data_2LVY # _entry.id 2LVY # _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 2LVY RCSB RCSB102899 BMRB 18593 WWPDB D_1000102899 # _pdbx_database_related.db_id 18593 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LVY _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-07-13 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _audit_author.name 'Baraguey, C.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure. ; _citation.journal_abbrev Org.Biomol.Chem. _citation.journal_volume 11 _citation.page_first 2638 _citation.page_last 2647 _citation.year 2013 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1477-0520 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23455628 _citation.pdbx_database_id_DOI 10.1039/c3ob27005j # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Baraguey, C.' 1 primary 'Lescrinier, E.' 2 primary 'Lavergne, T.' 3 primary 'Debart, F.' 4 primary 'Herdewijn, P.' 5 primary 'Vasseur, J.J.' 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 ;RNA (5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3') ; 2919.889 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*CP*GP*UP*AP*GP*CP*GP*T)-3') ; 2885.794 1 ? ? ? ? # 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 yes 'CGC(UPV)ACGC(DT)' CGCXACGCT A ? 2 polyribonucleotide no no 'GCGUAGCG(DT)' GCGUAGCGT B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 C n 1 4 UPV n 1 5 A n 1 6 C n 1 7 G n 1 8 C n 1 9 DT n 2 1 G n 2 2 C n 2 3 G n 2 4 U n 2 5 A n 2 6 G n 2 7 C n 2 8 G n 2 9 DT n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2LVY 2LVY 1 ? ? ? 2 PDB 2LVY 2LVY 2 ? ? ? # 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 2LVY A 1 ? 9 ? 2LVY 1 ? 9 ? 1 9 2 2 2LVY B 1 ? 9 ? 2LVY 10 ? 18 ? 10 18 # 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 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 UPV 'RNA linking' n ;2'-O-{[(2,2-dimethylpropanoyl)oxy]methyl}uridine 5'-(dihydrogen phosphate) ; ? 'C15 H23 N2 O11 P' 438.324 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D DQF-COSY' 1 2 1 '2D 1H-31P HETCOR' 1 3 1 '2D 1H-1H NOESY' 2 4 2 '2D 1H-1H NOESY' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 0 6.7 ambient ? 293 K 2 0 6.7 ambient ? 283 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '0.9 mM duplex, 100% D2O' 1 '100% D2O' '0.9 mM duplex, 90% H2O/10% D2O' 2 '90% H2O/10% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 500 Bruker Avance 1 'Bruker Avance' 600 Bruker Avance 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2LVY _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LVY _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2LVY _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' X-PLOR_NIH 2.25 1 'Schwieters, Kuszewski, Tjandra and Clore' refinement X-PLOR_NIH 2.25 2 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2LVY _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LVY _struct.title ;Solution Structure of a RNA Duplex Containing a 2'-O-Pivaloyloxymethyl Modification ; _struct.pdbx_descriptor "5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3'" _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LVY _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, modification' # 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 ? # _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 3 "O3'" ? ? ? 1_555 A UPV 4 P ? ? A C 3 A UPV 4 1_555 ? ? ? ? ? ? ? 1.610 ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 1 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 1 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 1 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A C 1 N4 ? ? ? 1_555 B DT 9 O4 ? ? A C 1 B DT 18 1_555 ? ? ? ? ? ? 'C-DT MISPAIR' ? ? hydrog5 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 2 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 2 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 2 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 6 N1 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 6 O6 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 6 N2 ? ? A C 3 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 4 N3 ? ? A A 5 B U 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 4 O4 ? ? A A 5 B U 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 B U 4 N3 ? ? A C 6 B U 13 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 B U 4 O4 ? ? A C 6 B U 13 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 2 O2 ? ? A G 7 B C 11 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? hydrog16 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 8 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B G 1 N1 ? ? A DT 9 B G 10 1_555 ? ? ? ? ? ? 