0.0879 _pdbx_refine_tls.S[2][3] -0.0038 _pdbx_refine_tls.S[3][1] 0.7874 _pdbx_refine_tls.S[3][2] 0.4599 _pdbx_refine_tls.S[3][3] 0.0534 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.selection_details 1 1 A 1 A 1 A 16 A 16 ? 'X-RAY DIFFRACTION' ? 2 1 B 17 B 1 B 32 B 16 ? 'X-RAY DIFFRACTION' ? 3 1 A 17 C 1 A 18 E 1 ? 'X-RAY DIFFRACTION' ? # 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 SO4 S S N N 111 SO4 O1 O N N 112 SO4 O2 O N N 113 SO4 O3 O N N 114 SO4 O4 O N N 115 U OP3 O N N 116 U P P N N 117 U OP1 O N N 118 U OP2 O N N 119 U "O5'" O N N 120 U "C5'" C N N 121 U "C4'" C N R 122 U "O4'" O N N 123 U "C3'" C N S 124 U "O3'" O N N 125 U "C2'" C N R 126 U "O2'" O N N 127 U "C1'" C N R 128 U N1 N N N 129 U C2 C N N 130 U O2 O N N 131 U N3 N N N 132 U C4 C N N 133 U O4 O N N 134 U C5 C N N 135 U C6 C N N 136 U HOP3 H N N 137 U HOP2 H N N 138 U "H5'" H N N 139 U "H5''" H N N 140 U "H4'" H N N 141 U "H3'" H N N 142 U "HO3'" H N N 143 U "H2'" H N N 144 U "HO2'" H N N 145 U "H1'" H N N 146 U H3 H N N 147 U H5 H N N 148 U H6 H N N 149 XUG O6 O N N 150 XUG C6 C N N 151 XUG C5 C Y N 152 XUG N7 N Y N 153 XUG C8 C Y N 154 XUG N1 N N N 155 XUG C2 C N N 156 XUG N2 N N N 157 XUG N3 N N N 158 XUG C4 C Y N 159 XUG N9 N Y N 160 XUG "C1'" C N R 161 XUG "O4'" O N N 162 XUG "C2'" C N R 163 XUG "SE2'" SE N N 164 XUG "CA'" C N N 165 XUG "C3'" C N R 166 XUG "O3'" O N N 167 XUG "C4'" C N R 168 XUG "C5'" C N N 169 XUG "O5'" O N N 170 XUG P P N N 171 XUG OP1 O N N 172 XUG OP2 O N N 173 XUG OP3 O N N 174 XUG H8 H N N 175 XUG HN1 H N N 176 XUG HN21 H N N 177 XUG HN22 H N N 178 XUG "H1'" H N N 179 XUG "H2'" H N N 180 XUG "HA'1" H N N 181 XUG "HA'2" H N N 182 XUG "HA'3" H N N 183 XUG "H3'" H N N 184 XUG "HO3'" H N N 185 XUG "H4'" H N N 186 XUG "H5'" H N N 187 XUG "H5''" H N N 188 XUG HOP2 H N N 189 XUG HOP3 H N N 190 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 SO4 S O1 doub N N 116 SO4 S O2 doub N N 117 SO4 S O3 sing N N 118 SO4 S O4 sing N N 119 U OP3 P sing N N 120 U OP3 HOP3 sing N N 121 U P OP1 doub N N 122 U P OP2 sing N N 123 U P "O5'" sing N N 124 U OP2 HOP2 sing N N 125 U "O5'" "C5'" sing N N 126 U "C5'" "C4'" sing N N 127 U "C5'" "H5'" sing N N 128 U "C5'" "H5''" sing N N 129 U "C4'" "O4'" sing N N 130 U "C4'" "C3'" sing N N 131 U "C4'" "H4'" sing N N 132 U "O4'" "C1'" sing N N 133 U "C3'" "O3'" sing N N 134 U "C3'" "C2'" sing N N 135 U "C3'" "H3'" sing N N 136 U "O3'" "HO3'" sing N N 137 U "C2'" "O2'" sing N N 138 U "C2'" "C1'" sing N N 139 U "C2'" "H2'" sing N N 140 U "O2'" "HO2'" sing N N 141 U "C1'" N1 sing N N 142 U "C1'" "H1'" sing N N 143 U N1 C2 sing N N 144 U N1 C6 sing N N 145 U C2 O2 doub N N 146 U C2 N3 sing N N 147 U N3 C4 sing N N 148 U N3 H3 sing N N 149 U C4 O4 doub N N 150 U C4 C5 sing N N 151 U C5 C6 doub N N 152 U C5 H5 sing N N 153 U C6 H6 sing N N 154 XUG O6 C6 doub N N 155 XUG C6 C5 sing N N 156 