data_2PLB # _entry.id 2PLB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 2PLB pdb_00002plb 10.2210/pdb2plb/pdb NDB AD0070 ? ? RCSB RCSB042504 ? ? WWPDB D_1000042504 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 115D 'D-(GG[Br]UA[Br]UACC), with the two Br replacing THY methyl groups' unspecified PDB 1VJ4 'D-(GGTATACC) initial structure' unspecified PDB 2PKV 'D-(GGTATACC) ambient pressure' unspecified PDB 2PL4 'D-(GGTATACC) under 0.55 GPA hydrostatic pressure' unspecified PDB 2PL8 'D-(GGTATACC) under 1.04 GPA hydrostatic pressure' unspecified PDB 2PLO 'D-(GTATACC) LOW TEMPERATURE (100K)' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2PLB _pdbx_database_status.recvd_initial_deposition_date 2007-04-19 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Prange, T.' 1 'Girard, E.' 2 'Kahn, R.' 3 'Fourme, R.' 4 # 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 'Adaptation of the base-paired double-helix molecular architecture to extreme pressure.' 'Nucleic Acids Res.' 35 4800 4808 2007 NARHAD UK 0305-1048 0389 ? 17617642 10.1093/nar/gkm511 1 'Coexistence of A-and B-Form DNA in a Single Crystal Lattice' Nature 337 190 193 1989 NATUAS UK 0028-0836 0006 ? 2911354 10.1038/337190a0 2 'High-pressure protein crystallography (HPPX): Instrumentation, methodology and results on lysozyme crystals' 'J.Synchrotron Radia.' 8 1149 1156 2001 JSYRES DK 0909-0495 1210 ? 11524565 10.1107/S0909049501011037 3 ;High pressure macromolecular crystallography: The 140 MPa crystal structure at 2.3 A resolution of urate oxidase, A 135 KD tetrameric assembly ; 'BIOCHEM.BIOPHYS.ACTA PROTEINS & PROTEOMICS' 1764 391 397 2006 ? NE 1570-9639 ? ? 16478683 10.1016/j.bbapap.2006.01.006 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Girard, E.' 1 ? primary 'Prange, T.' 2 ? primary 'Dhaussy, A.C.' 3 ? primary 'Migianu-Griffoni, E.' 4 ? primary 'Lecouvey, M.' 5 ? primary 'Chervin, J.C.' 6 ? primary 'Mezouar, M.' 7 ? primary 'Kahn, R.' 8 ? primary 'Fourme, R.' 9 ? 1 'Doucet, J.' 10 ? 1 'Benoit, J.-P.' 11 ? 1 'Cruse, W.B.T.' 12 ? 1 'Prange, T.' 13 ? 1 'Kennard, O.' 14 ? 2 'Fourme, R.' 15 ? 2 'Kahn, R.' 16 ? 2 'Mezouar, M.' 17 ? 2 'Girard, E.' 18 ? 2 'Horentrup, C.' 19 ? 2 'Prange, T.' 20 ? 2 'Ascone, I.' 21 ? 3 ;Colloc'h, N. ; 22 ? 3 'Girard, E.' 23 ? 3 'Dhaussy, A.C.' 24 ? 3 'Kahn, R.' 25 ? 3 'Ascone, I.' 26 ? 3 'Mezouar, M.' 27 ? 3 'Fourme, R.' 28 ? # _cell.entry_id 2PLB _cell.length_a 42.830 _cell.length_b 42.830 _cell.length_c 40.300 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2PLB _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _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 "5'-D(*DGP*DGP*DTP*DAP*DTP*DAP*DCP*DC)-3'" 2426.617 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 water nat water 18.015 76 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DG)(DG)(DT)(DA)(DT)(DA)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GGTATACC _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 DG n 1 2 DG n 1 3 DT n 1 4 DA n 1 5 DT n 1 6 DA n 1 7 DC n 1 8 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'synthetic DNA octamer' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2PLB _struct_ref.pdbx_db_accession 2PLB _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 2PLB A 1 ? 8 ? 2PLB 1 ? 8 ? 1 8 2 1 2PLB B 1 ? 8 ? 2PLB 1 ? 8 ? 