data_1SI3 # _entry.id 1SI3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1SI3 NDB PR0112 RCSB RCSB021726 WWPDB D_1000021726 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1SI2 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1SI3 _pdbx_database_status.recvd_initial_deposition_date 2004-02-27 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ye, K.' 1 'Ma, J.B.' 2 'Patel, D.' 3 # _citation.id primary _citation.title 'Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain.' _citation.journal_abbrev Nature _citation.journal_volume 429 _citation.page_first 318 _citation.page_last 322 _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 15152257 _citation.pdbx_database_id_DOI 10.1038/nature02519 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Ma, J.B.' 1 primary 'Ye, K.' 2 primary 'Patel, D.J.' 3 # _cell.entry_id 1SI3 _cell.length_a 99.799 _cell.length_b 99.799 _cell.length_c 34.933 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SI3 _symmetry.space_group_name_H-M 'P 64' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3'" 2808.703 1 ? ? ? ? 2 polymer man 'Eukaryotic translation initiation factor 2C 1' 17377.562 1 ? ? 'PAZ domain (residues 225-369)' ? 3 water nat water 18.015 15 ? ? ? ? # _entity_name_com.entity_id 2 _entity_name_com.name 'eIF2C 1, eIF-2C 1, Putative RNA-binding protein Q99, Argonaute1' # 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 CGUGACUCU CGUGACUCU B ? 2 'polypeptide(L)' no yes ;GSH(MSE)AQPVIEF(MSE)CEVLDIRNIDEQPKPLTDSQRVRFTKEIKGLKVEVTHCGQ(MSE)KRKYRVCNVTRRPAS HQTFPLQLESGQTVECTVAQYFKQKYNLQLKYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTST(MSE)IK ATARS ; ;GSHMAQPVIEFMCEVLDIRNIDEQPKPLTDSQRVRFTKEIKGLKVEVTHCGQMKRKYRVCNVTRRPASHQTFPLQLESGQ TVECTVAQYFKQKYNLQLKYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIKATARS ; A ? # 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 U n 1 4 G n 1 5 A n 1 6 C n 1 7 U n 1 8 C n 1 9 U n 2 1 GLY n 2 2 SER n 2 3 HIS n 2 4 MSE n 2 5 ALA n 2 6 GLN n 2 7 PRO n 2 8 VAL n 2 9 ILE n 2 10 GLU n 2 11 PHE n 2 12 MSE n 2 13 CYS n 2 14 GLU n 2 15 VAL n 2 16 LEU n 2 17 ASP n 2 18 ILE n 2 19 ARG n 2 20 ASN n 2 21 ILE n 2 22 ASP n 2 23 GLU n 2 24 GLN n 2 25 PRO n 2 26 LYS n 2 27 PRO n 2 28 LEU n 2 29 THR n 2 30 ASP n 2 31 SER n 2 32 GLN n 2 33 ARG n 2 34 VAL n 2 35 ARG n 2 36 PHE n 2 37 THR n 2 38 LYS n 2 39 GLU n 2 40 ILE n 2 41 LYS n 2 42 GLY n 2 43 LEU n 2 44 LYS n 2 45 VAL n 2 46 GLU n 2 47 VAL n 2 48 THR n 2 49 HIS n 2 50 CYS n 2 51 GLY n 2 52 GLN n 2 53 MSE n 2 54 LYS n 2 55 ARG n 2 56 LYS n 2 57 TYR n 2 58 ARG n 2 59 VAL n 2 60 CYS n 2 61 ASN n 2 62 VAL n 2 63 THR n 2 64 ARG n 2 65 ARG n 2 66 PRO n 2 67 ALA n 2 68 SER n 2 69 HIS n 2 70 GLN n 2 71 THR n 2 72 PHE n 2 73 PRO n 2 74 LEU n 2 75 GLN n 2 76 LEU n 2 77 GLU n 2 78 SER n 2 79 GLY n 2 80 GLN n 2 81 THR n 2 82 VAL n 2 83 