data_2XSL # _entry.id 2XSL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2XSL pdb_00002xsl 10.2210/pdb2xsl/pdb PDBE EBI-45994 ? ? WWPDB D_1290045994 ? ? # 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 2011-08-10 2 'Structure model' 1 1 2012-08-15 3 'Structure model' 1 2 2019-07-17 4 'Structure model' 1 3 2024-05-01 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' Other 6 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' diffrn_source 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_database_status 6 4 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_pdbx_database_status.status_code_sf' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2XSL _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2010-10-29 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Oberthuer, D.' 1 'Eichert, A.' 2 'Erdmann, V.A.' 3 'Fuerste, J.P.' 4 'Betzel, C.' 5 'Foerster, C.' 6 # _citation.id primary _citation.title 'The Crystal Structure of a Thermus Thermophilus tRNA(Gly) Acceptor Stem Microhelix at 1.6 A Resolution.' _citation.journal_abbrev Biochem.Biophys.Res.Commun. _citation.journal_volume 404 _citation.page_first 245 _citation.page_last ? _citation.year 2011 _citation.journal_id_ASTM BBRCA9 _citation.country US _citation.journal_id_ISSN 0006-291X _citation.journal_id_CSD 0146 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21114959 _citation.pdbx_database_id_DOI 10.1016/J.BBRC.2010.11.101 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Oberthur, D.' 1 ? primary 'Eichert, A.' 2 ? primary 'Erdmann, V.A.' 3 ? primary 'Furste, J.P.' 4 ? primary 'Betzel, C.' 5 ? primary 'Forster, C.' 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 "5'-R(*GP*CP*GP*GP*GP*AP*G)-3'" 2315.459 2 ? ? 'MICROHELIX, RESIDUES 1-7' ? 2 polymer syn "5'-R(*CP*UP*CP*CP*CP*GP*C)-3'" 2132.323 2 ? ? 'MICROHELIX, RESIDUES 66-72' ? 3 water nat water 18.015 88 ? ? ? ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 TRNAGLY 2 TRNAGLY # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GCGGGAG GCGGGAG A,C ? 2 polyribonucleotide no no CUCCCGC CUCCCGC B,D ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 G n 1 4 G n 1 5 G n 1 6 A n 1 7 G n 2 1 C n 2 2 U n 2 3 C n 2 4 C n 2 5 C n 2 6 G n 2 7 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? 'THERMUS THERMOPHILUS' ? 274 ? 2 1 sample ? ? 'THERMUS THERMOPHILUS' ? 274 ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 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 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 A 6 6 6 A A A . n A 1 7 G 7 7 7 G G A . n B 2 1 C 1 66 66 C C B . n B 2 2 U 2 67 67 U U B . n B 2 3 C 3 68 68 C C B . n B 2 4 C 4 69 69 C C B . n B 2 5 C 5 70 70 C C B . n B 2 6 G 6 71 71 G G B . n B 2 7 C 7 72 72 C C B . n C 1 1 G 1 1 1 G G C . n C 1 2 C 2 2 2 C C C . n C 1 3 G 3 3 3 G G C . n C 1 4 G 4 4 4 G G C . n C 1 5 G 5 5 5 G G C . n C 1 6 A 6 6 6 A A C . n C 1 7 G 7 7 7 G G C . n D 2 1 C 1 66 66 C C D . n D 2 2 U 2 67 67 U U D . n D 2 3 C 3 68 68 C C D . n D 2 4 C 4 69 69 C C D . n D 2 5 C 5 70 70 C C D . n D 2 6 G 6 71 71 G G D . n D 2 7 C 7 72 72 C C D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 3 HOH 1 2001 2001 HOH HOH A . E 3 HOH 2 2002 2002 HOH HOH A . E 3 HOH 3 2003 2003 HOH HOH A . E 3 HOH 4 2004 2004 HOH HOH A . E 3 HOH 5 2005 2005 HOH HOH A . E 3 HOH 6 2006 2006 HOH HOH A . E 3 HOH 7 2007 2007 HOH HOH A . E 3 HOH 8 2008 2008 HOH HOH A . E 3 HOH 