1 8 # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # _exptl.entry_id 2PLB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.11 _exptl_crystal.density_percent_sol 41.84 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details ;20 mg of DNA dissolved in 0.2 ml of 15% MPD solution cacodylate buffer 10-2 M. Additives: 10-5 M sodium azide, 10-2 M MgCl2, 2.10-2 M spermine chloride. Reservoir: same solution but 50 % MPD, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K ; _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 '15% MPD' ? ? ? 1 2 1 'cacodylate buffer' ? ? ? 1 3 1 'sodium azide' ? ? ? 1 4 1 MgCl2 ? ? ? 1 5 1 'spermine chloride' ? ? ? 1 6 2 '50% MPD' ? ? ? 1 7 2 'cacodylate buffer' ? ? ? 1 8 2 'sodium azide' ? ? ? 1 9 2 MgCl2 ? ? ? 1 10 2 'spermine chloride' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 295 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'MAR scanner 345 mm plate' _diffrn_detector.pdbx_collection_date 2006-11-10 _diffrn_detector.details '2 crystals, parallel beam, no focusing' # _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 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.3738 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID27' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID27 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.3738 # _reflns.entry_id 2PLB _reflns.observed_criterion_sigma_F 2 _reflns.observed_criterion_sigma_I 4 _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 10 _reflns.number_all 5582 _reflns.number_obs 5518 _reflns.percent_possible_obs 98.5 _reflns.pdbx_Rmerge_I_obs 0.047 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 11.4 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.1 _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 1.6 _reflns_shell.d_res_low 1.65 _reflns_shell.percent_possible_all 99. _reflns_shell.Rmerge_I_obs 0.331 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.2 _reflns_shell.pdbx_redundancy 3.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 490 _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 2PLB _refine.ls_number_reflns_obs 5518 _refine.ls_number_reflns_all 5582 _refine.pdbx_ls_sigma_I 4 _refine.pdbx_ls_sigma_F 2 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 1.60 _refine.ls_percent_reflns_obs 99.9 _refine.ls_R_factor_obs 0.1866 _refine.ls_R_factor_all 0.219 _refine.ls_R_factor_R_work 0.1806 _refine.ls_R_factor_R_free 0.222 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 440 _refine.ls_number_parameters 1747 _refine.ls_number_restraints 1776 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details 'One sugar and one phosphate group are disordered (two positions). The spermine molecule is also disordered' _refine.pdbx_starting_model 2PL8 _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model 'individual restrained B factors' _refine.pdbx_stereochemistry_target_values 'ENGH AND 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.