GLU n 2 84 CYS n 2 85 THR n 2 86 VAL n 2 87 ALA n 2 88 GLN n 2 89 TYR n 2 90 PHE n 2 91 LYS n 2 92 GLN n 2 93 LYS n 2 94 TYR n 2 95 ASN n 2 96 LEU n 2 97 GLN n 2 98 LEU n 2 99 LYS n 2 100 TYR n 2 101 PRO n 2 102 HIS n 2 103 LEU n 2 104 PRO n 2 105 CYS n 2 106 LEU n 2 107 GLN n 2 108 VAL n 2 109 GLY n 2 110 GLN n 2 111 GLU n 2 112 GLN n 2 113 LYS n 2 114 HIS n 2 115 THR n 2 116 TYR n 2 117 LEU n 2 118 PRO n 2 119 LEU n 2 120 GLU n 2 121 VAL n 2 122 CYS n 2 123 ASN n 2 124 ILE n 2 125 VAL n 2 126 ALA n 2 127 GLY n 2 128 GLN n 2 129 ARG n 2 130 CYS n 2 131 ILE n 2 132 LYS n 2 133 LYS n 2 134 LEU n 2 135 THR n 2 136 ASP n 2 137 ASN n 2 138 GLN n 2 139 THR n 2 140 SER n 2 141 THR n 2 142 MSE n 2 143 ILE n 2 144 LYS n 2 145 ALA n 2 146 THR n 2 147 ALA n 2 148 ARG n 2 149 SER 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 EIF2C1 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _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 pET19b _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # 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 I2C1_HUMAN Q9UL18 2 ;AQPVIEFMCEVLDIRNIDEQPKPLTDSQRVRFTKEIKGLKVEVTHCGQMKRKYRVCNVTRRPASHQTFPLQLESGQTVEC TVAQYFKQKYNLQLKYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIKATARS ; 225 ? 2 PDB 1SI3 1SI3 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 1SI3 A 5 ? 149 ? Q9UL18 225 ? 369 ? 225 369 2 2 1SI3 B 1 ? 9 ? 1SI3 401 ? 409 ? 401 409 # 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 1SI3 GLY A 1 ? UNP Q9UL18 ? ? 'CLONING ARTIFACT' 221 1 1 1SI3 SER A 2 ? UNP Q9UL18 ? ? 'CLONING ARTIFACT' 222 2 1 1SI3 HIS A 3 ? UNP Q9UL18 ? ? 'CLONING ARTIFACT' 223 3 1 1SI3 MSE A 4 ? UNP Q9UL18 ? ? 'CLONING ARTIFACT' 224 4 1 1SI3 MSE A 12 ? UNP Q9UL18 MET 232 'MODIFIED RESIDUE' 232 5 1 1SI3 MSE A 53 ? UNP Q9UL18 MET 273 'MODIFIED RESIDUE' 273 6 1 1SI3 MSE A 142 ? UNP Q9UL18 MET 362 'MODIFIED RESIDUE' 362 7 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 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 1SI3 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 50 _exptl_crystal.description ? _exptl_crystal.density_Matthews 2.49 # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.60 _exptl_crystal_grow.pdbx_details 'PEG 1000, POTASSIUM CHLORIDE, HEPES-NAOH, DITHIOTHREITOL, pH 7.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 'PEG 1000' ? ? ? 1 2 1 'POTASSIUM CHLORIDE' ? ? ? 1 3 1 HEPES-NAOH ? ? ? 1 4 1 DITHIOTHREITOL ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2003-10-18 _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 'SI 111' _diffrn_radiation.pdbx_diffrn_protocol SAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9796 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-BM' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-BM _diffrn_source.pdbx_wavelength 0.9796 _diffrn_source.pdbx_wavelength_list 