9 2009 2009 HOH HOH A . E 3 HOH 10 2010 2010 HOH HOH A . E 3 HOH 11 2011 2011 HOH HOH A . E 3 HOH 12 2012 2012 HOH HOH A . E 3 HOH 13 2013 2013 HOH HOH A . E 3 HOH 14 2014 2014 HOH HOH A . E 3 HOH 15 2015 2015 HOH HOH A . E 3 HOH 16 2016 2016 HOH HOH A . E 3 HOH 17 2017 2017 HOH HOH A . E 3 HOH 18 2018 2018 HOH HOH A . E 3 HOH 19 2019 2019 HOH HOH A . E 3 HOH 20 2020 2020 HOH HOH A . E 3 HOH 21 2021 2021 HOH HOH A . E 3 HOH 22 2022 2022 HOH HOH A . F 3 HOH 1 2001 2001 HOH HOH B . F 3 HOH 2 2002 2002 HOH HOH B . F 3 HOH 3 2003 2003 HOH HOH B . F 3 HOH 4 2004 2004 HOH HOH B . F 3 HOH 5 2005 2005 HOH HOH B . F 3 HOH 6 2006 2006 HOH HOH B . F 3 HOH 7 2007 2007 HOH HOH B . F 3 HOH 8 2008 2008 HOH HOH B . F 3 HOH 9 2009 2009 HOH HOH B . F 3 HOH 10 2010 2010 HOH HOH B . F 3 HOH 11 2011 2011 HOH HOH B . F 3 HOH 12 2012 2012 HOH HOH B . F 3 HOH 13 2013 2013 HOH HOH B . F 3 HOH 14 2014 2014 HOH HOH B . F 3 HOH 15 2015 2015 HOH HOH B . F 3 HOH 16 2016 2016 HOH HOH B . F 3 HOH 17 2017 2017 HOH HOH B . G 3 HOH 1 2001 2001 HOH HOH C . G 3 HOH 2 2002 2002 HOH HOH C . G 3 HOH 3 2003 2003 HOH HOH C . G 3 HOH 4 2004 2004 HOH HOH C . G 3 HOH 5 2005 2005 HOH HOH C . G 3 HOH 6 2006 2006 HOH HOH C . G 3 HOH 7 2007 2007 HOH HOH C . G 3 HOH 8 2008 2008 HOH HOH C . G 3 HOH 9 2009 2009 HOH HOH C . G 3 HOH 10 2010 2010 HOH HOH C . G 3 HOH 11 2011 2011 HOH HOH C . G 3 HOH 12 2012 2012 HOH HOH C . G 3 HOH 13 2013 2013 HOH HOH C . G 3 HOH 14 2014 2014 HOH HOH C . G 3 HOH 15 2015 2015 HOH HOH C . G 3 HOH 16 2016 2016 HOH HOH C . G 3 HOH 17 2017 2017 HOH HOH C . G 3 HOH 18 2018 2018 HOH HOH C . G 3 HOH 19 2019 2019 HOH HOH C . G 3 HOH 20 2020 2020 HOH HOH C . G 3 HOH 21 2021 2021 HOH HOH C . G 3 HOH 22 2022 2022 HOH HOH C . G 3 HOH 23 2023 2023 HOH HOH C . G 3 HOH 24 2024 2024 HOH HOH C . G 3 HOH 25 2025 2025 HOH HOH C . H 3 HOH 1 2001 2001 HOH HOH D . H 3 HOH 2 2002 2002 HOH HOH D . H 3 HOH 3 2003 2003 HOH HOH D . H 3 HOH 4 2004 2004 HOH HOH D . H 3 HOH 5 2005 2005 HOH HOH D . H 3 HOH 6 2006 2006 HOH HOH D . H 3 HOH 7 2007 2007 HOH HOH D . H 3 HOH 8 2008 2008 HOH HOH D . H 3 HOH 9 2009 2009 HOH HOH D . H 3 HOH 10 2010 2010 HOH HOH D . H 3 HOH 11 2011 2011 HOH HOH D . H 3 HOH 12 2012 2012 HOH HOH D . H 3 HOH 13 2013 2013 HOH HOH D . H 3 HOH 14 2014 2014 HOH HOH D . H 3 HOH 15 2015 2015 HOH HOH D . H 3 HOH 16 2016 2016 HOH HOH D . H 3 HOH 17 2017 2017 HOH HOH D . H 3 HOH 18 2018 2018 HOH HOH D . H 3 HOH 19 2019 2019 HOH HOH D . H 3 HOH 20 2020 2020 HOH HOH D . H 3 HOH 21 2021 2021 HOH HOH D . H 3 HOH 22 2022 2022 HOH HOH D . H 3 HOH 23 2023 2023 HOH HOH D . H 3 HOH 24 2024 2024 HOH HOH D . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.5.0072 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 PHASER phasing . ? 4 # _cell.entry_id 2XSL _cell.length_a 26.187 _cell.length_b 29.015 _cell.length_c 29.534 _cell.angle_alpha 107.17 _cell.angle_beta 97.37 _cell.angle_gamma 96.55 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XSL _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 2XSL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.52 _exptl_crystal.density_percent_sol 62.59 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;0.5 MM RNA IN 40 MM SODIUM CACODYLATE, PH 7.0, 12 MM SPERMINE TETRA-HCL, 80 MM NACL AND 10 % (V/V) MPD, EQUILIBRATED AGAINST 35 % (V/V) MPD, ROOM TEMPERATURE. ; # _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 'MARRESEARCH