data_2F87 # _entry.id 2F87 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2F87 pdb_00002f87 10.2210/pdb2f87/pdb RCSB RCSB035572 ? ? WWPDB D_1000035572 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2F87 _pdbx_database_status.recvd_initial_deposition_date 2005-12-02 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Okada, K.' 1 'Takahashi, M.' 2 'Sakamoto, T.' 3 'Nakamura, K.' 4 'Kanai, A.' 5 'Kawai, G' 6 # _citation.id primary _citation.title 'Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus' _citation.journal_abbrev 'Nucleosides Nucleotides Nucleic Acids' _citation.journal_volume 25 _citation.page_first 383 _citation.page_last 395 _citation.year 2006 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1525-7770 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16838833 _citation.pdbx_database_id_DOI 10.1080/15257770600683979 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Okada, K.' 1 ? primary 'Takahashi, M.' 2 ? primary 'Sakamoto, T.' 3 ? primary 'Kawai, G.' 4 ? primary 'Nakamura, K.' 5 ? primary 'Kanai, A.' 6 ? # _cell.entry_id 2F87 _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2F87 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'SRP RNA' _entity.formula_weight 3906.400 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment pfHE6-12 _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GGCUGAAGGGCC _entity_poly.pdbx_seq_one_letter_code_can GGCUGAAGGGCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 U n 1 5 G n 1 6 A n 1 7 A n 1 8 G n 1 9 G n 1 10 G n 1 11 C n 1 12 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details ;The RNA fragment, pfHE6-12 was chemically synthesized by a phosphoramidite method, using an automatic DNA/RNA synthesizer, Expedite model 8909 (PerSeptive Biosystems). ; # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2F87 _struct_ref.pdbx_db_accession 2F87 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2F87 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2F87 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 12 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 1 '2D TOCSY' 1 3 1 DQF-COSY 1 4 1 ? 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 283 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 6.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength '50mM NaCl' _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '2.0mM RNA Buffer Na; 95% H2O, 5% D2O; 2.0mM RNA; 20mM Phosphate Buffer Na; 100% D2O' _pdbx_nmr_sample_details.solvent_system '95% H2O/5% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 DRX Bruker 500 ? 2 DRX Bruker 600 ? # _pdbx_nmr_refine.entry_id 2F87 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ;The structure is based on a total of 179 restraints, 127 are NOE-derived distance constraints, 34 dihedral angle restraints, 18 distance restraints from hydrogen bonds. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 2F87 _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques.' # _pdbx_nmr_ensemble.entry_id 2F87 _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 13 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 2F87 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'structure solution' Discover 97.0 ? 1 collection XwinNMR 2.6 ? 2 'data analysis' Felix 97.0 ? 3 refinement Discover 97.0 ? 