0.9796 # _reflns.entry_id 1SI3 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 2.60 _reflns.number_obs 6431 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.115 _reflns.pdbx_netI_over_sigmaI 28.6 _reflns.B_iso_Wilson_estimate 59.2 _reflns.pdbx_redundancy 12.6 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.60 _reflns_shell.d_res_low 2.69 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.663 _reflns_shell.meanI_over_sigI_obs 3.4 _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 1SI3 _refine.ls_number_reflns_obs 5908 _refine.ls_number_reflns_all 6310 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.83 _refine.ls_d_res_high 2.60 _refine.ls_percent_reflns_obs 93.6 _refine.ls_R_factor_obs 0.247 _refine.ls_R_factor_all 0.253 _refine.ls_R_factor_R_work 0.247 _refine.ls_R_factor_R_free 0.304 _refine.ls_R_factor_R_free_error 0.012 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 593 _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 58.9 _refine.aniso_B[1][1] 3.73 _refine.aniso_B[2][2] 3.73 _refine.aniso_B[3][3] -7.47 _refine.aniso_B[1][2] 4.90 _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 0.317842 _refine.solvent_model_param_bsol 35.0057 _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 SAD _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 1SI3 _refine_analyze.Luzzati_coordinate_error_obs 0.41 _refine_analyze.Luzzati_sigma_a_obs 0.48 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.59 _refine_analyze.Luzzati_sigma_a_free 0.58 _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 977 _refine_hist.pdbx_number_atoms_nucleic_acid 185 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 1177 _refine_hist.d_res_high 2.60 _refine_hist.d_res_low 19.83 # 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 21.0 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.17 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.60 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 2.77 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 1.90 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 3.00 2.50 ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 10 _refine_ls_shell.d_res_high 2.60 _refine_ls_shell.d_res_low 2.69 _refine_ls_shell.number_reflns_R_work 503 _refine_ls_shell.R_factor_R_work 0.396 _refine_ls_shell.percent_reflns_obs 89.8 _refine_ls_shell.R_factor_R_free 0.501 _refine_ls_shell.R_factor_R_free_error 0.066 _refine_ls_shell.percent_reflns_R_free 10.3 _refine_ls_shell.number_reflns_R_free 58 _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_REP.