data_1SJF # _entry.id 1SJF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.351 _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 1SJF pdb_00001sjf 10.2210/pdb1sjf/pdb NDB PR0118 ? ? RCSB RCSB021760 ? ? WWPDB D_1000021760 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1DRZ 'cleaved HDV ribozyme' unspecified PDB 1CX0 'cleaved HDV ribozyme' unspecified PDB 1VBX 'the same protein/RNA(C75U) complex in EDTA solution' unspecified PDB 1VBY 'the same protein/RNA(C75U) complex and Mn2+ bound' unspecified PDB 1VBZ 'the same protein/RNA(C75U) complex in Ba2+ solution' unspecified PDB 1VC0 'the same protein/RNA(C75U) complex in Imidazole and Sr2+ solutions' unspecified PDB 1SJF 'the same protein/RNA(C75U) complex in Cobalt Hexammine solution' unspecified PDB 1VC5 'the same protein/RNA(wild type) complex in EDTA solution' unspecified PDB 1VC6 'the same protein/RNA(C75U) complex in Imidazole and Mg2+ solutions' unspecified PDB 1VC7 'the same protein/RNA(C75U) complex in Sr2+ solution' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1SJF _pdbx_database_status.recvd_initial_deposition_date 2004-03-03 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _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 'Ke, A.' 1 'Zhou, K.' 2 'Ding, F.' 3 'Cate, J.H.D.' 4 'Doudna, J.A.' 5 # _citation.id primary _citation.title 'A conformational switch controls hepatitis delta virus ribozyme catalysis.' _citation.journal_abbrev Nature _citation.journal_volume 429 _citation.page_first 201 _citation.page_last 205 _citation.year 2004 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15141216 _citation.pdbx_database_id_DOI 10.1038/nature02522 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ke, A.' 1 ? primary 'Zhou, K.' 2 ? primary 'Ding, F.' 3 ? primary 'Cate, J.H.' 4 ? primary 'Doudna, J.A.' 5 ? # _cell.entry_id 1SJF _cell.length_a 108.754 _cell.length_b 108.754 _cell.length_c 188.381 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SJF _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 # 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 'Hepatitis Delta virus ribozyme' 24467.521 1 ? C75U ? ? 2 polymer man 'U1 small nuclear ribonucleoprotein A' 11498.472 1 ? Y31H/Q36R 'U1A_RBD(residues 1-100)' ? 3 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 4 water nat water 18.015 15 ? ? ? ? # _entity_name_com.entity_id 2 _entity_name_com.name 'U1 snRNP protein A, U1A protein, U1-A' # 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 GAUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGACU GAUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGACU B ? 2 'polypeptide(L)' no no ;MAVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK PMRIQYAKTDSDIIAKMKGT ; ;MAVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK PMRIQYAKTDSDIIAKMKGT ; A ? # 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 A n 1 3 U n 1 4 G n 1 5 G n 1 6 C n 1 7 C n 1 8 G n 1 9 G n 1 10 C n 1 11 A n 1 12 U n 1 13 G n 1 14 G n 1 15 U n 1 16 C n 1 17 C n 1 18 C n 1 19 A n 1 20 G n 1 21 C n 1 22 C n 1 23 U n 1 24 C n 1 25 C n 1 26 U n 1 27 C n 1 28 G n 1 29 C n 1 30 U n 1 31 G n 1 32 G n 1 33 C n 1 34 G n 1 35 C n 1 36 C n 1 37 G n 1 38 G n 1 39 C n 1 40 U n 1 41 G n 1 42 G n 1 43 G n 1 44 C n 1 45 A n 1 46 A n 1 47 C n 1 48 A n 1 49 C n 1 50 C n 1 51 A n 1 52 U n 1 53 U n 1 54 G n 1 55 C n 1 56 A n 1 57 C n 1 58 U n 1 59 C n 1 60 C n 1 61 G n 1 62 G n 1 63 U n 1 64 G n 1 65 G n 1 66 U n 1 67 G n 1 68 A n 1 69 A n 1 70 U n 1 71 G n 1 72 G n 1 73 G n 1 74 A n 1 75 C n 1 76 U n 2 1 MET n 2 2 ALA n 2 3 VAL n 2 4 PRO n 2 5 GLU n 2 6 THR n 2 7 ARG n 2 8 PRO n 2 9 ASN n 2 10 HIS n 2 11 THR n 2 12 ILE n 2 13 TYR n 2 14 ILE n 2 15 ASN n 2 16 ASN n 2 17 LEU n 2 18 ASN n 2 19 GLU n 2 20 LYS n 2 21 ILE n 2 22 LYS n 2 23 LYS n 2 24 ASP n 2 25 GLU n 2 26 LEU n 2 27 LYS n 2 28 LYS n 2 29 SER n 2 30 LEU n 2 31 HIS n 2 32 ALA n 2 33 ILE n 2 34 PHE n 2 35 SER n 2 36 ARG n 2 37 PHE n 2 38 GLY n 2 39 GLN n 2 40 ILE n 2 41 LEU n 2 42 ASP n 2 43 ILE n 2 44 LEU n 2 45 VAL n 2 46 SER n 2 47 ARG n 2 48 SER n 2 49 LEU n 2 50 LYS n 2 51 MET n 2 52 ARG n 2 53 GLY n 2 54 GLN n 2 55 ALA n 2 56 PHE n 2 57 VAL n 2 58 ILE n 2 59 PHE n 2 60 LYS n 2 61 GLU n 2 62 VAL n 