4 # _exptl.entry_id 2F87 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2F87 _struct.title 'Solution structure of a GAAG tetraloop in SRP RNA from Pyrococcus furiosus' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 2F87 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'SRP, GNRR, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _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 A C 12 N3 ? ? A G 1 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 12 O2 ? ? A G 1 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 12 N4 ? ? A G 1 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 11 N3 ? ? A G 2 A C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 11 O2 ? ? A G 2 A C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 11 N4 ? ? A G 2 A C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 10 N1 ? ? A C 3 A G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 10 O6 ? ? A C 3 A G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 10 N2 ? ? A C 3 A G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 N3 ? ? ? 1_555 A G 9 O6 ? ? A U 4 A G 9 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog11 hydrog ? ? A U 4 O2 ? ? ? 1_555 A G 9 N1 ? ? A U 4 A G 9 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog12 hydrog ? ? A U 4 O2 ? ? ? 1_555 A G 10 N2 ? ? A U 4 A G 10 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A G 8 N7 ? ? A G 5 A G 8 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 2F87 _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 # _atom_sites.entry_id 2F87 _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 1.000000 _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] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 U 4 4 4 U U 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 A 7 7 7 A A A . n A 1 8 G 8 8 8 G G A . n A 1 9 G 9 9 9 G G A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 2006-08-08 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' # 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 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 116.83 108.50 8.33 0.70 N 2 1 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 116.40 108.50 7.90 0.70 N 3 1 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 112.79 108.50 4.29 0.70 N 4 1 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 113.06 108.50 4.56 0.70 N 5 1 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.86 108.50 6.36 0.70 N 6 2 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 116.69 108.50 8.19 0.70 N 7 2 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 116.35 108.50 7.85 0.70 N 8 2 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 112.71 108.50 4.21 0.70 N 9 2 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 113.02 108.50 4.52 0.70 N 10 2 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.91 108.50 6.41 0.70 N 11 3 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 115.92 108.50 7.42 0.70 N 12 3 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 114.47 108.50 5.97 0.70 N 13 3 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 114.97 108.50 6.47 0.70 N 14 3 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 112.87 108.50 4.37 0.70 N 15 3 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 112.92 108.50 4.42 0.70 N 16 3 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.34 108.50 5.84 0.70 N 17 4 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 116.55 108.50 8.05 0.70 N 18 4 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 116.36 108.50 7.86 0.70 N 19 4 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 112.71 108.50 4.21 0.70 N 20 4 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 112.84 108.50 4.34 0.70 N 21 4 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 113.25 108.50 4.75 0.70 N 22 4 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.75 108.50 6.25 0.70 N 23 5 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 