data_1ME1 # _entry.id 1ME1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1ME1 RCSB RCSB016843 WWPDB D_1000016843 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1ME0 _pdbx_database_related.details ;CHIMERIC HAIRPIN WITH 2',5'-LINKED RNA LOOP AND DNA STEM ; _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1ME1 _pdbx_database_status.recvd_initial_deposition_date 2002-08-07 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Denisov, A.Y.' 1 'Hannoush, R.N.' 2 'Gehring, K.' 3 'Damha, M.J.' 4 # _citation.id primary _citation.title ;A Novel RNA Motif Based on the Structure of Unusually Stable 2',5'-Linked r(UUCG) Loops ; _citation.journal_abbrev J.AM.CHEM.SOC. _citation.journal_volume 125 _citation.page_first 11525 _citation.page_last 11531 _citation.year 2003 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 13129354 _citation.pdbx_database_id_DOI 10.1021/ja036207k # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Denisov, A.Y.' 1 primary 'Hannoush, R.N.' 2 primary 'Gehring, K.' 3 primary 'Damha, M.J.' 4 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-R(*GP*GP*AP*CP*(U25)P*(U25)P*(C25)P*(5GP)P*GP*UP*CP*C)-3'" _entity.formula_weight 3804.296 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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 'GGAC(U5P)(U5P)(C5P)(5GP)GUCC' _entity_poly.pdbx_seq_one_letter_code_can GGACXXXXGUCC _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 A n 1 4 C n 1 5 U5P n 1 6 U5P n 1 7 C5P n 1 8 5GP n 1 9 G n 1 10 U 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 'Solid phase synthesis, phosphoramidite chemistry' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1ME1 _struct_ref.pdbx_db_accession 1ME1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1ME1 _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 1ME1 _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 5GP non-polymer . "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 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 C5P non-polymer . "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 U5P non-polymer . "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 DQF-COSY # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 288 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '1.5 mM hairpin' _pdbx_nmr_sample_details.solvent_system 'D2O, H2O/D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model DRX _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1ME1 _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details 'Structures were refined by NMR-restrained molecular dynamics (12 ps, 300-1000 K) with final energy minimization' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1ME1 _pdbx_nmr_details.text 'Structure was determined using standard 2D homo- and heteronuclear techniques: 2D-NOESY, DQF-COSY, TOCSY, H,C-HMQC, H,P-HetCOSY' # _pdbx_nmr_ensemble.entry_id 1ME1 _pdbx_nmr_ensemble.conformers_calculated_total_number 20 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, 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 1ME1 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average, lowest energy' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal X-PLOR 3.851 refinement Brunger 1 X-PLOR ? 'data analysis' Brunger 2 # _exptl.entry_id 1ME1 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_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 . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1ME1 _struct.title ;Chimeric hairpin with 2',5'-linked RNA loop and RNA stem ; _struct.pdbx_descriptor "5'-R(*GP*GP*AP*CP*(U25)P*(U25)P*(C25)P*(5GP)P*GP*UP*CP*C)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1ME1 _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;Hairpin, (2', 5')-RNA, 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 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A C 4 "O3'" ? ? ? 1_555 A U5P 5 P ? ? A C 4 A U5P 5 1_555 ? ? ? ? ? ? ? 1.615 ? covale2 covale ? ? A U5P 5 "O2'" ? ? ? 1_555 A U5P 6 P ? ? A U5P 5 A U5P 6 1_555 ? ? ? ? ? ? ? 1.610 ? covale3 covale ? ? A U5P 6 "O2'" ? ? ? 1_555 A C5P 7 P ? ? A U5P 6 A C5P 7 1_555 ? ? ? ? ? ? ? 1.614 ? covale4 covale ? ? A C5P 7 "O2'" ? ? ? 1_555 A 5GP 8 P ? ? A C5P 7 A 5GP 8 1_555 ? ? ? ? ? ? ? 1.619 ? covale5 covale ? ? A 5GP 8 "O2'" ? ? ? 1_555 A G 9 P ? ? A 5GP 8 A G 9 1_555 ? ? ? ? ? ? ? 1.615 ? 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 A 3 N1 ? ? ? 1_555 A U 10 N3 ? ? A A 3 A U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 10 O4 ? ? A A 3 A U 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 9 N1 ? ? A C 4 A G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 9 O6 ? ? A C 4 A G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 9 N2 ? ? A C 4 A G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1ME1 _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 1ME1 _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 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 U5P 5 5 5 U5P U5P A . n A 1 6 U5P 6 6 6 U5P U5P A . n A 1 7 C5P 7 7 7 C5P C5P A . n A 1 8 5GP 8 8 8 5GP 5GP A . n A 1 9 G 9 9 9 G G A . n A 1 10 U 10 10 10 U U 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 2003-08-19 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-08-24 # _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 ? # 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' 'Non-polymer description' # _pdbx_database_remark.id 400 _pdbx_database_remark.text ;COMPOUND NUCLOTIDES 5(U25), 6(U25), 7(C25), 8(5GP) HAS A NON-STANDARD 2'-5' LINKAGE. ; # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 H21 A G 1 ? ? O2 A C 12 ? ? 