XUG C6 N1 sing N N 157 XUG C5 N7 sing Y N 158 XUG C5 C4 doub Y N 159 XUG N7 C8 doub Y N 160 XUG C8 N9 sing Y N 161 XUG C8 H8 sing N N 162 XUG N1 C2 sing N N 163 XUG N1 HN1 sing N N 164 XUG C2 N2 sing N N 165 XUG C2 N3 doub N N 166 XUG N2 HN21 sing N N 167 XUG N2 HN22 sing N N 168 XUG N3 C4 sing N N 169 XUG C4 N9 sing Y N 170 XUG N9 "C1'" sing N N 171 XUG "C1'" "O4'" sing N N 172 XUG "C1'" "C2'" sing N N 173 XUG "C1'" "H1'" sing N N 174 XUG "O4'" "C4'" sing N N 175 XUG "C2'" "SE2'" sing N N 176 XUG "C2'" "C3'" sing N N 177 XUG "C2'" "H2'" sing N N 178 XUG "SE2'" "CA'" sing N N 179 XUG "CA'" "HA'1" sing N N 180 XUG "CA'" "HA'2" sing N N 181 XUG "CA'" "HA'3" sing N N 182 XUG "C3'" "O3'" sing N N 183 XUG "C3'" "C4'" sing N N 184 XUG "C3'" "H3'" sing N N 185 XUG "O3'" "HO3'" sing N N 186 XUG "C4'" "C5'" sing N N 187 XUG "C4'" "H4'" sing N N 188 XUG "C5'" "O5'" sing N N 189 XUG "C5'" "H5'" sing N N 190 XUG "C5'" "H5''" sing N N 191 XUG "O5'" P sing N N 192 XUG P OP1 doub N N 193 XUG P OP2 sing N N 194 XUG P OP3 sing N N 195 XUG OP2 HOP2 sing N N 196 XUG OP3 HOP3 sing N N 197 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2H1M 'double helix' 2H1M 'a-form double helix' 2H1M '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 B C 16 1_555 -0.554 -0.087 -0.216 -4.666 -3.103 -1.392 1 A_G1:C32_B A 1 ? B 32 ? 19 1 1 A C 2 1_555 B G 15 1_555 0.242 -0.180 0.157 -0.287 -12.569 3.644 2 A_C2:G31_B A 2 ? B 31 ? 19 1 1 A A 3 1_555 B U 14 1_555 0.101 0.095 0.071 -1.328 -7.605 6.622 3 A_A3:U30_B A 3 ? B 30 ? 20 1 1 A XUG 4 1_555 B C 13 1_555 -0.644 0.028 0.023 -0.431 -20.488 7.071 4 A_XUG4:C29_B A 4 ? B 29 ? 19 1 1 A A 5 1_555 B U 12 1_555 0.029 0.142 -0.215 -3.971 -13.485 0.250 5 A_A5:U28_B A 5 ? B 28 ? 20 1 1 A G 6 1_555 B A 11 1_555 -1.015 -3.561 -0.367 13.030 6.985 96.380 6 A_G6:A27_B A 6 ? B 27 ? ? ? 1 A U 7 1_555 B A 10 1_555 -0.452 -0.173 0.290 -2.259 -19.965 1.891 7 A_U7:A26_B A 7 ? B 26 ? 20 1 1 A U 8 1_555 B A 9 1_555 -0.161 -0.019 0.660 -1.522 -15.573 11.850 8 A_U8:A25_B A 8 ? B 25 ? ? 1 1 A A 9 1_555 B U 8 1_555 -0.720 -0.049 0.615 3.686 -12.472 5.993 9 A_A9:U24_B A 9 ? B 24 ? 20 1 1 A A 10 1_555 B U 7 1_555 0.010 -0.065 0.162 0.623 -19.544 1.128 10 A_A10:U23_B A 10 ? B 23 ? 20 1 1 A U 12 1_555 B A 5 1_555 -0.002 -0.088 -0.161 2.070 -11.966 1.383 11 A_U12:A21_B A 12 ? B 21 ? 20 1 1 A C 13 1_555 B XUG 4 1_555 0.269 -0.187 -0.124 3.700 -18.307 -0.274 12 A_C13:XUG20_B A 13 ? B 20 ? 19 1 1 A U 14 1_555 B A 3 1_555 0.068 0.068 0.065 3.320 -4.995 7.689 13 A_U14:A19_B A 14 ? B 19 ? 20 1 1 A G 15 1_555 B C 2 1_555 -0.365 -0.224 0.175 -0.301 -13.913 2.748 14 A_G15:C18_B A 15 ? B 18 ? 19 1 1 A C 16 1_555 B G 1 1_555 1.108 -0.190 -0.319 9.301 -5.850 -1.964 15 A_C16:G17_B A 16 ? B 17 ? 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 B C 16 1_555 A C 2 1_555 B G 15 1_555 -0.194 -1.535 3.204 -4.193 0.299 38.179 -2.370 -0.218 3.195 0.456 6.386 38.401 1 AA_G1C2:G31C32_BB A 1 ? B 32 ? A 2 ? B 31 ? 