115.85 108.50 7.35 0.70 N 24 5 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 115.28 108.50 6.78 0.70 N 25 5 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 114.59 108.50 6.09 0.70 N 26 5 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 113.00 108.50 4.50 0.70 N 27 5 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.65 108.50 6.15 0.70 N 28 6 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 116.63 108.50 8.13 0.70 N 29 6 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 116.64 108.50 8.14 0.70 N 30 6 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.27 108.50 5.77 0.70 N 31 7 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 116.33 108.50 7.83 0.70 N 32 7 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 115.24 108.50 6.74 0.70 N 33 7 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 113.03 108.50 4.53 0.70 N 34 7 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.73 108.50 6.23 0.70 N 35 8 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 116.66 108.50 8.16 0.70 N 36 8 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 114.53 108.50 6.03 0.70 N 37 8 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 114.94 108.50 6.44 0.70 N 38 8 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 113.84 108.50 5.34 0.70 N 39 8 "O4'" A A 7 ? ? "C1'" A A 7 ? ? N9 A A 7 ? ? 112.77 108.50 4.27 0.70 N 40 8 "C5'" A C 11 ? ? "C4'" A C 11 ? ? "O4'" A C 11 ? ? 115.42 109.80 5.62 0.90 N 41 8 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 115.36 108.50 6.86 0.70 N 42 9 "O4'" A G 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 116.74 108.50 8.24 0.70 N 43 9 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 113.84 108.50 5.34 0.70 N 44 9 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 116.20 113.10 3.10 0.50 N 45 9 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 114.87 108.50 6.37 0.70 N 46 9 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 113.66 108.50 5.16 0.70 N 47 10 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 116.92 108.50 8.42 0.70 N 48 10 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 114.81 108.50 6.31 0.70 N 49 10 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 112.75 108.50 4.25 0.70 N 50 10 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.32 108.50 5.82 0.70 N 51 11 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 116.64 108.50 8.14 0.70 N 52 11 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 116.46 108.50 7.96 0.70 N 53 11 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 112.97 108.50 4.47 0.70 N 54 11 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 113.34 108.50 4.84 0.70 N 55 11 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.76 108.50 6.26 0.70 N 56 12 "C3'" A G 2 ? ? "C2'" A G 2 ? ? "C1'" A G 2 ? ? 106.35 101.50 4.85 0.80 N 57 12 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 116.65 108.50 8.15 0.70 N 58 12 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 116.50 108.50 8.00 0.70 N 59 12 "O4'" A U 4 ? ? "C1'" A U 4 ? ? N1 A U 4 ? ? 112.78 108.50 4.28 0.70 N 60 12 "O4'" A A 7 ? ? "C1'" A A 7 ? ? N9 A A 7 ? ? 113.51 108.50 5.01 0.70 N 61 12 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 112.81 108.50 4.31 0.70 N 62 12 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.53 108.50 6.03 0.70 N 63 13 "C3'" A G 2 ? ? "C2'" A G 2 ? ? "C1'" A G 2 ? ? 106.34 101.50 4.84 0.80 N 64 13 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 117.48 108.50 8.98 0.70 N 65 13 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 116.53 108.50 8.03 0.70 N 66 13 "O4'" A A 7 ? ? "C1'" A A 7 ? ? N9 A A 7 ? ? 