2 63 SER n 2 64 SER n 2 65 ALA n 2 66 THR n 2 67 ASN n 2 68 ALA n 2 69 LEU n 2 70 ARG n 2 71 SER n 2 72 MET n 2 73 GLN n 2 74 GLY n 2 75 PHE n 2 76 PRO n 2 77 PHE n 2 78 TYR n 2 79 ASP n 2 80 LYS n 2 81 PRO n 2 82 MET n 2 83 ARG n 2 84 ILE n 2 85 GLN n 2 86 TYR n 2 87 ALA n 2 88 LYS n 2 89 THR n 2 90 ASP n 2 91 SER n 2 92 ASP n 2 93 ILE n 2 94 ILE n 2 95 ALA n 2 96 LYS n 2 97 MET n 2 98 LYS n 2 99 GLY n 2 100 THR n # _entity_src_gen.entity_id 2 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _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 'RNA occurs from Hapatitis Delta Virus pathogen, in vitro transcription with pUc19' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP SNRPA_HUMAN P09012 2 ;MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK PMRIQYAKTDSDIIAKMKGT ; 1 ? 2 PDB 1SJF 1SJF 1 ? ? ? # 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 1SJF A 1 ? 100 ? P09012 1 ? 100 ? 1 100 2 2 1SJF B 1 ? 76 ? 1SJF 98 ? 173 ? 98 173 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 1SJF HIS A 31 ? UNP P09012 TYR 31 'engineered mutation' 31 1 1 1SJF ARG A 36 ? UNP P09012 GLN 36 'engineered mutation' 36 2 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 1SJF _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.24 _exptl_crystal.density_percent_sol 61.71 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'Cobalt Herxammine, NaCl, MPD, Sodium Cacodylate, Spermine-HCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'Cobalt Herxammine' ? ? ? 1 2 1 NaCl ? ? ? 1 3 1 MPD ? ? ? 1 4 1 'Sodium Cacodylate' ? ? ? 1 5 1 Spermine-HCl ? ? ? 1 6 2 'Cobalt Herxammine' ? ? ? 1 7 2 NaCl ? ? ? 1 8 2 MPD ? ? ? 1 9 2 'Sodium Cacodylate' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 80 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2003-03-30 _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 graphite _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0781 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0781 # _reflns.entry_id 1SJF _reflns.observed_criterion_sigma_I 2.7 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 42.1 _reflns.d_resolution_high 2.75 _reflns.number_obs 10826 _reflns.number_all 11441 _reflns.percent_possible_obs 95.3 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 31.8 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.75 _reflns_shell.d_res_low 2.92 _reflns_shell.percent_possible_all 88.0 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1SJF _refine.ls_number_reflns_obs 10826 _refine.ls_number_reflns_all 11441 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 2125045.11 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 42.12 _refine.ls_d_res_high 2.75 _refine.ls_percent_reflns_obs 94.6 _refine.ls_R_factor_obs 0.24 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.24 _refine.ls_R_factor_R_free 0.275 _refine.ls_R_factor_R_free_error 0.008 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 1078 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 79.1 _refine.aniso_B[1][1] -13.17 _refine.aniso_B[2][2] -13.17 _refine.aniso_B[3][3] 26.34 _refine.aniso_B[1][2] -1.70 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.297932 _refine.solvent_model_param_bsol 40.2266 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1SJF _refine_analyze.Luzzati_coordinate_error_obs 0.39 _refine_analyze.Luzzati_sigma_a_obs 0.67 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.48 _refine_analyze.Luzzati_sigma_a_free 0.72 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 762 _refine_hist.pdbx_number_atoms_nucleic_acid 1574 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 2365 _refine_hist.d_res_high 2.75 _refine_hist.d_res_low 42.12 # 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 c_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.2 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 28.6 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.47 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.47 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 2.86 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 1.49 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 2.35 2.