SX-165' _diffrn_detector.pdbx_collection_date ? _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 0.8123 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X13' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X13 _diffrn_source.pdbx_wavelength 0.8123 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2XSL _reflns.observed_criterion_sigma_I 1.7 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 36.00 _reflns.d_resolution_high 1.60 _reflns.number_obs 10142 _reflns.number_all ? _reflns.percent_possible_obs 94.7 _reflns.pdbx_Rmerge_I_obs 0.07 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 14.50 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.4 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.63 _reflns_shell.percent_possible_all 72.9 _reflns_shell.Rmerge_I_obs 0.35 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.70 _reflns_shell.pdbx_redundancy 2.1 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2XSL _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 9648 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 27.80 _refine.ls_d_res_high 1.59 _refine.ls_percent_reflns_obs 93.37 _refine.ls_R_factor_obs 0.23898 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23690 _refine.ls_R_factor_R_free 0.28033 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 485 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.952 _refine.correlation_coeff_Fo_to_Fc_free 0.927 _refine.B_iso_mean ? _refine.aniso_B[1][1] -0.01 _refine.aniso_B[2][2] -0.02 _refine.aniso_B[3][3] 0.00 _refine.aniso_B[1][2] -0.03 _refine.aniso_B[1][3] -0.03 _refine.aniso_B[2][3] -0.01 _refine.solvent_model_details 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 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.' _refine.pdbx_starting_model 'ARTIFICIAL RNA' _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 0.123 _refine.pdbx_overall_ESU_R_Free 0.123 _refine.overall_SU_ML 0.101 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 3.032 _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 588 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 88 _refine_hist.number_atoms_total 676 _refine_hist.d_res_high 1.59 _refine_hist.d_res_low 27.80 # 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 0.025 0.021 ? 654 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.138 3.000 ? 1014 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.109 0.200 ? 112 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.017 0.020 ? 292 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.149 3.000 ? 654 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 2.496 4.500 ? 1014 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.pdbx_refine_id _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso _refine_ls_restr_ncs.pdbx_asym_id _refine_ls_restr_ncs.pdbx_rms _refine_ls_restr_ncs.pdbx_weight 1 A 154 0.20 0.05 'tight positional' 1 1 'X-RAY DIFFRACTION' ? ? ? ? ? ? 1 B 154 0.20 0.05 'tight positional' 1 2 'X-RAY DIFFRACTION' ? ? ? ? ? ? 1 B 140 0.24 0.05 'tight positional' 2 3 'X-RAY DIFFRACTION' ? ? ? ? ? ? 2 D 140 0.24 0.05 'tight positional' 2 4 'X-RAY DIFFRACTION' ? ? ? ? ? ? 1 A 154 0.55 0.50 'tight thermal' 1 5 'X-RAY DIFFRACTION' ? ? ? ? ? ? 1 B 154 0.55 0.50 'tight thermal' 1 6 'X-RAY DIFFRACTION' ? ? ? ? ? ? 1 B 140 0.77 0.50 'tight thermal' 2 7 'X-RAY DIFFRACTION' ? ? ? ? ? ? 2 D 140 0.77 0.50 'tight thermal' 2 8 'X-RAY DIFFRACTION' ? ? ? ? ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.594 _refine_ls_shell.d_res_low 1.636 _refine_ls_shell.number_reflns_R_work 483 _refine_ls_shell.R_factor_R_work 0.453 _refine_ls_shell.percent_reflns_obs 62.62 _refine_ls_shell.R_factor_R_free 0.444 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 23 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _struct_ncs_dom.id _struct_ncs_dom.details _struct_ncs_dom.pdbx_ens_id 1 A 1 2 C 1 1 B 2 2 D 2 # loop_ _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.selection_details _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.end_auth_comp_id 1 A 1 A 7 1 1 ? ? ? ? ? ? ? ? 1 ? ? ? 2 C 1 C 7 1 1 ? ? ? ? ? ? ? ? 1 ? ? ? 1 B 8 B 14 1 1 ? ? ? ? ? ? ? ? 2 ? ? ? 2 D 8 D 14 1 1 ? ? ? ? ? ? ? ? 2 ? ? ? # loop_ _struct_ncs_ens.id _struct_ncs_ens.details 1 ? 2 ? # _database_PDB_matrix.entry_id 2XSL _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 2XSL _struct.title 'The crystal structure of a Thermus thermophilus tRNAGly acceptor stem microhelix at 1.6 Angstroem resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2XSL _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, IDENTITY ELEMENTS, GLYCYL-TRNA SYNTHETASE (GLYRS), RNA HYDRATION' # 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 1 ? D N N 2 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 GB NC_006461 1 ? ? 55979969 ? 2 GB NC_006461 2 ? ? 55979969 ? # 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 2XSL A 1 ? 7 ? 55979969 12366 ? 12372 ? 1 7 2 1 2XSL C 1 ? 7 ? 55979969 12366 ? 12372 ? 1 7 3 2 2XSL B 1 ? 7 ? 55979969 12431 ? 12437 ? 66 72 4 2 2XSL D 1 ? 7 ? 55979969 12431 ? 12437 ? 66 72 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 software_defined_assembly PISA dimeric 2 2 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 710 ? 1 MORE -4.4 ? 1 'SSA (A^2)' 2760 ? 2 'ABSA (A^2)' 710 ? 2 MORE -3.8 ? 2 'SSA (A^2)' 2750 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F 2 1 C,D,G,H # _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 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 1 B C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 1 B C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 1 B C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 2 B G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 2 B G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 2 B G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 3 B C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 3 B C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 3 B C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 4 B C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 4 B C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 4 B C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 5 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 5 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 5 B C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 6 N1 ? ? ? 1_555 B U 2 N3 ? ? A A 6 B U 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 6 N6 ? ? ? 1_555 B U 2 O4 ? ? A A 6 B U 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 7 B C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 7 B C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 7 B C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C G 1 N1 ? ? ? 1_555 D C 7 N3 ? ? C G 1 D C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C G 1 N2 ? ? ? 