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 3 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' 4 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' # _struct.entry_id 1SI3 _struct.title 'Crystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like duplex' _struct.pdbx_descriptor ;Eukaryotic translation initiation factor 2C 1/5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3' ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1SI3 _struct_keywords.pdbx_keywords 'GENE REGULATION/RNA' _struct_keywords.text 'PROTEIN-RNA COMPLEX, RNA INTERFERENCE, DOUBLE HELIX, OVERHANG, GENE REGULATION-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 ? # _struct_biol.id 1 _struct_biol.details ;The biological assemble consists of two PAZ domains bound to each end of a 9-mer siRNA-like duplex generated from the protein monomer and the 9-mer single stranded RNA in the asymmetric unit by the operation: -X+1,-Y+2,Z. ; _struct_biol.pdbx_parent_biol_id ? # 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 VAL B 8 ? ASP B 17 ? VAL A 228 ASP A 237 1 ? 10 HELX_P HELX_P2 2 THR B 29 ? LYS B 41 ? THR A 249 LYS A 261 1 ? 13 HELX_P HELX_P3 3 VAL B 86 ? LYS B 93 ? VAL A 306 LYS A 313 1 ? 8 # _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 covale1 covale ? ? B MSE 4 C ? ? ? 1_555 B ALA 5 N ? ? A MSE 224 A ALA 225 1_555 ? ? ? ? ? ? ? 1.328 ? covale2 covale ? ? B PHE 11 C ? ? ? 1_555 B MSE 12 N ? ? A PHE 231 A MSE 232 1_555 ? ? ? ? ? ? ? 1.331 ? covale3 covale ? ? B MSE 12 C ? ? ? 1_555 B CYS 13 N ? ? A MSE 232 A CYS 233 1_555 ? ? ? ? ? ? ? 1.326 ? covale4 covale ? ? B GLN 52 C ? ? ? 1_555 B MSE 53 N ? ? A GLN 272 A MSE 273 1_555 ? ? ? ? ? ? ? 1.321 ? covale5 covale ? ? B MSE 53 C ? ? ? 1_555 B LYS 54 N ? ? A MSE 273 A LYS 274 1_555 ? ? ? ? ? ? ? 1.331 ? hydrog1 hydrog ? ? A C 1 N4 ? ? ? 1_555 A U 7 O4 ? ? B C 401 B U 407 4_675 ? ? ? ? ? ? 'C-U MISPAIR' ? ? hydrog2 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 6 N3 ? ? B G 402 B C 406 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 6 O2 ? ? B G 402 B C 406 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 6 N4 ? ? B G 402 B C 406 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 7 O4 ? ? B G 402 B U 407 4_675 ? ? ? ? ? ? 'G-U MISPAIR' ? ? hydrog6 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 5 N1 ? ? B U 403 B A 405 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 5 N6 ? ? B U 403 B A 405 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 3 N3 ? ? B A 405 B U 403 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 3 O4 ? ? B A 405 B U 403 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 2 N1 ? ? B C 406 B G 402 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 2 O6 ? ? B C 406 B G 402 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 2 N2 ? ? B C 406 B G 402 4_675 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A U 7 O4 ? ? ? 1_555 A C 1 N4 ? ? B U 407 B C 401 4_675 ? ? ? ? ? ? 'U-C MISPAIR' ? ? hydrog14 hydrog ? ? A U 7 O4 ? ? ? 1_555 A G 2 N1 ? ? B U 407 B G 402 4_675 ? ? ? ? ? ? 