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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 2PLB _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 2 _refine_analyze.occupancy_sum_hydrogen 178.00 _refine_analyze.occupancy_sum_non_hydrogen 412.00 _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 0 _refine_hist.pdbx_number_atoms_nucleic_acid 322 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 76 _refine_hist.number_atoms_total 412 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 10.00 # 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 s_bond_d 0.013 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.030 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.0011 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.008 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.020 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.063 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.000 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 2PLB _pdbx_refine.R_factor_all_no_cutoff 0.219 _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff 0.2021 _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff 4600 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 2PLB _struct.title 'D(GTATACC) under hydrostatic pressure of 1.39 GPa' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2PLB _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, HIGH-PRESSURE' # 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 3 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 2 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 2 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 2 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 3 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 3 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 4 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 4 B DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 5 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 5 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 6 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 6 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 7 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 7 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 7 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id SPM _struct_site.pdbx_auth_seq_id 20 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 3 _struct_site.details 'BINDING SITE FOR RESIDUE SPM B 20' # 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 3 DT B 5 ? DT B 5 . ? 1_555 ? 2 AC1 3 DA B 6 ? DA B 6 . ? 1_555 ? 3 AC1 3 HOH E . ? HOH B 133 . ? 1_555 ? # _database_PDB_matrix.entry_id 2PLB _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 2PLB _atom_sites.fract_transf_matrix[1][1] 0.023348 _atom_sites.fract_transf_matrix[1][2] 0.013480 _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] 0.026960 _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] 0.024814 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n B 1 1 DG 1 1 1 DG G B . n B 1 2 DG 2 2 2 DG G B . n B 1 3 DT 3 3 3 DT T B . n B 1 4 DA 4 4 4 DA A B . n B 1 5 DT 5 5 5 DT T B . n B 1 6 DA 6 6 6 DA A B . n B 1 7 DC 7 7 7 DC C B . n B 1 8 DC 8 8 8 DC C B . 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 2 SPM 1 20 20 SPM SPM B . D 3 HOH 1 102 102 HOH HOH A . D 3 HOH 2 103 103 HOH HOH A . D 3 HOH 3 104 104 HOH HOH A . D 3 HOH 4 105 105 HOH HOH A . D 3 HOH 5 107 107 HOH HOH A . D 3 HOH 6 111 111 HOH HOH A . D 3 HOH 7 112 112 HOH HOH A . D 3 HOH 8 113 113 HOH HOH A . D 3 HOH 9 114 114 HOH HOH A . D 3 HOH 10 115 115 HOH HOH A . D 3 HOH 11 116 116 HOH HOH A . D 3 HOH 12 117 117 HOH HOH A . D 3 HOH 13 118 118 HOH HOH A . D 3 HOH 14 122 122 HOH HOH A . D 3 HOH 15 123 123 HOH HOH A . D 3 HOH 16 124 124 HOH HOH A . D 3 HOH 17 125 125 HOH HOH A . D 