113.15 108.50 4.65 0.70 N 67 13 "O4'" A G 10 ? ? "C1'" A G 10 ? ? N9 A G 10 ? ? 113.59 108.50 5.09 0.70 N 68 13 "O4'" A C 12 ? ? "C1'" A C 12 ? ? N1 A C 12 ? ? 114.86 108.50 6.36 0.70 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G A 1 ? ? 0.050 'SIDE CHAIN' 2 1 G A 2 ? ? 0.068 'SIDE CHAIN' 3 1 G A 5 ? ? 0.059 'SIDE CHAIN' 4 1 C A 12 ? ? 0.075 'SIDE CHAIN' 5 2 G A 1 ? ? 0.051 'SIDE CHAIN' 6 2 G A 2 ? ? 0.067 'SIDE CHAIN' 7 2 G A 5 ? ? 0.071 'SIDE CHAIN' 8 2 C A 12 ? ? 0.076 'SIDE CHAIN' 9 3 G A 2 ? ? 0.062 'SIDE CHAIN' 10 3 C A 3 ? ? 0.083 'SIDE CHAIN' 11 3 U A 4 ? ? 0.090 'SIDE CHAIN' 12 3 G A 5 ? ? 0.070 'SIDE CHAIN' 13 3 G A 10 ? ? 0.071 'SIDE CHAIN' 14 3 C A 12 ? ? 0.072 'SIDE CHAIN' 15 4 G A 1 ? ? 0.050 'SIDE CHAIN' 16 4 G A 2 ? ? 0.068 'SIDE CHAIN' 17 4 A A 6 ? ? 0.063 'SIDE CHAIN' 18 4 G A 8 ? ? 0.061 'SIDE CHAIN' 19 4 G A 9 ? ? 0.075 'SIDE CHAIN' 20 4 C A 12 ? ? 0.083 'SIDE CHAIN' 21 5 G A 2 ? ? 0.069 'SIDE CHAIN' 22 5 C A 3 ? ? 0.070 'SIDE CHAIN' 23 5 G A 9 ? ? 0.068 'SIDE CHAIN' 24 5 C A 12 ? ? 0.077 'SIDE CHAIN' 25 6 G A 1 ? ? 0.051 'SIDE CHAIN' 26 6 G A 2 ? ? 0.068 'SIDE CHAIN' 27 6 G A 5 ? ? 0.059 'SIDE CHAIN' 28 6 C A 12 ? ? 0.081 'SIDE CHAIN' 29 7 G A 2 ? ? 0.066 'SIDE CHAIN' 30 7 C A 3 ? ? 0.094 'SIDE CHAIN' 31 7 G A 9 ? ? 0.052 'SIDE CHAIN' 32 7 C A 12 ? ? 0.073 'SIDE CHAIN' 33 8 C A 3 ? ? 0.084 'SIDE CHAIN' 34 8 U A 4 ? ? 0.063 'SIDE CHAIN' 35 8 G A 5 ? ? 0.072 'SIDE CHAIN' 36 8 C A 11 ? ? 0.058 'SIDE CHAIN' 37 9 C A 3 ? ? 0.075 'SIDE CHAIN' 38 9 G A 5 ? ? 0.067 'SIDE CHAIN' 39 9 C A 12 ? ? 0.143 'SIDE CHAIN' 40 10 G A 2 ? ? 0.072 'SIDE CHAIN' 41 10 C A 3 ? ? 0.100 'SIDE CHAIN' 42 10 G A 5 ? ? 0.053 'SIDE CHAIN' 43 10 A A 6 ? ? 0.062 'SIDE CHAIN' 44 10 G A 8 ? ? 0.050 'SIDE CHAIN' 45 11 G A 1 ? ? 0.051 'SIDE CHAIN' 46 11 G A 2 ? ? 0.065 'SIDE CHAIN' 47 11 C A 3 ? ? 0.058 'SIDE CHAIN' 48 11 G A 5 ? ? 0.055 'SIDE CHAIN' 49 11 A A 6 ? ? 0.054 'SIDE CHAIN' 50 11 C A 12 ? ? 0.080 'SIDE CHAIN' 51 12 G A 2 ? ? 0.064 'SIDE CHAIN' 52 12 G A 9 ? ? 0.064 'SIDE CHAIN' 53 12 C A 12 ? ? 0.074 'SIDE CHAIN' 54 13 G A 2 ? ? 0.079 'SIDE CHAIN' 55 13 C A 3 ? ? 0.061 'SIDE CHAIN' 56 13 U A 4 ? ? 0.076 'SIDE CHAIN' 57 13 G A 9 ? ? 0.065 'SIDE CHAIN' 58 13 G A 10 ? ? 0.066 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2F87 'double helix' 2F87 'a-form double helix' 2F87 'hairpin loop' 2F87 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 12 1_555 -0.886 -0.246 -0.100 13.275 11.933 -1.762 1 A_G1:C12_A A 1 ? A 12 ? 19 1 1 A G 2 1_555 A C 11 1_555 0.401 0.062 -0.120 19.353 5.512 -1.699 2 A_G2:C11_A A 2 ? A 11 ? 19 1 1 A C 3 1_555 A G 10 1_555 0.823 -0.506 -1.039 -6.442 -6.020 3.448 3 A_C3:G10_A A 3 ? A 10 ? 19 1 1 A U 4 1_555 A G 9 1_555 1.588 -0.426 -0.615 6.775 15.614 -11.150 4 A_U4:G9_A A 4 ? A 9 ? 28 ? 1 A G 5 1_555 A G 8 1_555 7.520 -5.671 1.673 32.212 -0.608 -35.639 5 A_G5:G8_A A 5 ? A 8 ? ? ? # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 12 1_555 A G 2 1_555 A C 11 1_555 0.353 -1.878 3.063 -5.438 3.055 31.707 -3.864 -1.503 2.778 5.525 9.835 32.300 1 AA_G1G2:C11C12_AA A 1 ? A 12 ? A 2 ? A 11 ? 1 A G 2 1_555 A C 11 1_555 A C 3 1_555 A G 10 1_555 -0.486 -2.463 3.773 4.886 6.560 35.720 -4.893 1.497 3.195 10.525 -7.839 36.615 2 AA_G2C3:G10C11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A C 3 1_555 A G 10 1_555 A U 4 1_555 A G 9 1_555 -0.971 -0.717 3.100 -0.916 12.330 29.259 -3.381 1.624 2.621 23.149 1.720 31.711 3 AA_C3U4:G9G10_AA A 3 ? A 10 ? A 4 ? A 9 ? 1 A U 4 1_555 A G 9 1_555 A G 5 1_555 A G 8 1_555 -2.234 -1.676 2.605 -6.558 17.117 54.648 -2.458 2.052 2.264 18.084 6.928 57.415 4 AA_U4G5:G8G9_AA A 4 ? A 9 ? A 5 ? A 8 ? #