'U-G MISPAIR' ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 6 ? 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 A 4 5 ? anti-parallel A 5 6 ? 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 GLN B 6 ? PRO B 7 ? GLN A 226 PRO A 227 A 2 CYS B 122 ? ILE B 124 ? CYS A 342 ILE A 344 A 3 LYS B 44 ? VAL B 47 ? LYS A 264 VAL A 267 A 4 LYS B 56 ? PRO B 66 ? LYS A 276 PRO A 286 A 5 PRO B 104 ? VAL B 108 ? PRO A 324 VAL A 328 A 6 THR B 115 ? PRO B 118 ? THR A 335 PRO A 338 B 1 THR B 71 ? PRO B 73 ? THR A 291 PRO A 293 B 2 GLU B 83 ? THR B 85 ? GLU A 303 THR A 305 # 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 GLN B 6 ? N GLN A 226 O ILE B 124 ? O ILE A 344 A 2 3 O ASN B 123 ? O ASN A 343 N GLU B 46 ? N GLU A 266 A 3 4 N VAL B 45 ? N VAL A 265 O TYR B 57 ? O TYR A 277 A 4 5 N THR B 63 ? N THR A 283 O CYS B 105 ? O CYS A 325 A 5 6 N LEU B 106 ? N LEU A 326 O LEU B 117 ? O LEU A 337 B 1 2 N PHE B 72 ? N PHE A 292 O CYS B 84 ? O CYS A 304 # _database_PDB_matrix.entry_id 1SI3 _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 1SI3 _atom_sites.fract_transf_matrix[1][1] 0.010020 _atom_sites.fract_transf_matrix[1][2] 0.005785 _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] 0.011570 _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] 0.028626 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S SE # 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 1 401 401 C CYT B . n A 1 2 G 2 402 402 G GUA B . n A 1 3 U 3 403 403 U URI B . n A 1 4 G 4 404 404 G GUA B . n A 1 5 A 5 405 405 A ADE B . n A 1 6 C 6 406 406 C CYT B . n A 1 7 U 7 407 407 U URI B . n A 1 8 C 8 408 408 C CYT B . n A 1 9 U 9 409 409 U URI B . n B 2 1 GLY 1 221 ? ? ? A . n B 2 2 SER 2 222 ? ? ? A . n B 2 3 HIS 3 223 ? ? ? A . n B 2 4 MSE 4 224 224 MSE MSE A . n B 2 5 ALA 5 225 225 ALA ALA A . n B 2 6 GLN 6 226 226 GLN GLN A . n B 2 7 PRO 7 227 227 PRO PRO A . n B 2 8 VAL 8 228 228 VAL VAL A . n B 2 9 ILE 9 229 229 ILE ILE A . n B 2 10 GLU 10 230 230 GLU GLU A . n B 2 11 PHE 11 231 231 PHE PHE A . n B 2 12 MSE 12 232 232 MSE MSE A . n B 2 13 CYS 13 233 233 CYS CYS A . n B 2 14 GLU 14 234 234 GLU GLU A . n B 2 15 VAL 15 235 235 VAL VAL A . n B 2 16 LEU 16 236 236 LEU LEU A . n B 2 17 ASP 17 237 237 ASP ASP A . n B 2 18 ILE 18 238 238 ILE ILE A . n B 2 19 ARG 19 239 239 ARG ARG A . n B 2 20 ASN 20 240 240 ASN ASN A . n B 2 21 ILE 21 241 241 ILE ILE A . n B 2 22 ASP 22 242 242 ASP ASP A . n B 2 23 GLU 23 243 243 GLU GLU A . n B 2 24 GLN 24 244 244 GLN GLN A . n B 2 25 PRO 25 245 245 PRO PRO A . n B 2 26 LYS 26 246 246 LYS LYS A . n B 2 27 PRO 27 247 247 PRO PRO A . n B 2 28 LEU 28 248 248 LEU LEU A . n B 2 29 THR 29 249 249 THR THR A . n B 2 30 ASP 30 250 250 ASP ASP A . n B 2 31 SER 31 251 251 SER SER A . n B 2 32 GLN 32 252 252 GLN GLN A . n B 2 33 ARG 33 253 253 ARG ARG A . n B 2 34 VAL 34 254 254 VAL VAL A . n B 