data_1XJ9 # _entry.id 1XJ9 # _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 1XJ9 NDB UP0006 RCSB RCSB030416 WWPDB D_1000030416 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1PUP 'peptide nucleic acid duplex' unspecified PDB 1PDT 'Peptide nucleic acid complexed with DNA' unspecified PDB 1PNN 'peptide nucleic acid/DNA triplex' unspecified PDB 176D 'peptide nucleic acid complexed with RNA' unspecified PDB 1NR8 'A D-Lysine-Based Chiral Peptide nucleic acid/DNA Duplex' unspecified PDB 1RRU 'peptide nucleic acid with L-Lys in C-terminus' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1XJ9 _pdbx_database_status.recvd_initial_deposition_date 2004-09-23 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Petersson, B.' 1 'Nielsen, B.B.' 2 'Rasmussen, H.' 3 'Larsen, I.K.' 4 'Gajhede, M.' 5 'Nielsen, P.E.' 6 'Kastrup, J.S.' 7 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Crystal Structure of a Partly Self-Complementary Peptide Nucleic Acid (PNA) Oligomer Showing a Duplex-Triplex Network' J.Am.Chem.Soc. 127 1424 1430 2005 JACSAT US 0002-7863 0004 ? 15686374 10.1021/ja0458726 1 'Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution' Nat.Struct.Biol. 4 98 101 1997 NSBIEW US 1072-8368 2024 ? 9033585 10.1038/nsb0297-98 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Petersson, B.' 1 primary 'Nielsen, B.B.' 2 primary 'Rasmussen, H.' 3 primary 'Larsen, I.K.' 4 primary 'Gajhede, M.' 5 primary 'Nielsen, P.E.' 6 primary 'Kastrup, J.S.' 7 1 'Rasmussen, H.' 8 1 'Kastrup, J.S.' 9 1 'Nielsen, J.N.' 10 1 'Nielsen, J.M.' 11 1 'Nielsen, P.E.' 12 # _cell.entry_id 1XJ9 _cell.length_a 55.600 _cell.length_b 41.900 _cell.length_c 30.100 _cell.angle_alpha 90.00 _cell.angle_beta 117.70 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XJ9 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # 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 'peptide nucleic acid, (H-P(*GPN*TPN*APN*GPN*APN*TPN*CPN*APN*CPN*TPN)-LYS-NH2)' 2803.876 2 ? ? ? ? 2 water nat water 18.015 33 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name PNA # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(GPN)(TPN)(APN)(GPN)(APN)(TPN)(CPN)(APN)(CPN)(TPN)K' _entity_poly.pdbx_seq_one_letter_code_can XXXXXXXXXXK _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GPN n 1 2 TPN n 1 3 APN n 1 4 GPN n 1 5 APN n 1 6 TPN n 1 7 CPN n 1 8 APN n 1 9 CPN n 1 10 TPN n 1 11 LYS n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1XJ9 _struct_ref.pdbx_db_accession 1XJ9 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1XJ9 A 1 ? 11 ? 1XJ9 101 ? 111 ? 101 111 2 1 1XJ9 B 1 ? 11 ? 1XJ9 201 ? 211 ? 201 211 # 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 APN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE ? 'C11 H16 N7 O3 1' 294.290 CPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE ? 'C10 H16 N5 O4 1' 270.265 GPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE ? 'C11 H16 N7 O4 1' 310.289 HOH non-polymer . WATER ? 'H2 O' 18.015 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 TPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE ? 'C11 H17 N4 O5 1' 285.276 # _exptl.entry_id 1XJ9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # loop_ _exptl_crystal.id _exptl_crystal.density_meas _exptl_crystal.density_Matthews _exptl_crystal.density_percent_sol _exptl_crystal.description _exptl_crystal.F_000 _exptl_crystal.preparation 1 ? 