1_555 D C 7 O2 ? ? C G 1 D C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C G 1 O6 ? ? ? 1_555 D C 7 N4 ? ? C G 1 D C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? C C 2 N3 ? ? ? 1_555 D G 6 N1 ? ? C C 2 D G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? C C 2 N4 ? ? ? 1_555 D G 6 O6 ? ? C C 2 D G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? C C 2 O2 ? ? ? 1_555 D G 6 N2 ? ? C C 2 D G 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? C G 3 N1 ? ? ? 1_555 D C 5 N3 ? ? C G 3 D C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C G 3 N2 ? ? ? 1_555 D C 5 O2 ? ? C G 3 D C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C G 3 O6 ? ? ? 1_555 D C 5 N4 ? ? C G 3 D C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C G 4 N1 ? ? ? 1_555 D C 4 N3 ? ? C G 4 D C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C G 4 N2 ? ? ? 1_555 D C 4 O2 ? ? C G 4 D C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C G 4 O6 ? ? ? 1_555 D C 4 N4 ? ? C G 4 D C 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C G 5 N1 ? ? ? 1_555 D C 3 N3 ? ? C G 5 D C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C G 5 N2 ? ? ? 1_555 D C 3 O2 ? ? C G 5 D C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C G 5 O6 ? ? ? 1_555 D C 3 N4 ? ? C G 5 D C 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C A 6 N1 ? ? ? 1_555 D U 2 N3 ? ? C A 6 D U 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C A 6 N6 ? ? ? 1_555 D U 2 O4 ? ? C A 6 D U 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C G 7 N1 ? ? ? 1_555 D C 1 N3 ? ? C G 7 D C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C G 7 N2 ? ? ? 1_555 D C 1 O2 ? ? C G 7 D C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C G 7 O6 ? ? ? 1_555 D C 1 N4 ? ? C G 7 D C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 N3 A G 3 ? ? C4 A G 3 ? ? 1.418 1.350 0.068 0.007 N 2 1 "O5'" A G 4 ? ? "C5'" A G 4 ? ? 1.364 1.420 -0.056 0.009 N 3 1 N3 A G 4 ? ? C4 A G 4 ? ? 1.394 1.350 0.044 0.007 N 4 1 P A G 5 ? ? "O5'" A G 5 ? ? 1.503 1.593 -0.090 0.010 N 5 1 C2 A G 7 ? ? N3 A G 7 ? ? 1.386 1.323 0.063 0.008 N 6 1 P B U 67 ? ? "O5'" B U 67 ? ? 1.513 1.593 -0.080 0.010 N 7 1 N1 B C 69 ? ? C2 B C 69 ? ? 1.464 1.397 0.067 0.010 N 8 1 N3 B C 69 ? ? C4 B C 69 ? ? 1.290 1.335 -0.045 0.007 N 9 1 P B C 70 ? ? "O5'" B C 70 ? ? 1.532 1.593 -0.061 0.010 N 10 1 C2 C G 1 ? ? N3 C G 1 ? ? 1.382 1.323 0.059 0.008 N 11 1 C2 C G 3 ? ? N3 C G 3 ? ? 1.373 1.323 0.050 0.008 N 12 1 C5 C G 4 ? ? C6 C G 4 ? ? 1.355 1.419 -0.064 0.010 N 13 1 C5 C A 6 ? ? N7 C A 6 ? ? 1.345 1.388 -0.043 0.006 N 14 1 N9 C A 6 ? ? C4 C A 6 ? ? 1.413 1.374 0.039 0.006 N 15 1 "O3'" C G 7 ? ? "C3'" C G 7 ? ? 1.512 1.427 0.085 0.012 N 16 1 C2 C G 7 ? ? N3 C G 7 ? ? 1.383 1.323 0.060 0.008 N 17 1 "C1'" D C 68 ? ? N1 D C 68 ? ? 1.585 1.483 0.102 0.015 N 18 1 "O3'" D C 68 ? ? P D C 69 ? ? 1.534 1.607 -0.073 0.012 Y 19 1 "O5'" D C 69 ? ? "C5'" D C 69 ? ? 1.357 1.420 -0.063 0.009 N 20 1 N3 D C 70 ? ? C4 D C 70 ? ? 1.292 1.335 -0.043 0.007 N 21 1 C8 D G 71 ? ? N9 D G 71 ? ? 1.329 1.374 -0.045 0.007 N 22 1 N3 D C 72 ? ? C4 D C 72 ? ? 1.288 1.335 -0.047 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 OP1 A C 2 ? ? P A C 2 ? ? OP2 A C 2 ? ? 107.18 119.60 -12.42 1.50 N 2 1 "O5'" A C 2 ? ? P A C 2 ? ? OP2 A C 2 ? ? 121.42 110.70 10.72 1.20 N 3 1 P A C 2 ? ? "O5'" A C 2 ? ? "C5'" A C 2 ? ? 