2 35 ARG 35 255 255 ARG ARG A . n B 2 36 PHE 36 256 256 PHE PHE A . n B 2 37 THR 37 257 257 THR THR A . n B 2 38 LYS 38 258 258 LYS LYS A . n B 2 39 GLU 39 259 259 GLU GLU A . n B 2 40 ILE 40 260 260 ILE ILE A . n B 2 41 LYS 41 261 261 LYS LYS A . n B 2 42 GLY 42 262 262 GLY GLY A . n B 2 43 LEU 43 263 263 LEU LEU A . n B 2 44 LYS 44 264 264 LYS LYS A . n B 2 45 VAL 45 265 265 VAL VAL A . n B 2 46 GLU 46 266 266 GLU GLU A . n B 2 47 VAL 47 267 267 VAL VAL A . n B 2 48 THR 48 268 268 THR THR A . n B 2 49 HIS 49 269 269 HIS HIS A . n B 2 50 CYS 50 270 270 CYS CYS A . n B 2 51 GLY 51 271 271 GLY GLY A . n B 2 52 GLN 52 272 272 GLN GLN A . n B 2 53 MSE 53 273 273 MSE MSE A . n B 2 54 LYS 54 274 274 LYS LYS A . n B 2 55 ARG 55 275 275 ARG ARG A . n B 2 56 LYS 56 276 276 LYS LYS A . n B 2 57 TYR 57 277 277 TYR TYR A . n B 2 58 ARG 58 278 278 ARG ARG A . n B 2 59 VAL 59 279 279 VAL VAL A . n B 2 60 CYS 60 280 280 CYS CYS A . n B 2 61 ASN 61 281 281 ASN ASN A . n B 2 62 VAL 62 282 282 VAL VAL A . n B 2 63 THR 63 283 283 THR THR A . n B 2 64 ARG 64 284 284 ARG ARG A . n B 2 65 ARG 65 285 285 ARG ARG A . n B 2 66 PRO 66 286 286 PRO PRO A . n B 2 67 ALA 67 287 287 ALA ALA A . n B 2 68 SER 68 288 288 SER SER A . n B 2 69 HIS 69 289 289 HIS HIS A . n B 2 70 GLN 70 290 290 GLN GLN A . n B 2 71 THR 71 291 291 THR THR A . n B 2 72 PHE 72 292 292 PHE PHE A . n B 2 73 PRO 73 293 293 PRO PRO A . n B 2 74 LEU 74 294 294 LEU LEU A . n B 2 75 GLN 75 295 295 GLN GLN A . n B 2 76 LEU 76 296 ? ? ? A . n B 2 77 GLU 77 297 ? ? ? A . n B 2 78 SER 78 298 ? ? ? A . n B 2 79 GLY 79 299 ? ? ? A . n B 2 80 GLN 80 300 ? ? ? A . n B 2 81 THR 81 301 ? ? ? A . n B 2 82 VAL 82 302 302 VAL VAL A . n B 2 83 GLU 83 303 303 GLU GLU A . n B 2 84 CYS 84 304 304 CYS CYS A . n B 2 85 THR 85 305 305 THR THR A . n B 2 86 VAL 86 306 306 VAL VAL A . n B 2 87 ALA 87 307 307 ALA ALA A . n B 2 88 GLN 88 308 308 GLN GLN A . n B 2 89 TYR 89 309 309 TYR TYR A . n B 2 90 PHE 90 310 310 PHE PHE A . n B 2 91 LYS 91 311 311 LYS LYS A . n B 2 92 GLN 92 312 312 GLN GLN A . n B 2 93 LYS 93 313 313 LYS LYS A . n B 2 94 TYR 94 314 314 TYR TYR A . n B 2 95 ASN 95 315 315 ASN ASN A . n B 2 96 LEU 96 316 316 LEU LEU A . n B 2 97 GLN 97 317 317 GLN GLN A . n B 2 98 LEU 98 318 318 LEU LEU A . n B 2 99 LYS 99 319 319 LYS LYS A . n B 2 100 TYR 100 320 320 TYR TYR A . n B 2 101 PRO 101 321 321 PRO PRO A . n B 2 102 HIS 102 322 322 HIS HIS A . n B 2 103 LEU 103 323 323 LEU LEU A . n B 2 104 PRO 104 324 324 PRO PRO A . n B 2 105 CYS 105 325 325 CYS CYS A . n B 2 106 LEU 106 326 326 LEU LEU A . n B 2 107 GLN 107 327 327 GLN GLN A . n B 2 108 VAL 108 328 328 VAL VAL A . n B 2 109 GLY 109 329 329 GLY GLY A . n B 2 110 GLN 110 330 330 GLN GLN A . n B 2 111 GLU 111 331 331 GLU GLU A . n B 2 112 GLN 112 332 332 GLN GLN A . n B 2 113 LYS 113 333 333 LYS