2.77 55.59 ? ? ? 2 ? ? ? ? ? ? # loop_ _exptl_crystal_grow.crystal_id _exptl_crystal_grow.method _exptl_crystal_grow.temp _exptl_crystal_grow.temp_details _exptl_crystal_grow.pH _exptl_crystal_grow.pdbx_details _exptl_crystal_grow.pdbx_pH_range 1 'VAPOR DIFFUSION, HANGING DROP' 293 ? ? 'crystal 1: magnesium chloride, PEG 8000, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K' . 2 'VAPOR DIFFUSION, SITTING DROP' 293 ? ? 'crystal 2: isopropanol, calcium chloride, acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K' . # 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 'magnesium chloride' ? ? ? 1 2 1 'PEG 8000' ? ? ? 1 3 1 glycerol ? ? ? 1 4 1 H2O ? ? ? 1 5 2 'PEG 8000' ? ? ? 1 6 2 H2O ? ? ? 2 7 1 isopropanol ? ? ? 2 8 1 'calcium chloride' ? ? ? 2 9 1 acetate ? ? ? 2 10 1 H2O ? ? ? 2 11 2 isopropanol ? ? ? 2 12 2 'calcium chloride' ? ? ? 2 13 2 acetate ? ? ? 2 14 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 293 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1998-02-17 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0000 # _reflns.entry_id 1XJ9 _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 2.6 _reflns.d_resolution_low 30.0 _reflns.number_all 1839 _reflns.number_obs 1839 _reflns.percent_possible_obs 98.6 _reflns.pdbx_Rmerge_I_obs 0.045 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 22.4 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.0 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.60 _reflns_shell.d_res_low 2.69 _reflns_shell.percent_possible_all 95.6 _reflns_shell.Rmerge_I_obs 0.183 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.3 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 172 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1XJ9 _refine.ls_d_res_high 2.6 _refine.ls_d_res_low 27.0 _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 1839 _refine.ls_number_reflns_obs 1517 _refine.ls_number_reflns_R_free 141 _refine.ls_percent_reflns_obs 78.2 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.255 _refine.ls_R_factor_R_free 0.277 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct ;crystal 1: single wavelength protocol. crystal 2: MAD protocol with data collected on 5-bromo-uracil derivative crystal at 0.9177, 0.9185, 0.9110, 0.9218 A. the condition for crystal 2 was as follows. collection data: 05-NOV-2000, temperature(kelvin): 110, PH: 4.80, the details of the source of radiation: synchrotron, EMBL/DESY, HAMBURG beamline BW7A ; _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model Isotropic _refine.B_iso_mean 42.5 _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details 'Own parameter and topology files created' _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _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 1XJ9 _refine_analyze.Luzzati_coordinate_error_obs 0.36 _refine_analyze.Luzzati_sigma_a_obs 0.34 _refine_analyze.Luzzati_d_res_low_obs 5 _refine_analyze.Luzzati_coordinate_error_free 0.42 _refine_analyze.Luzzati_sigma_a_free 0.42 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_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 312 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 33 _refine_hist.number_atoms_total 345 _refine_hist.d_res_high 2.6 _refine_hist.d_res_low 27.0 # 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_angle_deg 1.3 