'DT-G MISPAIR' ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2LVY _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 C 1 1 1 C C 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 UPV 4 4 4 UPV UPV A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 G 7 7 7 G G A . n A 1 8 C 8 8 8 C C A . n A 1 9 DT 9 9 9 DT DT A . n B 2 1 G 1 10 10 G G B . n B 2 2 C 2 11 11 C C B . n B 2 3 G 3 12 12 G G B . n B 2 4 U 4 13 13 U U B . n B 2 5 A 5 14 14 A A B . n B 2 6 G 6 15 15 G G B . n B 2 7 C 7 16 16 C C B . n B 2 8 G 8 17 17 G G B . n B 2 9 DT 9 18 18 DT DT B . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id UPV _pdbx_struct_mod_residue.label_seq_id 4 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id UPV _pdbx_struct_mod_residue.auth_seq_id 4 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id U _pdbx_struct_mod_residue.details ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2013-04-10 # _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_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id duplex-1 0.9 ? mM ? 1 duplex-2 0.9 ? mM ? 2 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2LVY _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count 14 _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count 14 _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count 16 _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count 14 _pdbx_nmr_constraints.NA_other-angle_constraints_total_count 14 _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count 32 _pdbx_nmr_constraints.NOE_constraints_total 292 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 145 _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # 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 6 "HO2'" B A 14 ? ? "O4'" B G 15 ? ? 1.53 2 7 "HO2'" A A 5 ? ? "O4'" A C 6 ? ? 1.59 3 9 H21 A G 2 ? ? O2 B C 16 ? ? 1.56 4 12 "HO2'" B A 14 ? ? "O4'" B G 15 ? ? 1.55 5 13 O2 A C 8 ? ? H21 B G 10 ? ? 1.60 6 14 O2 A C 1 ? ? H21 B G 17 ? ? 1.56 7 16 O2 A C 3 ? ? H22 B G 15 ? ? 1.58 8 17 "HO2'" B A 14 ? ? "O4'" B G 15 ? ? 1.55 9 17 "HO2'" A C 3 ? ? "O4'" A UPV 4 ? ? 1.59 10 18 "HO2'" B G 15 ? ? "O4'" B C 16 ? ? 1.59 11 19 "HO2'" B G 15 ? ? "O4'" B C 16 ? ? 1.58 12 20 "HO2'" B U 13 ? ? "O4'" B A 14 ? ? 1.58 13 20 "HO2'" B G 15 ? ? "O4'" B C 16 ? ? 1.59 # 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 DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.60 108.30 2.30 0.30 N 2 1 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.56 108.30 2.26 0.30 N 3 1 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.15 122.90 -3.75 0.60 N 4 2 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.69 108.30 2.39 0.30 N 5 2 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.34 108.30 2.04 0.30 N 6 3 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.36 108.30 3.06 0.30 N 7 3 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.45 108.30 2.15 0.30 N 8 3 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.19 122.90 -3.71 0.60 N 9 4 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.55 108.30 2.25 0.30 N 10 4 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.11 122.90 -3.79 0.60 N 11 4 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.34 108.30 2.04 0.30 N 12 4 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.02 122.90 -3.88 0.60 N 13 5 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.36 108.30 3.06 0.30 N 14 5 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.38 108.30 2.08 0.30 N 15 6 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.48 108.30 3.18 0.30 N 16 6 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.39 108.30 2.09 0.30 N 17 6 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.25 122.90 -3.65 0.60 N 18 7 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.90 108.30 2.60 0.30 N 19 7 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.95 108.30 2.65 0.30 N 20 8 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.19 108.30 2.89 0.30 N 21 8 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.39 108.30 2.09 0.30 N 22 8 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.28 122.90 -3.62 0.60 N 23 9 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.39 108.30 3.09 0.30 N 24 9 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 111.15 108.30 2.85 0.30 N 25 9 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.71 