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.75 _refine_ls_shell.d_res_low 2.92 _refine_ls_shell.number_reflns_R_work 1495 _refine_ls_shell.R_factor_R_work 0.38 _refine_ls_shell.percent_reflns_obs 88.0 _refine_ls_shell.R_factor_R_free 0.397 _refine_ls_shell.R_factor_R_free_error 0.031 _refine_ls_shell.percent_reflns_R_free 9.8 _refine_ls_shell.number_reflns_R_free 162 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 DNA-RNA-MULTI-ENDO.PARAM ? 'X-RAY DIFFRACTION' 3 WATER_REP.PARAM ? 'X-RAY DIFFRACTION' 4 ION.PARAM ? 'X-RAY DIFFRACTION' 5 COHEX.PARAM ? 'X-RAY DIFFRACTION' # _struct.entry_id 1SJF _struct.title 'Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, in Cobalt Hexammine solution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1SJF _struct_keywords.pdbx_keywords TRANSLATION/RNA _struct_keywords.text 'HDV, ribozyme, RNA, U1A, precursor, TRANSLATION-RNA COMPLEX' # 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 3 ? D N N 3 ? E N N 4 ? F N N 4 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 LYS B 22 ? SER B 35 ? LYS A 22 SER A 35 1 ? 14 HELX_P HELX_P2 2 ARG B 36 ? GLY B 38 ? ARG A 36 GLY A 38 5 ? 3 HELX_P HELX_P3 3 GLU B 61 ? GLN B 73 ? GLU A 61 GLN A 73 1 ? 13 HELX_P HELX_P4 4 SER B 91 ? LYS B 96 ? SER A 91 LYS A 96 1 ? 6 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 4 N1 ? ? ? 1_555 A U 40 O2 ? ? B G 101 B U 137 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A G 4 O6 ? ? ? 1_555 A U 40 N3 ? ? B G 101 B U 137 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 39 N3 ? ? B G 102 B C 136 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 39 O2 ? ? B G 102 B C 136 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 39 N4 ? ? B G 102 B C 136 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 38 N1 ? ? B C 103 B G 135 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 38 O6 ? ? B C 103 B G 135 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 38 N2 ? ? B C 103 B G 135 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 6 N3 ? ? ? 1_555 A C 39 N4 ? ? B C 103 B C 136 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog10 hydrog ? ? A C 7 N3 ? ? ? 1_555 A G 37 N1 ? ? B C 104 B G 134 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 7 N4 ? ? ? 1_555 A G 37 O6 ? ? B C 104 B G 134 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 7 O2 ? ? ? 1_555 A G 37 N2 ? ? B C 104 B G 134 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 36 N3 ? ? B G 105 B C 133 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 36 O2 ? ? B G 105 B C 133 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 36 N4 ? ? B G 105 B C 133 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 9 N1 ? ? ? 1_555 A C 35 N3 ? ? B G 106 B C 132 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 9 N2 ? ? ? 1_555 A C 35 O2 ? ? B G 106 B C 132 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 9 O6 ? ? ? 1_555 A C 35 N4 ? ? B G 106 B C 132 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 34 N1 ? ? B C 107 B G 131 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 34 O6 ? ? B C 107 B G 131 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 34 N2 ? ? B C 107 B G 131 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 14 N1 ? ? ? 1_555 A C 75 N3 ? ? B G 111 B C 172 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog23 hydrog ? ? A U 15 N3 ? ? ? 1_555 A A 74 N1 ? ? B U 112 B A 171 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 15 O4 ? ? ? 1_555 A A 74 N6 ? ? B U 112 B A 171 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 73 N1 ? ? B C 113 B G 170 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 73 O6 ? ? B C 113 B G 170 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 73 N2 ? ? B C 113 B G 170 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 17 N3 ? ? ? 1_555 A G 72 N1 ? ? B C 114 B G 169 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 17 N4 ? ? ? 1_555 A G 72 O6 ? ? B C 114 B G 169 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 17 O2 ? ? ? 1_555 A G 72 N2 ? ? B C 114 B G 169 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 18 N3 ? ? ? 1_555 A G 71 N1 ? ? B C 115 B G 168 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 18 N4 ? ? ? 