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.60 _refine_ls_shell.d_res_low 2.86 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.344 _refine_ls_shell.percent_reflns_obs 70.9 _refine_ls_shell.R_factor_R_free 0.401 _refine_ls_shell.R_factor_R_free_error 0.092 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 22 _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 ? # _struct.entry_id 1XJ9 _struct.title 'Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network' _struct.pdbx_descriptor "5'-D(*(GPN)P*(TPN)*(APN)*(GPN)*(APN)*(TPN)*(CPN)*(APN)*(CPN)*(TPN)*(LYS)*(NH2))-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1XJ9 _struct_keywords.pdbx_keywords 'PEPTIDE NUCLEIC ACID' _struct_keywords.text 'PNA, peptide nucleic acid, partly self-complementary, duplex-triplex complex, right-handed, left-handed' # 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 1 ? C N N 2 ? D N N 2 ? # loop_ _struct_biol.id _struct_biol.details _struct_biol.pdbx_parent_biol_id 1 ;THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. A right-handed duplex (from chain A) is generated with the symmetry operation: -x+2, y, -z+1. ; ? 2 'A left-handed duplex (from chain B) is generated with the symmetry operation: -x+1, y, -z' ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A APN 3 "C'" A ? ? 1_555 A GPN 4 "N1'" A ? A APN 103 A GPN 104 1_555 ? ? ? ? ? ? ? 1.336 ? covale2 covale ? ? A APN 3 "C'" B ? ? 1_555 A GPN 4 "N1'" B ? A APN 103 A GPN 104 1_555 ? ? ? ? ? ? ? 1.332 ? covale3 covale ? ? A GPN 4 "C'" ? ? ? 1_555 A APN 5 "N1'" ? ? A GPN 104 A APN 105 1_555 ? ? ? ? ? ? ? 1.325 ? covale4 covale ? ? A APN 5 "C'" ? ? ? 1_555 A TPN 6 "N1'" ? ? A APN 105 A TPN 106 1_555 ? ? ? ? ? ? ? 1.329 ? covale5 covale ? ? A TPN 6 "C'" ? ? ? 1_555 A CPN 7 "N1'" ? ? A TPN 106 A CPN 107 1_555 ? ? ? ? ? ? ? 1.337 ? covale6 covale ? ? A CPN 7 "C'" A ? ? 1_555 A APN 8 "N1'" A ? A CPN 107 A APN 108 1_555 ? ? ? ? ? ? ? 1.324 ? covale7 covale ? ? A CPN 7 "C'" B ? ? 1_555 A APN 8 "N1'" B ? A CPN 107 A APN 108 1_555 ? ? ? ? ? ? ? 1.328 ? covale8 covale ? ? A APN 8 "C'" A ? ? 1_555 A CPN 9 "N1'" A ? A APN 108 A CPN 109 1_555 ? ? ? ? ? ? ? 1.333 ? covale9 covale ? ? A APN 8 "C'" B ? ? 1_555 A CPN 9 "N1'" B ? A APN 108 A CPN 109 1_555 ? ? ? ? ? ? ? 1.311 ? covale10 covale ? ? A CPN 9 "C'" ? ? ? 1_555 A TPN 10 "N1'" ? ? A CPN 109 A TPN 110 1_555 ? ? ? ? ? ? ? 1.333 ? covale11 covale ? ? A TPN 10 "C'" ? ? ? 1_555 A LYS 11 N ? ? A TPN 110 A LYS 111 1_555 ? ? ? ? ? ? ? 1.329 ? covale12 covale ? ? B APN 3 "C'" A ? ? 1_555 B GPN 4 "N1'" A ? B APN 203 B GPN 204 1_555 ? ? ? ? ? ? ? 1.339 ? covale13 covale ? ? B APN 3 "C'" B ? ? 1_555 B GPN 4 "N1'" B ? B APN 203 B GPN 204 1_555 ? ? ? ? ? ? ? 1.334 ? covale14 covale ? ? B GPN 4 "C'" ? ? ? 1_555 B APN 5 "N1'" ? ? B GPN 204 B APN 205 1_555 ? ? ? ? ? ? ? 1.335 ? covale15 covale ? ? B APN 5 "C'" ? ? ? 1_555 B TPN 6 "N1'" ? ? B APN 205 B TPN 206 1_555 ? ? ? ? ? ? ? 1.339 ? covale16 covale ? ? B TPN 6 "C'" ? ? ? 1_555 B CPN 7 "N1'" ? ? B TPN 206 B CPN 207 1_555 ? ? ? ? ? ? ? 1.316 ? covale17 covale ? ? B CPN 7 "C'" A ? ? 1_555 B APN 8 "N1'" A ? B CPN 207 B APN 208 1_555 ? ? ? ? ? ? ? 1.325 ? covale18 covale ? ? B CPN 7 "C'" B ? ? 1_555 B APN 8 "N1'" B ? B CPN 207 B APN 208 1_555 ? ? ? ? ? ? ? 1.297 ? covale19 covale ? ? B APN 8 "C'" A ? ? 1_555 B CPN 9 "N1'" A ? B APN 208 B CPN 209 1_555 ? ? ? ? ? ? ? 