122.90 -4.19 0.60 N 26 10 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.81 108.30 2.51 0.30 N 27 10 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 111.07 108.30 2.77 0.30 N 28 11 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.44 108.30 2.14 0.30 N 29 11 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 111.11 108.30 2.81 0.30 N 30 11 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.92 122.90 -3.98 0.60 N 31 12 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.91 108.30 2.61 0.30 N 32 12 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.20 122.90 -3.70 0.60 N 33 13 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.19 108.30 2.89 0.30 N 34 13 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.08 122.90 -3.82 0.60 N 35 13 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.76 108.30 2.46 0.30 N 36 14 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.96 108.30 2.66 0.30 N 37 14 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.67 108.30 2.37 0.30 N 38 14 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.90 122.90 -4.00 0.60 N 39 15 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.60 108.30 2.30 0.30 N 40 15 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.07 122.90 -3.83 0.60 N 41 15 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.21 108.30 1.91 0.30 N 42 15 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.99 122.90 -3.91 0.60 N 43 16 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.77 108.30 2.47 0.30 N 44 16 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.26 122.90 -3.64 0.60 N 45 16 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.79 108.30 2.49 0.30 N 46 16 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.15 122.90 -3.75 0.60 N 47 17 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.50 108.30 2.20 0.30 N 48 17 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.23 108.30 1.93 0.30 N 49 17 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.17 122.90 -3.73 0.60 N 50 18 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.88 108.30 2.58 0.30 N 51 18 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.92 108.30 2.62 0.30 N 52 19 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.63 108.30 2.33 0.30 N 53 19 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.56 108.30 2.26 0.30 N 54 20 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.88 108.30 2.58 0.30 N 55 20 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 110.89 108.30 2.59 0.30 N 56 20 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.04 122.90 -3.86 0.60 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LVY 'double helix' 2LVY '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 C 1 1_555 B G 8 1_555 1.197 -0.854 -1.349 1.860 15.409 -8.888 1 A_C1:G17_B A 1 ? B 17 ? 19 1 1 A G 2 1_555 B C 7 1_555 -0.393 -0.877 -2.082 -16.729 5.213 -13.288 2 A_G2:C16_B A 2 ? B 16 ? 19 1 1 A C 3 1_555 B G 6 1_555 0.266 -0.437 -0.624 -7.829 0.697 -3.174 3 A_C3:G15_B A 3 ? B 15 ? 19 1 1 A A 5 1_555 B U 4 1_555 0.061 -0.298 -0.520 3.857 -0.115 -1.705 4 A_A5:U13_B A 5 ? B 13 ? 20 1 1 A C 6 1_555 B G 3 1_555 1.118 -0.289 -0.857 26.147 -13.130 6.635 5 A_C6:G12_B A 6 ? B 12 ? 19 1 1 A G 7 1_555 B C 2 1_555 -0.634 -0.286 -1.430 -27.920 1.900 1.621 6 A_G7:C11_B A 7 ? B 11 ? 19 1 1 A C 8 1_555 B G 1 1_555 1.144 -0.516 -0.547 -1.760 18.379 -10.968 7 A_C8:G10_B A 8 ? B 10 ? 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 C 1 1_555 B G 8 1_555 A G 2 1_555 B C 7 1_555 -0.085 -1.285 5.160 4.152 -6.514 24.945 0.045 2.031 5.238 -14.638 -9.331 26.096 1 AA_C1G2:C16G17_BB A 1 ? B 17 ? A 2 ? B 16 ? 1 A G 2 1_555 B C 7 1_555 A C 3 1_555 B G 6 1_555 0.751 -1.492 3.541 -5.708 -9.687 36.505 -0.904 -1.961 3.652 -15.031 8.857 38.141 2 AA_G2C3:G15C16_BB A 2 ? B 16 ? A 3 ? B 15 ? 1 A C 3 1_555 B G 6 1_555 A A 5 1_555 B U 4 1_555 -0.279 -2.175 6.906 0.668 3.319 59.079 -2.557 0.354 6.783 3.363 -0.677 59.168 3 AA_C3A5:U13G15_BB A 3 ? B 15 ? A 5 ? B 13 ? 1 A A 5 1_555 B U 4 1_555 A C 6 1_555 B G 3 1_555 1.062 -1.177 2.912 1.755 -4.704 34.119 -1.312 -1.540 3.091 -7.963 -2.971 34.475 4 AA_A5C6:G12U13_BB A 5 ? B 13 ? A 6 ? B 12 ? 1 A C 6 1_555 B G 3 1_555 A G 7 1_555 B C 2 1_555 -0.317 -2.715 5.310 0.343 6.957 23.242 -9.774 0.917 4.320 16.791 -0.827 24.250 5 AA_C6G7:C11G12_BB A 6 ? B 12 ? A 7 ? B 11 ? 1 A G 7 1_555 B C 2 1_555 A C 8 1_555 B G 1 1_555 -1.619 -1.120 2.881 -3.101 -2.894 37.406 -1.394 2.142 3.076 -4.494 4.816 37.637 6 AA_G7C8:G10C11_BB A 7 ? B 11 ? A 8 ? B 10 ? #