132.75 120.90 11.85 1.60 N 4 1 "C3'" A C 2 ? ? "C2'" A C 2 ? ? "C1'" A C 2 ? ? 96.94 101.30 -4.36 0.70 N 5 1 C5 A C 2 ? ? C6 A C 2 ? ? N1 A C 2 ? ? 125.02 121.00 4.02 0.50 N 6 1 N3 A C 2 ? ? C4 A C 2 ? ? N4 A C 2 ? ? 122.61 118.00 4.61 0.70 N 7 1 OP1 A G 4 ? ? P A G 4 ? ? OP2 A G 4 ? ? 129.18 119.60 9.58 1.50 N 8 1 "O5'" A G 4 ? ? P A G 4 ? ? OP2 A G 4 ? ? 91.14 105.70 -14.56 0.90 N 9 1 C5 A G 4 ? ? C6 A G 4 ? ? O6 A G 4 ? ? 123.62 128.60 -4.98 0.60 N 10 1 C6 A G 5 ? ? C5 A G 5 ? ? N7 A G 5 ? ? 134.63 130.40 4.23 0.60 N 11 1 N3 A G 7 ? ? C2 A G 7 ? ? N2 A G 7 ? ? 124.56 119.90 4.66 0.70 N 12 1 C4 B C 66 ? ? C5 B C 66 ? ? C6 B C 66 ? ? 114.31 117.40 -3.09 0.50 N 13 1 C5 B C 66 ? ? C6 B C 66 ? ? N1 B C 66 ? ? 124.15 121.00 3.15 0.50 N 14 1 "O5'" B U 67 ? ? P B U 67 ? ? OP1 B U 67 ? ? 100.29 105.70 -5.41 0.90 N 15 1 "O4'" B U 67 ? ? "C1'" B U 67 ? ? N1 B U 67 ? ? 100.93 108.20 -7.27 0.80 N 16 1 C2 B U 67 ? ? N3 B U 67 ? ? C4 B U 67 ? ? 131.57 127.00 4.57 0.60 N 17 1 C4 B U 67 ? ? C5 B U 67 ? ? C6 B U 67 ? ? 113.35 119.70 -6.35 0.60 N 18 1 C5 B U 67 ? ? C6 B U 67 ? ? N1 B U 67 ? ? 127.50 122.70 4.80 0.50 N 19 1 C6 B C 68 ? ? N1 B C 68 ? ? C2 B C 68 ? ? 116.88 120.30 -3.42 0.40 N 20 1 N1 B C 68 ? ? C2 B C 68 ? ? N3 B C 68 ? ? 124.01 119.20 4.81 0.70 N 21 1 N1 B C 68 ? ? C2 B C 68 ? ? O2 B C 68 ? ? 114.56 118.90 -4.34 0.60 N 22 1 "O5'" B C 69 ? ? P B C 69 ? ? OP1 B C 69 ? ? 98.49 105.70 -7.21 0.90 N 23 1 "O4'" B C 69 ? ? "C1'" B C 69 ? ? N1 B C 69 ? ? 115.07 108.50 6.57 0.70 N 24 1 N1 B C 69 ? ? C2 B C 69 ? ? N3 B C 69 ? ? 124.34 119.20 5.14 0.70 N 25 1 C2 B C 69 ? ? N3 B C 69 ? ? C4 B C 69 ? ? 114.57 119.90 -5.33 0.50 N 26 1 C4 B C 69 ? ? C5 B C 69 ? ? C6 B C 69 ? ? 125.43 117.40 8.03 0.50 N 27 1 C5 B C 69 ? ? C6 B C 69 ? ? N1 B C 69 ? ? 114.67 121.00 -6.33 0.50 N 28 1 N3 B C 69 ? ? C2 B C 69 ? ? O2 B C 69 ? ? 114.63 121.90 -7.27 0.70 N 29 1 N3 B C 69 ? ? C4 B C 69 ? ? N4 B C 69 ? ? 113.20 118.00 -4.80 0.70 N 30 1 C5 B C 69 ? ? C4 B C 69 ? ? N4 B C 69 ? ? 124.55 120.20 4.35 0.70 N 31 1 "O4'" B C 70 ? ? "C1'" B C 70 ? ? N1 B C 70 ? ? 102.98 108.20 -5.22 0.80 N 32 1 N3 B C 70 ? ? C4 B C 70 ? ? C5 B C 70 ? ? 124.86 121.90 2.96 0.40 N 33 1 C4 B C 70 ? ? C5 B C 70 ? ? C6 B C 70 ? ? 112.55 117.40 -4.85 0.50 N 34 1 N9 B G 71 ? ? C4 B G 71 ? ? C5 B G 71 ? ? 108.13 105.40 2.73 0.40 N 35 1 N3 B G 71 ? ? C2 B G 71 ? ? N2 B G 71 ? ? 114.81 119.90 -5.09 0.70 N 36 1 C2 B C 72 ? ? N3 B C 72 ? ? C4 B C 72 ? ? 123.78 119.90 3.88 0.50 N 37 1 C4 B C 72 ? ? C5 B C 72 ? ? C6 B C 72 ? ? 112.85 117.40 -4.55 0.50 N 38 1 C5 B C 72 ? ? C6 B C 72 ? ? N1 B C 72 ? ? 124.55 121.00 3.55 0.50 N 39 1 N1 B C 72 ? ? C2 B C 72 ? ? O2 B C 72 ? ? 124.40 118.90 5.50 0.60 N 40 1 C5 C G 1 ? ? C6 C G 1 ? ? N1 C G 1 ? ? 115.50 111.50 4.00 0.50 N 41 1 N7 C G 1 ? ? C8 C G 1 ? ? N9 C G 1 ? ? 116.15 113.10 3.05 0.50 N 42 1 C8 C G 1 ? ? N9 C G 1 ? ? C4 C G 1 ? ? 103.72 106.40 -2.68 0.40 N 43 1 N3 C G 1 ? ? C2 C G 1 ? ? N2 C G 1 ? ? 124.85 119.90 4.95 0.70 N 44 1 OP1 C C 2 ? ? P C C 2 ? ? OP2 C C 2 ? ? 108.44 119.60 -11.16 1.50 N 45 1 "O3'" C C 2 ? ? P C G 3 ? ? OP2 C G 3 ? ? 118.46 110.50 7.96 1.10 Y 46 1 C2 C G 3 ? ? N3 C G 3 ? ? C4 C G 3 ? ? 107.78 111.90 -4.12 0.50 N 47 1 N3 C G 3 ? ? C4 C G 3 ? ? C5 C G 3 ? ? 131.73 128.60 3.13 0.50 N 48 1 C4 C G 3 ? ? C5 C G 3 ? ? N7 C G 3 ? ? 113.51 110.80 2.71 0.40 N 49 1 N9 C G 3 ? ? C4 C G 3 ? ? C5 C G 3 ? ? 102.47 105.40 -2.93 0.40 N 50 1 N1 C G 3 ? ? C2 C G 3 ? ? N2 C G 3 ? ? 