1.56 2 2 H21 A G 1 ? ? O2 A C 12 ? ? 1.57 3 2 O2 A C 4 ? ? H21 A G 9 ? ? 1.60 4 3 H21 A G 2 ? ? O2 A C 11 ? ? 1.59 5 3 O2 A C 4 ? ? H21 A G 9 ? ? 1.60 6 4 O2 A C 4 ? ? H21 A G 9 ? ? 1.57 7 4 O2 A U5P 5 ? ? HN1 A 5GP 8 ? ? 1.60 8 5 H21 A G 1 ? ? O2 A C 12 ? ? 1.58 9 5 "HO2'" A C 11 ? ? "O4'" A C 12 ? ? 1.59 10 5 O2 A C 4 ? ? H21 A G 9 ? ? 1.59 11 5 O2 A U5P 5 ? ? HN1 A 5GP 8 ? ? 1.60 12 6 H21 A G 2 ? ? O2 A C 11 ? ? 1.56 13 6 HN3 A U5P 5 ? ? O6 A 5GP 8 ? ? 1.57 14 6 "HO3'" A C5P 7 ? ? O2P A 5GP 8 ? ? 1.59 15 6 H61 A A 3 ? ? O4 A U 10 ? ? 1.59 16 7 O2 A C 4 ? ? H21 A G 9 ? ? 1.56 17 7 H21 A G 2 ? ? O2 A C 11 ? ? 1.57 18 7 H21 A G 1 ? ? O2 A C 12 ? ? 1.58 19 8 "HO2'" A G 2 ? ? "O5'" A A 3 ? ? 1.54 20 8 O2 A C 4 ? ? H21 A G 9 ? ? 1.56 21 8 "HO2'" A G 1 ? ? "O4'" A G 2 ? ? 1.57 22 8 O2 A U5P 5 ? ? HN1 A 5GP 8 ? ? 1.59 23 8 H21 A G 1 ? ? O2 A C 12 ? ? 1.60 24 9 O2 A C 4 ? ? H21 A G 9 ? ? 1.58 25 9 O2 A U5P 5 ? ? HN1 A 5GP 8 ? ? 1.60 26 10 "HO3'" A C5P 7 ? ? O2P A 5GP 8 ? ? 1.54 27 10 "HO2'" A U 10 ? ? "O4'" A C 11 ? ? 1.57 28 10 "HO2'" A C 11 ? ? "O4'" A C 12 ? ? 1.57 29 10 HN3 A U5P 5 ? ? O6 A 5GP 8 ? ? 1.60 # 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 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.54 113.10 4.44 0.50 N 2 1 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 104.00 106.40 -2.40 0.40 N 3 1 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.94 113.10 4.84 0.50 N 4 1 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.87 106.40 -2.53 0.40 N 5 1 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 118.10 113.80 4.30 0.50 N 6 1 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.50 113.10 4.40 0.50 N 7 1 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.96 106.40 -2.44 0.40 N 8 2 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.46 113.10 4.36 0.50 N 9 2 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 118.00 113.10 4.90 0.50 N 10 2 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.83 106.40 -2.57 0.40 N 11 2 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 118.00 113.80 4.20 0.50 N 12 2 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.53 113.10 4.43 0.50 N 13 2 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.86 106.40 -2.54 0.40 N 14 3 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.87 113.10 4.77 0.50 N 15 3 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.82 106.40 -2.58 0.40 N 16 3 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.64 113.10 4.54 0.50 N 17 3 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.87 106.40 -2.53 0.40 N 18 3 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.80 113.80 4.00 0.50 N 19 3 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.57 113.10 4.47 0.50 N 20 3 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.77 106.40 -2.63 0.40 N 21 4 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.83 113.10 4.73 0.50 N 22 4 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.81 106.40 -2.59 0.40 N 23 4 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.59 113.10 4.49 0.50 N 24 4 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.95 106.40 -2.45 0.40 N 25 4 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.70 113.80 3.90 0.50 N 26 4 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.51 113.10 4.41 0.50 N 27 4 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.95 106.40 -2.45 0.40 N 28 5 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.45 113.10 4.35 0.50 N 29 5 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.97 113.10 4.87 0.50 N 30 5 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.87 106.40 -2.53 0.40 N 31 5 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 118.17 113.80 4.37 0.50 N 32 5 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.56 113.10 4.46 0.50 N 33 5 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.91 106.40 -2.49 0.40 N 34 6 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.91 113.10 4.81 0.50 N 35 6 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.77 106.40 -2.63 0.40 N 36 6 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.64 113.10 4.54 0.50 N 37 6 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.84 106.40 -2.56 0.40 N 38 6 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.73 113.80 3.93 0.50 N 39 6 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.60 113.10 4.50 0.50 N 40 6 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.80 106.40 -2.60 0.40 N 41 7 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.59 113.10 4.49 0.50 N 42 7 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.88 113.10 4.78 0.50 N 43 7 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.97 106.40 -2.43 0.40 N 44 7 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 118.09 113.80 4.29 0.50 N 45 7 