1 A C 2 1_555 B G 15 1_555 A A 3 1_555 B U 14 1_555 -0.281 -1.516 3.041 0.879 13.549 31.922 -4.301 0.586 2.225 23.359 -1.516 34.620 2 AA_C2A3:U30G31_BB A 2 ? B 31 ? A 3 ? B 30 ? 1 A A 3 1_555 B U 14 1_555 A XUG 4 1_555 B C 13 1_555 0.717 -1.678 3.119 1.984 12.540 24.472 -6.118 -1.096 2.076 27.355 -4.328 27.525 3 AA_A3XUG4:C29U30_BB A 3 ? B 30 ? A 4 ? B 29 ? 1 A XUG 4 1_555 B C 13 1_555 A A 5 1_555 B U 12 1_555 -0.914 -1.140 3.283 -1.295 9.498 38.761 -2.733 1.195 2.962 14.050 1.915 39.884 4 AA_XUG4A5:U28C29_BB A 4 ? B 29 ? A 5 ? B 28 ? 1 A A 5 1_555 B U 12 1_555 A G 6 1_555 B A 11 1_555 1.814 2.897 0.353 172.720 -36.448 -13.085 -1.521 0.569 -1.129 18.542 87.867 -176.547 5 AA_A5G6:A27U28_BB A 5 ? B 28 ? A 6 ? B 27 ? 1 A G 6 1_555 B A 11 1_555 A U 7 1_555 B A 10 1_555 -0.760 -3.259 -1.866 131.181 -113.073 84.735 -1.916 0.050 -0.113 -57.261 -66.431 174.969 6 AA_G6U7:A26A27_BB A 6 ? B 27 ? A 7 ? B 26 ? 1 A U 7 1_555 B A 10 1_555 A U 8 1_555 B A 9 1_555 0.656 -1.293 3.171 -1.909 5.839 33.451 -3.081 -1.407 2.870 10.038 3.282 33.995 7 AA_U7U8:A25A26_BB A 7 ? B 26 ? A 8 ? B 25 ? 1 A U 8 1_555 B A 9 1_555 A A 9 1_555 B U 8 1_555 -0.270 -1.425 2.602 -2.042 13.111 31.219 -3.958 0.228 1.882 23.098 3.597 33.857 8 AA_U8A9:U24A25_BB A 8 ? B 25 ? A 9 ? B 24 ? 1 A A 9 1_555 B U 8 1_555 A A 10 1_555 B U 7 1_555 -0.222 -1.415 3.302 3.188 4.874 35.461 -2.975 0.805 3.057 7.936 -5.190 35.921 9 AA_A9A10:U23U24_BB A 9 ? B 24 ? A 10 ? B 23 ? 1 A A 10 1_555 B U 7 1_555 A U 12 1_555 B A 5 1_555 0.236 -3.438 6.224 4.105 8.598 61.074 -4.088 0.122 5.745 8.406 -4.013 61.742 10 AA_A10U12:A21U23_BB A 10 ? B 23 ? A 12 ? B 21 ? 1 A U 12 1_555 B A 5 1_555 A C 13 1_555 B XUG 4 1_555 0.475 -1.245 3.101 0.933 10.620 35.909 -3.196 -0.630 2.650 16.776 -1.473 37.408 11 AA_U12C13:XUG20A21_BB A 12 ? B 21 ? A 13 ? B 20 ? 1 A C 13 1_555 B XUG 4 1_555 A U 14 1_555 B A 3 1_555 -0.492 -1.806 3.287 -3.086 10.749 28.264 -5.428 0.371 2.488 21.002 6.029 30.354 12 AA_C13U14:A19XUG20_BB A 13 ? B 20 ? A 14 ? B 19 ? 1 A U 14 1_555 B A 3 1_555 A G 15 1_555 B C 2 1_555 0.118 -1.527 3.109 0.374 11.439 29.646 -4.617 -0.157 2.373 21.378 -0.700 31.732 13 AA_U14G15:C18A19_BB A 14 ? B 19 ? A 15 ? B 18 ? 1 A G 15 1_555 B C 2 1_555 A C 16 1_555 B G 1 1_555 0.384 -1.480 3.106 5.898 0.757 40.688 -2.186 0.064 3.103 1.082 -8.428 41.102 14 AA_G15C16:G17C18_BB A 15 ? B 18 ? A 16 ? B 17 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'Similar RNA structure from the crystal grown in different conditions.' # _atom_sites.entry_id 2H1M _atom_sites.fract_transf_matrix[1][1] 0.021592 _atom_sites.fract_transf_matrix[1][2] 0.012466 _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] 0.024932 _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] 0.007791 _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 N O P S SE # loop_