109.31 116.20 -6.89 0.90 N 51 1 N3 C G 3 ? ? C2 C G 3 ? ? N2 C G 3 ? ? 126.49 119.90 6.59 0.70 N 52 1 C5 C G 3 ? ? C6 C G 3 ? ? O6 C G 3 ? ? 123.45 128.60 -5.15 0.60 N 53 1 "O5'" C G 4 ? ? P C G 4 ? ? OP2 C G 4 ? ? 99.25 105.70 -6.45 0.90 N 54 1 C8 C G 4 ? ? N9 C G 4 ? ? C4 C G 4 ? ? 109.15 106.40 2.75 0.40 N 55 1 N3 C G 4 ? ? C2 C G 4 ? ? N2 C G 4 ? ? 124.93 119.90 5.03 0.70 N 56 1 C5 C G 4 ? ? C6 C G 4 ? ? O6 C G 4 ? ? 124.29 128.60 -4.31 0.60 N 57 1 "C4'" C G 5 ? ? "C3'" C G 5 ? ? "C2'" C G 5 ? ? 95.97 102.60 -6.63 1.00 N 58 1 C5 C G 5 ? ? C6 C G 5 ? ? O6 C G 5 ? ? 124.57 128.60 -4.03 0.60 N 59 1 C6 C A 6 ? ? N1 C A 6 ? ? C2 C A 6 ? ? 124.01 118.60 5.41 0.60 N 60 1 C5 C A 6 ? ? C6 C A 6 ? ? N1 C A 6 ? ? 114.00 117.70 -3.70 0.50 N 61 1 C8 C A 6 ? ? N9 C A 6 ? ? C4 C A 6 ? ? 103.00 105.80 -2.80 0.40 N 62 1 C5 C G 7 ? ? C6 C G 7 ? ? N1 C G 7 ? ? 114.71 111.50 3.21 0.50 N 63 1 C4 C G 7 ? ? C5 C G 7 ? ? N7 C G 7 ? ? 113.69 110.80 2.89 0.40 N 64 1 C5 C G 7 ? ? N7 C G 7 ? ? C8 C G 7 ? ? 101.04 104.30 -3.26 0.50 N 65 1 N3 C G 7 ? ? C2 C G 7 ? ? N2 C G 7 ? ? 124.18 119.90 4.28 0.70 N 66 1 C6 D C 66 ? ? N1 D C 66 ? ? C2 D C 66 ? ? 116.81 120.30 -3.49 0.40 N 67 1 C5 D C 66 ? ? C4 D C 66 ? ? N4 D C 66 ? ? 125.02 120.20 4.82 0.70 N 68 1 N1 D U 67 ? ? C2 D U 67 ? ? O2 D U 67 ? ? 118.21 122.80 -4.59 0.70 N 69 1 "C3'" D C 69 ? ? "C2'" D C 69 ? ? "C1'" D C 69 ? ? 96.09 101.30 -5.21 0.70 N 70 1 N3 D C 69 ? ? C4 D C 69 ? ? C5 D C 69 ? ? 118.26 121.90 -3.64 0.40 N 71 1 C4 D C 69 ? ? C5 D C 69 ? ? C6 D C 69 ? ? 121.41 117.40 4.01 0.50 N 72 1 C5 D C 69 ? ? C4 D C 69 ? ? N4 D C 69 ? ? 124.46 120.20 4.26 0.70 N 73 1 C6 D G 71 ? ? N1 D G 71 ? ? C2 D G 71 ? ? 121.24 125.10 -3.86 0.60 N 74 1 C4 D G 71 ? ? C5 D G 71 ? ? N7 D G 71 ? ? 108.17 110.80 -2.63 0.40 N 75 1 N3 D G 71 ? ? C2 D G 71 ? ? N2 D G 71 ? ? 115.52 119.90 -4.38 0.70 N 76 1 C6 D C 72 ? ? N1 D C 72 ? ? C2 D C 72 ? ? 117.17 120.30 -3.13 0.40 N 77 1 C2 D C 72 ? ? N3 D C 72 ? ? C4 D C 72 ? ? 123.07 119.90 3.17 0.50 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 U OP3 O N N 114 U P P N N 115 U OP1 O N N 116 U OP2 O N N 117 U "O5'" O N N 118 U "C5'" C N N 119 U "C4'" C N R 120 U "O4'" O N N 121 U "C3'" C N S 122 U "O3'" O N N 123 U "C2'" C N R 124 U "O2'" O N N 125 U "C1'" C N R 126 U N1 N N N 127 U C2 C N N 128 U O2 O N N 129 U N3 N N N 130 U C4 C N N 131 U O4 O N N 132 U C5 C N N 133 U C6 C N N 134 U HOP3 H N N 135 U HOP2 H N N 136 U "H5'" H N N 137 U "H5''" H N N 138 U "H4'" H N N 139 U "H3'" H N N 140 U "HO3'" H N N 141 U "H2'" H N N 142 U "HO2'" H N N 143 U "H1'" H N N 144 U H3 H N N 145 U H5 H N N 146 U H6 H N N 147 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # _ndb_struct_conf_na.entry_id 2XSL _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 7 1_555 -0.164 -0.202 0.034 -0.652 -3.998 -1.425 1 A_G1:C72_B A 1 ? B 72 ? 19 1 1 A C 2 1_555 B G 6 1_555 0.229 -0.179 0.168 1.346 -9.038 1.375 2 A_C2:G71_B A 2 ? B 71 ? 19 1 1 A G 3 1_555 B C 5 1_555 -0.136 -0.195 -0.181 -2.362 -9.479 -4.238 3 A_G3:C70_B A 3 ? B 70 ? 19 1 1 A G 4 1_555 B C 4 1_555 -0.176 -0.106 0.018 -4.545 -10.473 2.429 4 A_G4:C69_B A 4 ? B 69 ? 19 1 1 A G 5 1_555 B C 3 1_555 -0.195 -0.117 -0.007 -5.332 -14.796 3.178 5 A_G5:C68_B A 5 ? B 68 ? 19 1 1 A A 6 1_555 B U 2 1_555 -0.172 0.018 -0.191 -6.739 -11.908 -0.656 6 A_A6:U67_B A 6 ? B 67 ? 20 1 1 A G 7 1_555 B C 1 1_555 -0.357 -0.140 0.062 -5.983 -12.176 -2.394 7 A_G7:C66_B A 7 ? B 66 ? 