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.36 113.10 4.26 0.50 N 46 7 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 104.00 106.40 -2.40 0.40 N 47 8 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.58 113.10 4.48 0.50 N 48 8 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.97 106.40 -2.43 0.40 N 49 8 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.91 113.10 4.81 0.50 N 50 8 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.93 106.40 -2.47 0.40 N 51 8 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.97 113.80 4.17 0.50 N 52 8 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.35 113.10 4.25 0.50 N 53 8 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.89 106.40 -2.51 0.40 N 54 9 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.63 113.10 4.53 0.50 N 55 9 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.86 106.40 -2.54 0.40 N 56 9 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 118.08 113.10 4.98 0.50 N 57 9 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.80 106.40 -2.60 0.40 N 58 9 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 118.03 113.80 4.23 0.50 N 59 9 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.55 113.10 4.45 0.50 N 60 9 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.88 106.40 -2.52 0.40 N 61 10 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.59 113.10 4.49 0.50 N 62 10 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.92 113.10 4.82 0.50 N 63 10 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 118.08 113.80 4.28 0.50 N 64 10 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.37 113.10 4.27 0.50 N 65 10 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.96 106.40 -2.44 0.40 N # loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.08 2 1 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.18 3 1 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 4.15 4 1 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.55 5 2 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.23 6 2 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.20 7 2 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 4.14 8 2 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.52 9 3 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.20 10 3 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.17 11 3 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 4.11 12 3 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.52 13 4 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.04 14 4 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.18 15 4 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 4.15 16 4 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.50 17 5 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.21 18 5 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.20 19 5 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 4.15 20 5 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.52 21 6 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.27 22 6 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.18 23 6 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 3.07 24 6 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.52 25 7 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.06 26 7 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.19 27 7 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 4.15 28 7 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.53 29 8 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.05 30 8 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.18 31 8 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 4.15 32 8 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.48 33 9 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.07 34 9 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.18 35 9 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 4.16 36 9 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.43 37 10 "O3'" A U5P 5 ? ? P A U5P 6 ? ? 3.18 38 10 "O3'" A U5P 6 ? ? P A C5P 7 ? ? 4.19 39 10 "O3'" A C5P 7 ? ? P A 5GP 8 ? ? 3.06 40 10 "O3'" A 5GP 8 ? ? P A G 9 ? ? 3.52 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1ME1 'a-form double helix' 1ME1 'hairpin loop' # 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 -0.379 -0.326 -0.340 -13.203 -3.782 1.107 1 A_G1:C12_A A 1 ? A 12 ? 19 1 1 A G 2 1_555 A C 11 1_555 -1.287 -0.500 -0.196 0.316 -4.781 4.841 2 A_G2:C11_A A 2 ? A 11 ? 19 1 1 A A 3 1_555 A U 10 1_555 -0.162 -0.402 -0.162 9.817 -7.317 -2.526 3 A_A3:U10_A A 3 ? A 10 ? 20 1 1 A C 4 1_555 A G 9 1_555 0.769 -0.191 -0.284 1.433 -3.632 5.464 4 A_C4:G9_A A 4 ? A 9 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 12 1_555 A G 2 1_555 A C 11 1_555 -0.104 -1.276 2.858 -2.735 0.304 31.374 -2.401 -0.253 2.844 0.561 5.045 31.491 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 A 3 1_555 A U 10 1_555 -1.670 0.168 2.744 -4.450 10.813 42.655 -0.660 1.858 2.855 14.540 5.984 44.156 2 AA_G2A3:U10C11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A A 3 1_555 A U 10 1_555 A C 4 1_555 A G 9 1_555 1.545 -1.810 3.111 2.094 14.150 36.134 -4.226 -2.106 2.348 21.792 -3.225 38.774 3 AA_A3C4:G9U10_AA A 3 ? A 10 ? A 4 ? A 9 ? #