1.316 ? covale20 covale ? ? B APN 8 "C'" B ? ? 1_555 B CPN 9 "N1'" B ? B APN 208 B CPN 209 1_555 ? ? ? ? ? ? ? 1.307 ? covale21 covale ? ? B CPN 9 "C'" ? ? ? 1_555 B TPN 10 "N1'" ? ? B CPN 209 B TPN 210 1_555 ? ? ? ? ? ? ? 1.336 ? covale22 covale ? ? B TPN 10 "C'" ? ? ? 1_555 B LYS 11 N ? ? B TPN 210 B LYS 211 1_555 ? ? ? ? ? ? ? 1.328 ? hydrog1 hydrog ? ? A GPN 4 N1 ? ? ? 1_555 A CPN 7 N3 ? ? A GPN 104 A CPN 107 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A GPN 4 N2 ? ? ? 1_555 A CPN 7 O2 ? ? A GPN 104 A CPN 107 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A GPN 4 O6 ? ? ? 1_555 A CPN 7 N4 ? ? A GPN 104 A CPN 107 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A APN 5 N1 ? ? ? 1_555 A TPN 6 N3 ? ? A APN 105 A TPN 106 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A APN 5 N6 ? ? ? 1_555 A TPN 6 O4 ? ? A APN 105 A TPN 106 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A TPN 6 N3 ? ? ? 1_555 A APN 5 N1 ? ? A TPN 106 A APN 105 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A TPN 6 O4 ? ? ? 1_555 A APN 5 N6 ? ? A TPN 106 A APN 105 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A CPN 7 N3 ? ? ? 1_555 A GPN 4 N1 ? ? A CPN 107 A GPN 104 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A CPN 7 N4 ? ? ? 1_555 A GPN 4 O6 ? ? A CPN 107 A GPN 104 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A CPN 7 O2 ? ? ? 1_555 A GPN 4 N2 ? ? A CPN 107 A GPN 104 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1XJ9 _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 1XJ9 _atom_sites.fract_transf_matrix[1][1] 0.017986 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009443 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023866 _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] 0.037523 _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 # 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 GPN 1 101 ? ? ? A . n A 1 2 TPN 2 102 ? ? ? A . n A 1 3 APN 3 103 103 APN APN A . n A 1 4 GPN 4 104 104 GPN GPN A . n A 1 5 APN 5 105 105 APN APN A . n A 1 6 TPN 6 106 106 TPN TPN A . n A 1 7 CPN 7 107 107 CPN CPN A . n A 1 8 APN 8 108 108 APN APN A . n A 1 9 CPN 9 109 109 CPN CPN A . n A 1 10 TPN 10 110 110 TPN TPN A . n A 1 11 LYS 11 111 111 LYS LYS A . n B 1 1 GPN 1 201 ? ? ? B . n B 1 2 TPN 2 202 ? ? ? B . n B 1 3 APN 3 203 203 APN APN B . n B 1 4 GPN 4 204 204 GPN GPN B . n B 1 5 APN 5 205 205 APN APN B . n B 1 6 TPN 6 206 206 TPN TPN B . n B 1 7 CPN 7 207 207 CPN CPN B . n B 1 8 APN 8 208 208 APN APN B . n B 1 9 CPN 9 209 209 CPN CPN B . n B 1 10 TPN 10 210 210 TPN TPN B . n B 1 11 LYS 11 211 211 LYS LYS B . 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 A APN 3 A APN 103 ? DA ? 2 A GPN 4 A GPN 104 ? DG ? 3 A APN 5 A APN 105 ? DA ? 4 A TPN 6 A TPN 106 ? DT ? 5 A CPN 7 A CPN 107 ? DC ? 6 A APN 8 A APN 108 ? DA ? 7 A CPN 9 A CPN 109 ? DC ? 8 A TPN 10 A TPN 110 ? DT ? 9 B APN 3 B APN 203 ? DA ? 10 B GPN 4 B GPN 204 ? DG ? 11 B APN 5 B APN 205 ? DA ? 12 B TPN 6 B TPN 206 ? DT ? 13 B CPN 7 B CPN 207 ? DC ? 14 B APN 8 B APN 208 ? DA ? 15 B CPN 9 B CPN 209 ? DC ? 