1_555 A G 71 O6 ? ? B C 115 B G 168 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 18 O2 ? ? ? 1_555 A G 71 N2 ? ? B C 115 B G 168 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A A 19 N1 ? ? ? 1_555 A U 70 N3 ? ? B A 116 B U 167 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A A 19 N6 ? ? ? 1_555 A U 70 O4 ? ? B A 116 B U 167 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 20 N1 ? ? ? 1_555 A C 33 N3 ? ? B G 117 B C 130 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 20 N2 ? ? ? 1_555 A C 33 O2 ? ? B G 117 B C 130 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 20 O6 ? ? ? 1_555 A C 33 N4 ? ? B G 117 B C 130 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 21 N3 ? ? ? 1_555 A G 32 N1 ? ? B C 118 B G 129 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 21 N4 ? ? ? 1_555 A G 32 O6 ? ? B C 118 B G 129 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 21 O2 ? ? ? 1_555 A G 32 N2 ? ? B C 118 B G 129 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 22 N3 ? ? ? 1_555 A G 31 N1 ? ? B C 119 B G 128 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 22 N4 ? ? ? 1_555 A G 31 O6 ? ? B C 119 B G 128 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 22 O2 ? ? ? 1_555 A G 31 N2 ? ? B C 119 B G 128 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 24 N3 ? ? ? 1_555 A G 42 N1 ? ? B C 121 B G 139 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 24 N4 ? ? ? 1_555 A G 42 O6 ? ? B C 121 B G 139 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 24 O2 ? ? ? 1_555 A G 42 N2 ? ? B C 121 B G 139 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 24 O2 ? ? ? 1_555 A A 45 N6 ? ? B C 121 B A 142 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog49 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 41 N1 ? ? B C 122 B G 138 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 41 O6 ? ? B C 122 B G 138 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 41 N2 ? ? B C 122 B G 138 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 32 N2 ? ? ? 1_555 A A 69 N3 ? ? B G 129 B A 166 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog53 hydrog ? ? A G 43 N3 ? ? ? 1_555 A A 45 N6 ? ? B G 140 B A 142 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog54 hydrog ? ? A G 43 N2 ? ? ? 1_555 A G 65 O6 ? ? B G 140 B G 162 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog55 hydrog ? ? A C 44 O2 ? ? ? 1_555 A C 47 N4 ? ? B C 141 B C 144 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog56 hydrog ? ? A C 44 N4 ? ? ? 1_555 A G 64 O6 ? ? B C 141 B G 161 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog57 hydrog ? ? A A 46 N1 ? ? ? 1_555 A G 65 N1 ? ? B A 143 B G 162 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog58 hydrog ? ? A A 46 N6 ? ? ? 1_555 A G 65 O6 ? ? B A 143 B G 162 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog59 hydrog ? ? A C 47 N3 ? ? ? 1_555 A G 64 N1 ? ? B C 144 B G 161 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A C 47 N4 ? ? ? 1_555 A G 64 O6 ? ? B C 144 B G 161 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A C 47 O2 ? ? ? 1_555 A G 64 N2 ? ? B C 144 B G 161 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A A 48 N1 ? ? ? 1_555 A U 63 N3 ? ? B A 145 B U 160 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A A 48 N6 ? ? ? 1_555 A U 63 O4 ? ? B A 145 B U 160 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A C 49 N3 ? ? ? 1_555 A G 62 N1 ? ? B C 146 B G 159 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A C 49 N4 ? ? ? 1_555 A G 62 O6 ? ? B C 146 B G 159 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 49 O2 ? ? ? 1_555 A G 62 N2 ? ? B C 146 B G 159 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 50 N3 ? ? ? 1_555 A G 61 N1 ? ? B C 147 B G 158 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 50 N4 ? ? ? 1_555 A G 61 O6 ? ? B C 147 B G 158 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A C 50 O2 ? ? ? 1_555 A G 61 N2 ? ? B C 147 B G 158 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A U 58 O2 ? ? ? 