LYS A . n B 2 114 HIS 114 334 334 HIS HIS A . n B 2 115 THR 115 335 335 THR THR A . n B 2 116 TYR 116 336 336 TYR TYR A . n B 2 117 LEU 117 337 337 LEU LEU A . n B 2 118 PRO 118 338 338 PRO PRO A . n B 2 119 LEU 119 339 339 LEU LEU A . n B 2 120 GLU 120 340 340 GLU GLU A . n B 2 121 VAL 121 341 341 VAL VAL A . n B 2 122 CYS 122 342 342 CYS CYS A . n B 2 123 ASN 123 343 343 ASN ASN A . n B 2 124 ILE 124 344 344 ILE ILE A . n B 2 125 VAL 125 345 345 VAL VAL A . n B 2 126 ALA 126 346 346 ALA ALA A . n B 2 127 GLY 127 347 347 GLY GLY A . n B 2 128 GLN 128 348 348 GLN GLN A . n B 2 129 ARG 129 349 349 ARG ARG A . n B 2 130 CYS 130 350 ? ? ? A . n B 2 131 ILE 131 351 ? ? ? A . n B 2 132 LYS 132 352 ? ? ? A . n B 2 133 LYS 133 353 ? ? ? A . n B 2 134 LEU 134 354 ? ? ? A . n B 2 135 THR 135 355 ? ? ? A . n B 2 136 ASP 136 356 ? ? ? A . n B 2 137 ASN 137 357 ? ? ? A . n B 2 138 GLN 138 358 ? ? ? A . n B 2 139 THR 139 359 ? ? ? A . n B 2 140 SER 140 360 ? ? ? A . n B 2 141 THR 141 361 ? ? ? A . n B 2 142 MSE 142 362 ? ? ? A . n B 2 143 ILE 143 363 ? ? ? A . n B 2 144 LYS 144 364 ? ? ? A . n B 2 145 ALA 145 365 ? ? ? A . n B 2 146 THR 146 366 ? ? ? A . n B 2 147 ALA 147 367 ? ? ? A . n B 2 148 ARG 148 368 ? ? ? A . n B 2 149 SER 149 369 ? ? ? A . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 B MSE 4 A MSE 224 ? MET SELENOMETHIONINE 2 B MSE 12 A MSE 232 ? MET SELENOMETHIONINE 3 B MSE 53 A MSE 273 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 4_675 -x+1,-y+2,z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 172.8569385446 0.0000000000 0.0000000000 1.0000000000 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 2004-05-25 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 # _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' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SCALEPACK 'data scaling' . ? 2 CNS refinement 1.1 ? 3 HKL-2000 'data reduction' . ? 4 CNS phasing 1.1 ? 5 # 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 ASN A 240 ? ? -92.47 38.44 2 1 PRO A 245 ? ? -79.10 29.75 3 1 ASN A 281 ? ? 176.21 171.60 4 1 LYS A 333 ? ? -160.35 -16.11 # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id U _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 407 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.067 _pdbx_validate_planes.type 'SIDE CHAIN' # 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 A MSE 224 ? CG ? B MSE 4 CG 2 1 Y 1 A MSE 224 ? SE ? B MSE 4 SE 3 1 Y 1 A MSE 224 ? CE ? B MSE 4 CE 4 1 Y 1 A GLN 295 ? CG ? B GLN 75 CG 5 1 Y 1 A GLN 295 ? CD ? B GLN 75 CD 6 1 Y 1 A GLN 295 ? OE1 ? B GLN 75 OE1 7 1 Y 1 A GLN 295 ? NE2 ? B GLN 75 NE2 # 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 A GLY 221 ? B GLY 1 2 1 Y 1 A SER 222 ? B SER 2 3 1 Y 1 A HIS 223 ? B HIS 3 4 1 Y 1 A LEU 296 ? B LEU 76 5 1 Y 1 A GLU 297 ? B GLU 77 6 