19 1 1 C G 1 1_555 D C 7 1_555 -0.279 -0.246 0.093 -1.558 -5.877 -0.617 8 C_G1:C72_D C 1 ? D 72 ? 19 1 1 C C 2 1_555 D G 6 1_555 0.269 -0.160 0.023 5.588 -11.659 0.996 9 C_C2:G71_D C 2 ? D 71 ? 19 1 1 C G 3 1_555 D C 5 1_555 -0.230 -0.090 -0.342 -7.397 -10.292 3.750 10 C_G3:C70_D C 3 ? D 70 ? 19 1 1 C G 4 1_555 D C 4 1_555 -0.051 -0.099 -0.276 -5.007 -4.239 -1.815 11 C_G4:C69_D C 4 ? D 69 ? 19 1 1 C G 5 1_555 D C 3 1_555 -0.124 -0.121 -0.104 -5.884 -13.247 3.897 12 C_G5:C68_D C 5 ? D 68 ? 19 1 1 C A 6 1_555 D U 2 1_555 0.035 -0.138 -0.254 -10.917 -8.538 -0.917 13 C_A6:U67_D C 6 ? D 67 ? 20 1 1 C G 7 1_555 D C 1 1_555 -0.252 -0.328 0.111 -5.376 -11.124 -3.064 14 C_G7:C66_D C 7 ? D 66 ? 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 7 1_555 A C 2 1_555 B G 6 1_555 -0.181 -1.892 3.278 -1.677 1.750 33.565 -3.550 0.043 3.183 3.026 2.899 33.650 1 AA_G1C2:G71C72_BB A 1 ? B 72 ? A 2 ? B 71 ? 1 A C 2 1_555 B G 6 1_555 A G 3 1_555 B C 5 1_555 -0.684 -1.746 3.290 0.748 8.695 29.451 -4.888 1.429 2.660 16.648 -1.433 30.690 2 AA_C2G3:C70G71_BB A 2 ? B 71 ? A 3 ? B 70 ? 1 A G 3 1_555 B C 5 1_555 A G 4 1_555 B C 4 1_555 0.580 -1.599 3.350 -1.974 5.999 30.630 -4.074 -1.440 2.949 11.207 3.687 31.259 3 AA_G3G4:C69C70_BB A 3 ? B 70 ? A 4 ? B 69 ? 1 A G 4 1_555 B C 4 1_555 A G 5 1_555 B C 3 1_555 0.749 -1.715 3.248 3.619 7.866 30.654 -4.482 -0.743 2.801 14.519 -6.680 31.825 4 AA_G4G5:C68C69_BB A 4 ? B 69 ? A 5 ? B 68 ? 1 A G 5 1_555 B C 3 1_555 A A 6 1_555 B U 2 1_555 -0.807 -1.203 3.334 1.395 5.059 33.165 -2.903 1.624 3.086 8.794 -2.426 33.567 5 AA_G5A6:U67C68_BB A 5 ? B 68 ? A 6 ? B 67 ? 1 A A 6 1_555 B U 2 1_555 A G 7 1_555 B C 1 1_555 0.520 -1.629 3.266 0.194 7.122 30.226 -4.336 -0.936 2.821 13.425 -0.367 31.035 6 AA_A6G7:C66U67_BB A 6 ? B 67 ? A 7 ? B 66 ? 1 C G 1 1_555 D C 7 1_555 C C 2 1_555 D G 6 1_555 -0.111 -1.643 3.111 -1.614 1.595 34.674 -2.980 -0.046 3.036 2.672 2.704 34.746 7 CC_G1C2:G71C72_DD C 1 ? D 72 ? C 2 ? D 71 ? 1 C C 2 1_555 D G 6 1_555 C G 3 1_555 D C 5 1_555 0.392 -1.759 3.540 2.352 9.714 29.257 -5.197 -0.277 2.846 18.561 -4.495 30.882 8 CC_C2G3:C70G71_DD C 2 ? D 71 ? C 3 ? D 70 ? 1 C G 3 1_555 D C 5 1_555 C G 4 1_555 D C 4 1_555 -0.445 -1.754 3.253 -0.567 5.000 31.407 -4.075 0.713 2.953 9.163 1.039 31.798 9 CC_G3G4:C69C70_DD C 3 ? D 70 ? C 4 ? D 69 ? 1 C G 4 1_555 D C 4 1_555 C G 5 1_555 D C 3 1_555 0.955 -1.807 3.304 0.471 6.968 28.978 -4.896 -1.765 2.817 13.675 -0.924 29.790 10 CC_G4G5:C68C69_DD C 4 ? D 69 ? C 5 ? D 68 ? 1 C G 5 1_555 D C 3 1_555 C A 6 1_555 D U 2 1_555 -0.792 -1.562 3.314 0.989 8.549 35.386 -3.639 1.400 2.850 13.813 -1.598 36.385 11 CC_G5A6:U67C68_DD C 5 ? D 68 ? C 6 ? D 67 ? 1 C A 6 1_555 D U 2 1_555 C G 7 1_555 D C 1 1_555 0.330 -1.727 3.141 0.605 4.694 28.431 -4.434 -0.539 2.832 9.474 -1.221 28.814 12 CC_A6G7:C66U67_DD C 6 ? D 67 ? C 7 ? D 66 ? # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type other _pdbx_initial_refinement_model.source_name ? _pdbx_initial_refinement_model.details 'ARTIFICIAL RNA' # _atom_sites.entry_id 2XSL _atom_sites.fract_transf_matrix[1][1] 0.038187 _atom_sites.fract_transf_matrix[1][2] 0.004385 _atom_sites.fract_transf_matrix[1][3] 0.006656 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.034691 _atom_sites.fract_transf_matrix[2][3] 0.011493 _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] 0.035966 _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 # loop_