1_555 A C 60 N4 ? ? B U 155 B C 157 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ILE B 40 ? VAL B 45 ? ILE A 40 VAL A 45 A 2 GLN B 54 ? PHE B 59 ? GLN A 54 PHE A 59 A 3 THR B 11 ? ASN B 15 ? THR A 11 ASN A 15 A 4 ARG B 83 ? TYR B 86 ? ARG A 83 TYR A 86 B 1 PRO B 76 ? PHE B 77 ? PRO A 76 PHE A 77 B 2 LYS B 80 ? PRO B 81 ? LYS A 80 PRO A 81 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N LEU B 41 ? N LEU A 41 O ILE B 58 ? O ILE A 58 A 2 3 O ALA B 55 ? O ALA A 55 N ILE B 14 ? N ILE A 14 A 3 4 N ASN B 15 ? N ASN A 15 O ARG B 83 ? O ARG A 83 B 1 2 N PHE B 77 ? N PHE A 77 O LYS B 80 ? O LYS A 80 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B NCO 201 ? 7 'BINDING SITE FOR RESIDUE NCO B 201' AC2 Software B NCO 202 ? 4 'BINDING SITE FOR RESIDUE NCO B 202' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 7 U A 3 ? U B 100 . ? 1_555 ? 2 AC1 7 U A 23 ? U B 120 . ? 1_555 ? 3 AC1 7 U A 26 ? U B 123 . ? 1_555 ? 4 AC1 7 C A 27 ? C B 124 . ? 1_555 ? 5 AC1 7 G A 28 ? G B 125 . ? 1_555 ? 6 AC1 7 G A 31 ? G B 128 . ? 1_555 ? 7 AC1 7 U A 66 ? U B 163 . ? 1_555 ? 8 AC2 4 ARG B 52 ? ARG A 52 . ? 1_555 ? 9 AC2 4 C A 44 ? C B 141 . ? 1_555 ? 10 AC2 4 G A 61 ? G B 158 . ? 1_555 ? 11 AC2 4 G A 62 ? G B 159 . ? 1_555 ? # _database_PDB_matrix.entry_id 1SJF _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 1SJF _atom_sites.fract_transf_matrix[1][1] 0.009195 _atom_sites.fract_transf_matrix[1][2] 0.005309 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.010618 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.005308 _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 CO N O P S # 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 98 ? ? ? B . n A 1 2 A 2 99 99 A ADE B . n A 1 3 U 3 100 100 U URI B . n A 1 4 G 4 101 101 G GUA B . n A 1 5 G 5 102 102 G GUA B . n A 1 6 C 6 103 103 C CYT B . n A 1 7 C 7 104 104 C CYT B . n A 1 8 G 8 105 105 G GUA B . n A 1 9 G 9 106 106 G GUA B . n A 1 10 C 10 107 107 C CYT B . n A 1 11 A 11 108 108 A ADE B . n A 1 12 U 12 109 109 U URI B . n A 1 13 G 13 110 110 G GUA B . n A 1 14 G 14 111 111 G GUA B . n A 1 15 U 15 112 112 U URI B . n A 1 16 C 16 113 113 C CYT B . n A 1 17 C 17 114 114 C CYT B . n A 1 18 C 18 115 115 C CYT B . n A 1 19 A 19 116 116 A ADE B . n A 1 20 G 20 117 117 G GUA B . n A 1 21 C 21 118 118 C CYT B . n A 1 22 C 22 119 119 C CYT B . n A 1 23 U 23 120 120 U URI B . n A 1 24 C 24 121 121 C CYT B . n A 1 25 C 25 122 122 C CYT B . n A 1 26 U 26 123 123 U URI B . n A 1 27 C 27 124 124 C CYT B . n A 1 28 G 28 125 125 G GUA B . n A 1 29 C 29 126 126 C CYT B . n A 1 30 U 30 127 127 U URI B . n A 1 31 G 31 128 128 G GUA B . n A 1 32 G 32 129 129 G GUA B . n A 1 33 C 33 130 130 C CYT B . n A 1 34 G 34 131 131 G GUA B . n A 1 35 C 35 132 132 C CYT B . n A 1 36 C 36 133 133 C CYT B . n A 1 37 G 37 134 134 G GUA B . n A 1 38 G 38 135 135 G GUA B . n A 1 39 C 39 136 136 C CYT B . n A 1 40 U 40 137 137 U URI B . n A 1 41 G 41 138 138 G GUA B . n A 1 42 G 42 139 139 G GUA B . n A 1 43 G 43 140 140 G GUA B . n A 1 44 C 44 141 141 C CYT B . n A 1 45 A 45 142 142 A ADE B . n A 1 46 A 46 143 143 A ADE B . n A 1 47 C 47 144 144 C CYT B . n A 1 48 A 48 145 145 A ADE B . n A 1 49 C 49 146 146 C CYT B . n A 1 50 C 50 147 147 C CYT B . n A 1 51 A 51 148 148 A ADE B . n A 1 52 U 52 149 149 U URI B . n A 1 53 U 53 150 150 U URI B . n A 1 54 G 54 151 151 G GUA B . n A 1 55 C 55 152 152 C CYT B . n A 1 56 A 56 153 153 A ADE B . n A 1 57 C 57 154 154 C CYT B . n A 1 58 U 58 155 155 U URI B . n A 1 59 C 59 156 156 C CYT B . n A 1 60 C 60 157 157 C CYT B . n A 1 61 G 61 158 158 G GUA B . n A 1 62 G 62 159 159 G GUA B . n A 1 63 U 63 160 160 U URI B . n A 1 64 G 64 161 161 G GUA B . n A 1 65 G 65 162 162 G GUA B . n A 1 66 U 66 163 163 U URI B . n A 1 67 G 67 164 164 G GUA B . n A 1 68 A 68 165 165 A ADE B . n A 1 69 A 69 166 166 A ADE B . n A 1 70 U 70 167 167 U URI B . n A 1 71 G 71 168 168 G GUA B . n A 1 72 G 72 169 169 G GUA B . n A 1 73 G 73 170 170 G GUA B . n A 1 74 A 74 171 171 A ADE B . n A 1 75 C 75 172 172 C CYT B . n A 1 76 U 76 173 ? ? ? B . n B 2 1 MET 1 1 ? ? ? A . n B 2 2 ALA 2 2 ? ? ? A . n B 2 3 VAL 3 3 ? ? ? A . n B 2 4 PRO 4 4 4 PRO PRO A . n B 2 5 GLU 5 5 5 GLU ALA A . n B 2 6 THR 6 6 6 THR THR A . n B 2 7 ARG 7 7 7 ARG ARG A . n B 2 8 PRO 8 8 8 PRO PRO A . n B 2 9 ASN 9 9 9 ASN ASN A . n B 2 10 HIS 10 10 10 HIS HIS A . n B 2 11 THR 11 11 11 THR THR A . n B 2 12 ILE 12 12 12 ILE ILE A . n B 2 13 TYR 13 13 13 TYR TYR A . n B 2 14 ILE 14 14 14 ILE ILE A . n B 2 15 ASN 15 15 15 ASN ASN A . n B 2 16 ASN 16 16 16 ASN ASN A . n B 2 17 LEU 17 17 17 LEU LEU A . n B 2 18 ASN 18 18 18 ASN ASN A . n B 2 19 GLU 19 19 19 GLU GLU A . n B 2 20 LYS 20 20 20 LYS ALA A . n B 2 21 ILE 21 21 21 ILE ILE A . n B 2 22 LYS 22 22 22 LYS LYS A . n B 2 23 LYS 23 23 23 LYS LYS A . n B 2 24 ASP 24 24 24 ASP ASP A . n B 2 25 GLU 25 25 25 GLU GLU A . n B 2 26 LEU 26 26 26 LEU LEU A . n B 2 27 LYS 27 27 27 LYS LYS A . n B 2 28 LYS 28 28 28 LYS LYS A . n B 2 29 SER 29 29 29 SER SER A . n B 2 30 LEU 30 30 30 LEU LEU A . n B 2 31 HIS 31 31 31 HIS HIS A . n B 2 32 ALA 32 32 32 ALA ALA A . n B 2 33 ILE 33 33 33 ILE ILE A . n B 2 34 PHE 34 34 34 PHE PHE A . n B 2 35 SER 35 35 35 SER SER A . n B 2 36 ARG 36 36 36 ARG ARG A . n B 2 37 PHE 37 37 37 PHE PHE A . n B 2 38 GLY 38 38 38 GLY GLY A . n B 2 39 GLN 39 39 39 GLN GLN A . n B 2 40 ILE 40 40 40 ILE ILE A . n B 2 41 LEU 41 41 41 LEU LEU A . n B 2 42 ASP 42 42 42 ASP ASP A . n B 2 43 ILE 43 43 43 ILE ILE A . n B 2 44 LEU 44 44 44 LEU LEU A . n B 2 45 VAL 45 45 45 VAL VAL A . n B 2 46 SER 46 46 46 SER SER A . n B 2 47 ARG 47 47 47 ARG ARG A . n B 2 48 SER 48 48 48 SER SER A . n B 2 49 LEU 49 49 49 LEU LEU A . n B 2 50 LYS 50 50 50 LYS LYS A . n B 2 51 MET 51 51 51 MET MET A . n B 2 52 ARG 52 52 52 ARG ARG A . n B 2 53 GLY 53 53 53 GLY GLY A . n B 2 54 GLN 54 54 54 GLN GLN A . n B 2 55 ALA 55 55 55 ALA ALA A . n B 2 56 PHE 56 56 56 PHE PHE A . n B 2 57 VAL 57 57 57 VAL VAL A . n B 2 58 ILE 58 58 58 ILE ILE A . n B 2 59 PHE 59 59 59 PHE PHE A . n B 2 60 LYS 60 60 60 LYS LYS A . n B 2 61 GLU 61 61 61 GLU GLU A . n B 2 62 VAL 62 62 62 VAL VAL A . n B 2 63 SER 63 63 63 SER SER A . n B 2 64 SER 64 64 64 SER SER A . n B 2 65 ALA 65 65 65 ALA ALA A . n B 2 66 THR 66 66 66 THR THR A . n B 2 67 ASN 67 67 67 ASN ASN A . n B 2 68 ALA 68 68 68 ALA ALA A . n B 2 69 LEU 69 69 69 LEU LEU A . n B 2 70 ARG 70 70 70 ARG ARG A . n B 2 71 SER 71 71 71 SER SER A . n B 2 72 MET 72 72 72 MET MET A . n B 2 73 GLN 73 73 73 GLN GLN A . n B 2 74 GLY 74 74 74 GLY GLY A . n B 2 75 PHE 75 75 75 PHE PHE A . n B 2 76 PRO 76 76 76 PRO PRO A . n B 2 77 PHE 77 77 77 PHE PHE A . n B 2 78 TYR 78 78 78 TYR TYR A . n B 2 79 ASP 79 79 79 ASP ASP A . n B 2 80 LYS 80 80 80 LYS LYS A . n B 2 81 PRO 81 81 81 PRO PRO A . n B 2 82 MET 82 82 82 MET MET A . n B 2 83 ARG 83 83 83 ARG ARG A . n B 2 84 ILE 84 84 84 ILE ILE A . n B 2 85 GLN 85 85 85 GLN GLN A . n B 2 86 TYR 86 86 86 TYR TYR A . n B 2 87 ALA 87 87 87 ALA ALA A . n B 2 88 LYS 88 88 88 LYS LYS A . n B 2 89 THR 89 89 89 THR THR A . n B 2 90 ASP 90 90 90 ASP ASP A . n B 2 91 SER 91 91 91 SER SER A . n B 2 92 ASP 92 92 92 ASP ASP A . n B 2 93 ILE 93 93 93 ILE ILE A . n B 2 94 ILE 94 94 94 ILE ILE A . n B 2 95 ALA 95 95 95 ALA ALA A . n B 2 96 LYS 96 96 96 LYS LYS A . n B 2 97 MET 97 97 97 MET MET A . n B 2 98 LYS 98 98 98 LYS ALA A . n B 2 99 GLY 99 99 ? ? ? A . n B 2 100 THR 100 100 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 NCO 1 201 201 NCO NCO B . D 3 NCO 1 202 202 NCO NCO B . E 4 HOH 1 13 13 HOH HOH B . E 4 HOH 2 14 14 HOH HOH B . E 4 HOH 3 15 15 HOH HOH B . F 4 HOH 1 101 1 HOH HOH A . F 4 HOH 2 102 2 HOH HOH A . F 4 HOH 3 103 3 HOH HOH A . F 4 HOH 4 104 4 HOH HOH A . F 4 HOH 5 105 5 HOH HOH A . F 4 HOH 6 106 6 HOH HOH A . F 4 HOH 7 107 7 HOH HOH A . F 4 HOH 8 108 8 HOH HOH A . F 4 HOH 9 109 9 HOH HOH A . F 4 HOH 10 110 10 HOH HOH A . F 4 HOH 11 111 11 HOH HOH A . F 4 HOH 12 112 12 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _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 2004-05-18 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2021-11-10 # _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 ? _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' 'Database references' 4 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' struct_ref_seq_dif 3 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_ref_seq_dif.details' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 HKL-2000 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 AMoRE phasing . ? 