1 Y 1 A SER 298 ? B SER 78 7 1 Y 1 A GLY 299 ? B GLY 79 8 1 Y 1 A GLN 300 ? B GLN 80 9 1 Y 1 A THR 301 ? B THR 81 10 1 Y 1 A CYS 350 ? B CYS 130 11 1 Y 1 A ILE 351 ? B ILE 131 12 1 Y 1 A LYS 352 ? B LYS 132 13 1 Y 1 A LYS 353 ? B LYS 133 14 1 Y 1 A LEU 354 ? B LEU 134 15 1 Y 1 A THR 355 ? B THR 135 16 1 Y 1 A ASP 356 ? B ASP 136 17 1 Y 1 A ASN 357 ? B ASN 137 18 1 Y 1 A GLN 358 ? B GLN 138 19 1 Y 1 A THR 359 ? B THR 139 20 1 Y 1 A SER 360 ? B SER 140 21 1 Y 1 A THR 361 ? B THR 141 22 1 Y 1 A MSE 362 ? B MSE 142 23 1 Y 1 A ILE 363 ? B ILE 143 24 1 Y 1 A LYS 364 ? B LYS 144 25 1 Y 1 A ALA 365 ? B ALA 145 26 1 Y 1 A THR 366 ? B THR 146 27 1 Y 1 A ALA 367 ? B ALA 147 28 1 Y 1 A ARG 368 ? B ARG 148 29 1 Y 1 A SER 369 ? B SER 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1SI3 'double helix' 1SI3 '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 A U 7 4_675 0.255 0.162 -1.973 -24.273 -22.411 -37.448 1 B_C401:U407_B B 401 ? B 407 ? ? ? 1 A G 2 1_555 A C 6 4_675 -0.327 0.128 -0.199 -15.620 -9.505 1.374 2 B_G402:C406_B B 402 ? B 406 ? 19 1 1 A U 3 1_555 A A 5 4_675 0.184 0.080 0.250 13.876 -3.768 8.264 3 B_U403:A405_B B 403 ? B 405 ? 20 1 1 A C 1 1_555 A U 7 1_555 0.255 0.162 -1.973 -24.273 -22.411 -37.448 4 B_C401:U407_B B 401 ? B 407 ? ? ? 1 A G 2 1_555 A C 6 1_555 -0.327 0.128 -0.199 -15.620 -9.505 1.374 5 B_G402:C406_B B 402 ? B 406 ? 19 1 1 A U 3 1_555 A A 5 1_555 0.184 0.080 0.250 13.876 -3.768 8.264 6 B_U403:A405_B B 403 ? B 405 ? 20 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 A U 7 4_675 A G 2 1_555 A C 6 4_675 1.540 -0.943 3.156 -13.254 15.348 25.498 -3.818 -4.595 1.435 29.534 25.504 32.474 1 BB_C401G402:C406U407_BB B 401 ? B 407 ? B 402 ? B 406 ? 1 A G 2 1_555 A C 6 4_675 A U 3 1_555 A A 5 4_675 0.671 -1.487 2.699 -7.044 -2.624 33.391 -2.189 -2.054 2.614 -4.496 12.069 34.203 2 BB_G402U403:A405C406_BB B 402 ? B 406 ? B 403 ? B 405 ? 1 A C 1 1_555 A U 7 1_555 A G 2 1_555 A C 6 1_555 1.540 -0.943 3.156 -13.254 15.348 25.498 -3.818 -4.595 1.435 29.534 25.504 32.474 3 BB_C401G402:C406U407_BB B 401 ? B 407 ? B 402 ? B 406 ? 1 A G 2 1_555 A C 6 1_555 A U 3 1_555 A A 5 1_555 0.671 -1.487 2.699 -7.044 -2.624 33.391 -2.189 -2.054 2.614 -4.496 12.069 34.203 4 BB_G402U403:A405C406_BB B 402 ? B 406 ? B 403 ? B 405 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # 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 HOH 1 501 501 HOH WAT A . C 3 HOH 2 502 502 HOH WAT A . C 3 HOH 3 503 503 HOH WAT A . C 3 HOH 4 504 504 HOH WAT A . C 3 HOH 5 505 505 HOH WAT A . C 3 HOH 6 506 506 HOH WAT A . C 3 HOH 7 507 507 HOH WAT A . C 3 HOH 8 508 508 HOH WAT A . C 3 HOH 9 509 509 HOH WAT A . C 3 HOH 10 510 510 HOH WAT A . C 3 HOH 11 511 511 HOH WAT A . C 3 HOH 12 512 512 HOH WAT A . C 3 HOH 13 513 513 HOH WAT A . C 3 HOH 14 514 514 HOH WAT A . C 3 HOH 15 515 515 HOH WAT A . #