3 HOH 18 126 126 HOH HOH A . D 3 HOH 19 129 129 HOH HOH A . D 3 HOH 20 136 136 HOH HOH A . D 3 HOH 21 139 139 HOH HOH A . D 3 HOH 22 140 140 HOH HOH A . D 3 HOH 23 143 143 HOH HOH A . D 3 HOH 24 144 144 HOH HOH A . D 3 HOH 25 145 145 HOH HOH A . D 3 HOH 26 148 148 HOH HOH A . D 3 HOH 27 150 150 HOH HOH A . D 3 HOH 28 151 151 HOH HOH A . D 3 HOH 29 152 152 HOH HOH A . D 3 HOH 30 153 153 HOH HOH A . D 3 HOH 31 158 158 HOH HOH A . D 3 HOH 32 159 159 HOH HOH A . D 3 HOH 33 160 160 HOH HOH A . D 3 HOH 34 161 161 HOH HOH A . D 3 HOH 35 162 162 HOH HOH A . D 3 HOH 36 163 163 HOH HOH A . D 3 HOH 37 165 165 HOH HOH A . D 3 HOH 38 167 167 HOH HOH A . D 3 HOH 39 169 169 HOH HOH A . D 3 HOH 40 170 170 HOH HOH A . D 3 HOH 41 171 171 HOH HOH A . D 3 HOH 42 172 172 HOH HOH A . D 3 HOH 43 176 176 HOH HOH A . E 3 HOH 1 101 101 HOH HOH B . E 3 HOH 2 106 106 HOH HOH B . E 3 HOH 3 108 108 HOH HOH B . E 3 HOH 4 109 109 HOH HOH B . E 3 HOH 5 110 110 HOH HOH B . E 3 HOH 6 119 119 HOH HOH B . E 3 HOH 7 120 120 HOH HOH B . E 3 HOH 8 121 121 HOH HOH B . E 3 HOH 9 127 127 HOH HOH B . E 3 HOH 10 128 128 HOH HOH B . E 3 HOH 11 130 130 HOH HOH B . E 3 HOH 12 131 131 HOH HOH B . E 3 HOH 13 132 132 HOH HOH B . E 3 HOH 14 133 133 HOH HOH B . E 3 HOH 15 134 134 HOH HOH B . E 3 HOH 16 135 135 HOH HOH B . E 3 HOH 17 137 137 HOH HOH B . E 3 HOH 18 138 138 HOH HOH B . E 3 HOH 19 141 141 HOH HOH B . E 3 HOH 20 142 142 HOH HOH B . E 3 HOH 21 146 146 HOH HOH B . E 3 HOH 22 147 147 HOH HOH B . E 3 HOH 23 149 149 HOH HOH B . E 3 HOH 24 154 154 HOH HOH B . E 3 HOH 25 155 155 HOH HOH B . E 3 HOH 26 156 156 HOH HOH B . E 3 HOH 27 157 157 HOH HOH B . E 3 HOH 28 164 164 HOH HOH B . E 3 HOH 29 166 166 HOH HOH B . E 3 HOH 30 168 168 HOH HOH B . E 3 HOH 31 173 173 HOH HOH B . E 3 HOH 32 174 174 HOH HOH B . E 3 HOH 33 175 175 HOH HOH B . # _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 # _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 2007-07-24 2 'Structure model' 1 1 2008-01-17 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-30 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' # 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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 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_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELX 'model building' . ? 1 SHELXL-97 refinement . ? 2 AUTOMAR 'data collection' . ? 3 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 110.13 108.30 1.83 0.30 N 2 1 N3 A DT 3 ? ? C2 A DT 3 ? ? O2 A DT 3 ? ? 126.17 122.30 3.87 0.60 N 3 1 N1 A DA 4 ? ? C2 A DA 4 ? ? N3 A DA 4 ? ? 133.34 129.30 4.04 0.50 N 4 1 C2 A DA 4 ? ? N3 A DA 4 ? ? C4 A DA 4 ? ? 107.30 110.60 -3.30 0.50 N 5 1 "O4'" A DT 5 ? ? "C4'" A DT 5 ? ? "C3'" A DT 5 ? ? 101.95 104.50 -2.55 0.40 N 6 1 "O5'" A DA 6 ? ? "C5'" A DA 6 ? ? "C4'" A DA 6 ? A 102.82 109.40 -6.58 0.80 N 7 1 N1 A DA 6 ? ? C6 A DA 6 ? ? N6 A DA 6 ? ? 122.26 118.60 3.66 0.60 N 8 1 "C3'" A DA 6 ? B "O3'" A DA 6 ? B P A DC 7 ? B 129.39 119.70 9.69 1.20 Y 9 1 P A DC 7 ? A "O5'" A DC 7 ? A "C5'" A DC 7 ? A 132.84 120.90 11.94 1.60 N 10 1 C6 A DC 7 ? ? N1 A DC 7 ? ? C2 A DC 7 ? ? 123.43 120.30 3.13 0.40 N 11 1 C2 B DA 4 ? ? N3 B DA 4 ? ? C4 B DA 4 ? ? 114.12 110.60 3.52 0.50 N 12 1 "O4'" B DA 6 ? ? "C4'" B DA 6 ? ? "C3'" B DA 6 ? ? 101.22 104.50 -3.28 0.40 N 13 1 N1 B DA 6 ? ? C6 B DA 6 ? ? N6 B DA 6 ? ? 