16 B TPN 10 B TPN 210 ? DT ? # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,C 2 1,3 B,D # 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' 2_756 -x+2,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 97.2082544237 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 26.6503481352 3 'crystal symmetry operation' 2_655 -x+1,y,-z -1.0000000000 0.0000000000 0.0000000000 55.6000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 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 2005-02-22 2 'Structure model' 1 1 2008-04-30 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' 'Non-polymer description' 3 3 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 SOLVE phasing . ? 3 CNS refinement . ? 4 # 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 LYS 111 ? C ? A LYS 11 C 2 1 Y 1 A LYS 111 ? O ? A LYS 11 O 3 1 Y 1 A LYS 111 ? CB ? A LYS 11 CB 4 1 Y 1 A LYS 111 ? CG ? A LYS 11 CG 5 1 Y 1 A LYS 111 ? CD ? A LYS 11 CD 6 1 Y 1 A LYS 111 ? CE ? A LYS 11 CE 7 1 Y 1 A LYS 111 ? NZ ? A LYS 11 NZ 8 1 Y 1 B LYS 211 ? C ? B LYS 11 C 9 1 Y 1 B LYS 211 ? O ? B LYS 11 O 10 1 Y 1 B LYS 211 ? CB ? B LYS 11 CB 11 1 Y 1 B LYS 211 ? CG ? B LYS 11 CG 12 1 Y 1 B LYS 211 ? CD ? B LYS 11 CD 13 1 Y 1 B LYS 211 ? CE ? B LYS 11 CE 14 1 Y 1 B LYS 211 ? NZ ? B LYS 11 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 A GPN 101 ? A GPN 1 2 1 Y 1 A TPN 102 ? A TPN 2 3 1 Y 1 B GPN 201 ? B GPN 1 4 1 Y 1 B TPN 202 ? B TPN 2 # _ndb_struct_conf_na.entry_id 1XJ9 _ndb_struct_conf_na.feature 'double 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 GPN 4 1_555 A CPN 7 2_756 -0.460 -0.253 -0.154 4.142 -0.290 -7.427 1 A_GPN104:CPN107_A A 104 ? A 107 ? 19 1 1 A APN 5 1_555 A TPN 6 2_756 0.140 -0.277 -0.287 2.628 -4.308 1.249 2 A_APN105:TPN106_A A 105 ? A 106 ? 20 1 1 A TPN 6 1_555 A APN 5 2_756 -0.140 -0.277 -0.287 -2.628 -4.308 1.249 3 A_TPN106:APN105_A A 106 ? A 105 ? 20 1 1 A CPN 7 1_555 A GPN 4 2_756 0.460 -0.253 -0.154 -4.142 -0.290 -7.427 4 A_CPN107:GPN104_A A 107 ? A 104 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A GPN 4 1_555 A CPN 7 2_756 A APN 5 1_555 A TPN 6 2_756 0.303 -2.710 3.383 0.126 1.592 22.204 -7.621 -0.737 3.185 4.127 -0.328 22.261 1 AA_GPN104APN105:TPN106CPN107_AA A 104 ? A 107 ? A 105 ? A 106 ? 1 A APN 5 1_555 A TPN 6 2_756 A TPN 6 1_555 A APN 5 2_756 0.000 -2.925 3.515 0.000 -4.562 15.349 -6.496 0.000 4.200 -16.607 0.000 16.009 2 AA_APN105TPN106:APN105TPN106_AA A 105 ? A 106 ? A 106 ? A 105 ? 1 A TPN 6 1_555 A APN 5 2_756 A CPN 7 1_555 A GPN 4 2_756 -0.303 -2.710 3.383 -0.126 1.592 22.204 -7.621 0.737 3.185 4.127 0.328 22.261 3 AA_TPN106CPN107:GPN104APN105_AA A 106 ? A 105 ? A 107 ? A 104 ? # _pdbx_entity_nonpoly.entity_id 2 _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 2 HOH 1 1 1 HOH HOH A . C 2 HOH 2 4 4 HOH HOH A . C 2 HOH 3 6 6 HOH HOH A . C 2 HOH 4 8 8 HOH HOH A . C 2 HOH 5 9 9 HOH HOH A . C 2 HOH 6 11 11 HOH HOH A . C 2 HOH 7 12 12 HOH HOH A . C 2 HOH 8 13 13 HOH HOH A . C 2 HOH 9 14 14 HOH HOH A . C 2 HOH 10 16 16 HOH HOH A . C 2 HOH 11 17 17 HOH HOH A . C 2 HOH 12 20 20 HOH HOH A . C 2 HOH 13 22 22 HOH HOH A . C 2 HOH 14 24 24 HOH HOH A . C 2 HOH 15 25 25 HOH HOH A . C 2 HOH 16 30 30 HOH HOH A . C 2 HOH 17 31 31 HOH HOH A . C 2 HOH 18 32 32 HOH HOH A . C 2 HOH 19 33 33 HOH HOH A . D 2 HOH 1 2 2 HOH HOH B . D 2 HOH 2 3 3 HOH HOH B . D 2 HOH 3 5 5 HOH HOH B . D 2 HOH 4 7 7 HOH HOH B . D 2 HOH 5 10 10 HOH HOH B . D 2 HOH 6 15 15 HOH HOH B . D 2 HOH 7 18 18 HOH HOH B . D 2 HOH 8 19 19 HOH HOH B . D 2 HOH 9 21 21 HOH HOH B . D 2 HOH 10 23 23 HOH HOH B . D 2 HOH 11 26 26 HOH HOH B . D 2 HOH 12 27 27 HOH HOH B . D 2 HOH 13 28 28 HOH HOH B . D 2 HOH 14 29 29 HOH HOH B . #