4 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N3 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 U _pdbx_validate_close_contact.auth_seq_id_1 120 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O6 _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 G _pdbx_validate_close_contact.auth_seq_id_2 125 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.05 # 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 "C2'" B C 152 ? ? "C3'" B C 152 ? ? "O3'" B C 152 ? ? 127.68 113.70 13.98 1.60 N 2 1 "C2'" B U 163 ? ? "C3'" B U 163 ? ? "O3'" B U 163 ? ? 123.98 113.70 10.28 1.60 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU A 5 ? ? 58.10 133.54 2 1 LYS A 96 ? ? -46.96 -9.86 3 1 MET A 97 ? ? -118.38 -84.42 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B A 99 ? P ? A A 2 P 2 1 Y 1 B A 99 ? OP1 ? A A 2 OP1 3 1 Y 1 B A 99 ? OP2 ? A A 2 OP2 4 1 Y 1 A GLU 5 ? CG ? B GLU 5 CG 5 1 Y 1 A GLU 5 ? CD ? B GLU 5 CD 6 1 Y 1 A GLU 5 ? OE1 ? B GLU 5 OE1 7 1 Y 1 A GLU 5 ? OE2 ? B GLU 5 OE2 8 1 Y 1 A LYS 20 ? CG ? B LYS 20 CG 9 1 Y 1 A LYS 20 ? CD ? B LYS 20 CD 10 1 Y 1 A LYS 20 ? CE ? B LYS 20 CE 11 1 Y 1 A LYS 20 ? NZ ? B LYS 20 NZ 12 1 Y 1 A LYS 98 ? CG ? B LYS 98 CG 13 1 Y 1 A LYS 98 ? CD ? B LYS 98 CD 14 1 Y 1 A LYS 98 ? CE ? B LYS 98 CE 15 1 Y 1 A LYS 98 ? NZ ? B LYS 98 NZ # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 B G 98 ? A G 1 2 1 Y 1 B U 173 ? A U 76 3 1 Y 1 A MET 1 ? B MET 1 4 1 Y 1 A ALA 2 ? B ALA 2 5 1 Y 1 A VAL 3 ? B VAL 3 6 1 Y 1 A GLY 99 ? B GLY 99 7 1 Y 1 A THR 100 ? B THR 100 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1SJF 'double helix' 1SJF 'a-form double helix' 1SJF 'bulge loop' 1SJF 'mismatched base pair' 1SJF 'triple 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 34 1_555 A C 10 1_555 -0.246 -0.195 -0.386 -8.847 2.337 -0.148 1 B_G131:C107_B B 131 ? B 107 ? 19 1 1 A C 35 1_555 A G 9 1_555 0.729 -0.407 -0.098 -6.562 -9.523 3.319 2 B_C132:G106_B B 132 ? B 106 ? 19 1 1 A C 36 1_555 A G 8 1_555 0.451 -0.332 0.925 -9.923 1.933 4.444 3 B_C133:G105_B B 133 ? B 105 ? 19 1 1 A G 37 1_555 A C 7 1_555 -0.272 -0.190 -0.709 -11.269 10.004 -1.331 4 B_G134:C104_B B 134 ? B 104 ? 19 1 1 A G 38 1_555 A C 6 1_555 0.064 0.035 -1.281 -14.420 0.928 0.466 5 B_G135:C103_B B 135 ? B 103 ? 19 1 1 A C 39 1_555 A G 5 1_555 0.213 -0.055 -1.061 7.849 -0.835 6.736 6 B_C136:G102_B B 136 ? B 102 ? 19 1 1 A U 40 1_555 A G 4 1_555 2.708 -0.643 -0.483 7.899 2.334 -13.039 7 B_U137:G101_B B 137 ? B 101 ? 28 ? 1 A G 41 1_555 A C 25 1_555 -0.007 -0.243 -0.337 -3.520 -11.239 -0.819 8 B_G138:C122_B B 138 ? B 122 ? 19 1 1 A G 42 1_555 A C 24 1_555 0.018 -0.012 -0.023 -19.929 -20.613 -4.034 9 B_G139:C121_B B 139 ? B 121 ? 19 1 1 A A 46 1_555 A G 65 1_555 -0.696 1.440 -0.703 6.213 -23.560 -0.434 10 B_A143:G162_B B 143 ? B 162 ? 8 1 1 A C 47 1_555 A G 64 1_555 0.029 -0.064 0.388 3.354 -13.737 1.653 11 B_C144:G161_B B 144 ? B 161 ? 19 1 1 A A 48 1_555 A U 63 1_555 -0.040 -0.247 0.177 0.439 -16.522 3.418 12 B_A145:U160_B B 145 ? B 160 ? 20 1 1 A C 49 1_555 A G 62 1_555 0.297 -0.249 -0.350 7.421 -12.795 2.085 13 B_C146:G159_B B 146 ? B 159 ? 19 1 1 A C 50 1_555 A G 61 1_555 0.289 -0.211 -0.084 -1.792 -1.045 -1.818 14 B_C147:G158_B B 147 ? B 158 ? 19 1 1 A G 14 1_555 A C 75 1_555 0.038 0.324 0.140 -10.819 -12.527 8.558 15 B_G111:C172_B B 111 ? B 172 ? ? 1 1 A U 15 1_555 A A 74 1_555 0.174 -0.227 -0.416 7.020 -12.076 -5.456 16 B_U112:A171_B B 112 ? B 171 ? 20 1 1 A C 16 1_555 A G 73 1_555 0.155 -0.142 -0.325 7.704 -7.579 -2.456 17 B_C113:G170_B B 113 ? B 170 ? 19 1 1 A C 17 1_555 A G 72 1_555 0.530 -0.260 0.052 -4.375 -8.513 -2.936 18 B_C114:G169_B B 114 ? B 169 ? 19 1 1 A C 18 1_555 A G 71 1_555 0.189 -0.265 0.020 -3.970 -1.583 -1.467 19 B_C115:G168_B B 115 ? B 168 ? 19 1 1 A A 19 1_555 A U 70 1_555 -0.272 -0.283 0.085 3.325 -6.023 6.459 20 B_A116:U167_B B 116 ? B 167 ? 20 1 1 A G 20 1_555 A C 33 1_555 -0.198 -0.072 0.090 -2.209 -22.127 6.217 21 B_G117:C130_B B 117 ? B 130 ? 19 1 1 A C 21 1_555 A G 32 1_555 -0.048 -0.303 -0.151 2.905 -22.953 1.603 22 B_C118:G129_B B 118 ? B 129 ? 19 1 1 A C 22 1_555 A G 31 1_555 -0.414 -0.333 0.815 -9.815 -13.861 -6.698 23 B_C119:G128_B B 119 ? B 128 ? 19 1 1 A U 58 1_555 A C 60 1_555 -4.619 -1.124 -0.815 6.264 24.210 49.528 24 B_U155:C157_B B 155 ? B 157 ? ? 5 # 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 34 1_555 A C 10 1_555 A C 35 1_555 A G 9 1_555 -0.602 -2.060 3.208 0.730 5.075 33.469 -4.302 1.144 2.861 8.749 -1.259 33.848 1 BB_G131C132:G106C107_BB B 131 ? B 107 ? B 132 ? B 106 ? 1 A C 35 1_555 A G 9 1_555 A C 36 1_555 A G 8 1_555 0.497 -2.355 3.103 -6.388 6.384 30.209 -5.364 -1.943 2.414 11.919 11.925 31.500 2 BB_C132C133:G105G106_BB B 132 ? B 106 ? B 133 ? B 105 ? 1 A C 36 1_555 A G 8 1_555 A G 37 1_555 A C 7 1_555 -0.603 -2.679 3.149 9.317 5.038 25.135 -6.766 3.275 2.219 10.976 -20.297 27.242 3 BB_C133G134:C104G105_BB B 133 ? B 105 ? B 134 ? B 104 ? 1 A G 37 1_555 A C 7 1_555 A G 38 1_555 A C 6 1_555 0.326 -1.521 3.707 1.737 5.722 27.199 -4.654 -0.225 3.337 11.984 -3.638 27.837 4 BB_G134G135:C103C104_BB B 134 ? B 104 ? B 135 ? B 103 ? 1 A G 38 1_555 A C 6 1_555 A C 39 1_555 A G 5 1_555 -0.508 -2.619 2.735 -4.784 3.704 25.743 -6.511 0.100 2.394 8.171 10.553 26.433 5 BB_G135C136:G102C103_BB B 135 ? B 103 ? B 136 ? B 102 ? 1 A C 39 1_555 A G 5 1_555 A U 40 1_555 A G 4 1_555 -0.628 -1.597 3.401 -4.239 11.523 42.941 -3.154 0.442 2.946 15.369 5.654 44.582 6 BB_C136U137:G101G102_BB B 136 ? B 102 ? B 137 ? B 101 ? 1 A U 40 1_555 A G 4 1_555 A G 41 1_555 A C 25 1_555 -1.580 -3.003 3.717 -2.238 0.496 6.950 -25.574 3.143 3.809 3.955 17.837 7.318 7 BB_U137G138:C122G101_BB B 137 ? B 101 ? B 138 ? B 122 ? 1 A G 41 1_555 A C 25 1_555 A G 42 1_555 A C 24 1_555 -0.363 -2.159 3.680 -2.535 8.655 32.174 -5.261 0.193 3.032 15.246 4.466 33.382 8 BB_G138G139:C121C122_BB B 138 ? B 122 ? B 139 ? B 121 ? 1 A G 42 1_555 A C 24 1_555 A A 46 1_555 A G 65 1_555 -5.560 -2.127 3.573 35.118 -3.993 85.950 -1.416 4.464 1.760 -2.830 -24.890 91.606 9 BB_G139A143:G162C121_BB B 139 ? B 121 ? B 143 ? B 162 ? 1 A A 46 1_555 A G 65 1_555 A C 47 1_555 A G 64 1_555 0.584 -0.510 3.210 -12.847 13.813 37.809 -2.045 -2.055 2.562 19.878 18.487 42.099 10 BB_A143C144:G161G162_BB B 143 ? B 162 ? B 144 ? B 161 ? 1 A C 47 1_555 A G 64 1_555 A A 48 1_555 A U 63 1_555 0.284 -1.868 3.298 3.083 8.895 32.239 -4.606 -0.017 2.716 15.608 -5.410 33.551 11 BB_C144A145:U160G161_BB B 144 ? B 161 ? B 145 ? B 160 ? 1 A A 48 1_555 A U 63 1_555 A C 49 1_555 A G 62 1_555 -0.052 -1.247 3.127 1.622 0.956 34.597 -2.234 0.324 3.086 1.607 -2.725 34.646 12 BB_A145C146:G159U160_BB B 145 ? B 160 ? B 146 ? B 159 ? 1 A C 49 1_555 A G 62 1_555 A C 50 1_555 A G 61 1_555 -0.095 -1.924 3.607 -2.248 4.978 30.150 -4.681 -0.290 3.254 9.472 4.278 30.629 13 BB_C146C147:G158G159_BB B 146 ? B 159 ? B 147 ? B 158 ? 1 A G 14 1_555 A C 75 1_555 A U 15 1_555 A A 74 1_555 -1.687 -1.299 2.792 -0.832 2.881 26.640 -3.428 3.459 2.689 6.227 1.798 26.805 14 BB_G111U112:A171C172_BB B 111 ? B 172 ? B 112 ? B 171 ? 1 A U 15 1_555 A A 74 1_555 A C 16 1_555 A G 73 1_555 0.531 -1.708 3.240 -5.798 4.707 32.040 -3.775 -1.871 2.831 8.386 10.330 32.877 15 BB_U112C113:G170A171_BB B 112 ? B 171 ? B 113 ? B 170 ? 1 A C 16 1_555 A G 73 1_555 A C 17 1_555 A G 72 1_555 -0.647 -2.074 3.512 -4.693 3.451 37.647 -3.641 0.362 3.370 5.308 7.220 38.079 16 BB_C113C114:G169G170_BB B 113 ? B 170 ? B 114 ? B 169 ? 1 A C 17 1_555 A G 72 1_555 A C 18 1_555 A G 71 1_555 -0.403 -1.892 3.191 0.427 4.884 30.204 -4.484 0.841 2.851 9.295 -0.813 30.590 17 BB_C114C115:G168G169_BB B 114 ? B 169 ? B 115 ? B 168 ? 1 A C 18 1_555 A G 71 1_555 A A 19 1_555 A U 70 1_555 0.194 -1.417 3.033 -0.442 3.513 22.653 -4.678 -0.627 2.779 8.874 1.118 22.925 18 BB_C115A116:U167G168_BB B 115 ? B 168 ? B 116 ? B 167 ? 1 A A 19 1_555 A U 70 1_555 A G 20 1_555 A C 33 1_555 0.745 -1.351 3.447 -1.132 6.905 43.217 -2.485 -1.110 3.185 9.302 1.524 43.753 19 BB_A116G117:C130U167_BB B 116 ? B 167 ? B 117 ? B 130 ? 1 A G 20 1_555 A C 33 1_555 A C 21 1_555 A G 32 1_555 0.208 -1.112 3.013 3.935 -1.007 35.602 -1.674 0.187 3.048 -1.641 -6.410 35.825 20 BB_G117C118:G129C130_BB B 117 ? B 130 ? B 118 ? B 129 ? 1 A C 21 1_555 A G 32 1_555 A C 22 1_555 A G 31 1_555 -0.211 -1.636 3.790 -4.238 4.594 34.527 -3.495 -0.368 3.550 7.661 7.069 35.071 21 BB_C118C119:G128G129_BB B 118 ? B 129 ? B 119 ? B 128 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'COBALT HEXAMMINE(III)' NCO 4 water HOH #