128.42 118.60 9.82 0.60 N 14 1 C5 B DA 6 ? ? C6 B DA 6 ? ? N6 B DA 6 ? ? 115.51 123.70 -8.19 0.80 N 15 1 "O4'" B DC 7 ? ? "C4'" B DC 7 ? ? "C3'" B DC 7 ? ? 101.93 104.50 -2.57 0.40 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 SPM N1 N N N 147 SPM C2 C N N 148 SPM C3 C N N 149 SPM C4 C N N 150 SPM N5 N N N 151 SPM C6 C N N 152 SPM C7 C N N 153 SPM C8 C N N 154 SPM C9 C N N 155 SPM N10 N N N 156 SPM C11 C N N 157 SPM C12 C N N 158 SPM C13 C N N 159 SPM N14 N N N 160 SPM HN11 H N N 161 SPM HN12 H N N 162 SPM H21 H N N 163 SPM H22 H N N 164 SPM H31 H N N 165 SPM H32 H N N 166 SPM H41 H N N 167 SPM H42 H N N 168 SPM HN5 H N N 169 SPM H61 H N N 170 SPM H62 H N N 171 SPM H71 H N N 172 SPM H72 H N N 173 SPM H81 H N N 174 SPM H82 H N N 175 SPM H91 H N N 176 SPM H92 H N N 177 SPM HN0 H N N 178 SPM H111 H N N 179 SPM H112 H N N 180 SPM H121 H N N 181 SPM H122 H N N 182 SPM H131 H N N 183 SPM H132 H N N 184 SPM HN41 H N N 185 SPM HN42 H N N 186 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 SPM N1 C2 sing N N 152 SPM N1 HN11 sing N N 153 SPM N1 HN12 sing N N 154 SPM C2 C3 sing N N 155 SPM C2 H21 sing N N 156 SPM C2 H22 sing N N 157 SPM C3 C4 sing N N 158 SPM C3 H31 sing N N 159 SPM C3 H32 sing N N 160 SPM C4 N5 sing N N 161 SPM C4 H41 sing N N 162 SPM C4 H42 sing N N 163 SPM N5 C6 sing N N 164 SPM N5 HN5 sing N N 165 SPM C6 C7 sing N N 166 SPM C6 H61 sing N N 167 SPM C6 H62 sing N N 168 SPM C7 C8 sing N N 169 SPM C7 H71 sing N N 170 SPM C7 H72 sing N N 171 SPM C8 C9 sing N N 172 SPM C8 H81 sing N N 173 SPM C8 H82 sing N N 174 SPM C9 N10 sing N N 175 SPM C9 H91 sing N N 176 SPM C9 H92 sing N N 177 SPM N10 C11 sing N N 178 SPM N10 HN0 sing N N 179 SPM C11 C12 sing N N 180 SPM C11 H111 sing N N 181 SPM C11 H112 sing N N 182 SPM C12 C13 sing N N 183 SPM C12 H121 sing N N 184 SPM C12 H122 sing N N 185 SPM C13 N14 sing N N 186 SPM C13 H131 sing N N 187 SPM C13 H132 sing N N 188 SPM N14 HN41 sing N N 189 SPM N14 HN42 sing N N 190 # _ndb_struct_conf_na.entry_id 2PLB _ndb_struct_conf_na.feature 'a-form 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 DG 1 1_555 B DC 8 1_555 -0.240 -0.164 -0.005 -3.725 -7.085 1.563 1 A_DG1:DC8_B A 1 ? B 8 ? 19 1 1 A DG 2 1_555 B DC 7 1_555 -0.333 -0.210 0.003 -7.307 -14.552 0.875 2 A_DG2:DC7_B A 2 ? B 7 ? 19 1 1 A DT 3 1_555 B DA 6 1_555 0.550 -0.484 -0.026 -3.255 -11.137 -4.449 3 A_DT3:DA6_B A 3 ? B 6 ? 20 1 1 A DA 4 1_555 B DT 5 1_555 0.157 -0.206 0.301 -5.054 -13.735 4.895 4 A_DA4:DT5_B A 4 ? B 5 ? 20 1 1 A DT 5 1_555 B DA 4 1_555 -0.042 -0.172 0.402 5.912 -14.373 6.430 5 A_DT5:DA4_B A 5 ? B 4 ? 20 1 1 A DA 6 1_555 B DT 3 1_555 0.106 -0.194 -0.042 11.375 -17.827 0.884 6 A_DA6:DT3_B A 6 ? B 3 ? 20 1 1 A DC 7 1_555 B DG 2 1_555 0.331 -0.147 0.022 9.570 -19.819 2.460 7 A_DC7:DG2_B A 7 ? B 2 ? 19 1 1 A DC 8 1_555 B DG 1 1_555 0.194 -0.266 0.011 5.953 -2.301 -2.994 8 A_DC8:DG1_B A 8 ? B 1 ? 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 DG 1 1_555 B DC 8 1_555 A DG 2 1_555 B DC 7 1_555 0.282 -2.017 3.133 -0.078 8.643 30.193 -5.151 -0.534 2.474 16.180 0.146 31.379 1 AA_DG1DG2:DC7DC8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A DG 2 1_555 B DC 7 1_555 A DT 3 1_555 B DA 6 1_555 -0.898 -1.225 3.018 -0.066 2.083 40.096 -2.001 1.301 2.955 3.036 0.096 40.148 2 AA_DG2DT3:DA6DC7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A DT 3 1_555 B DA 6 1_555 A DA 4 1_555 B DT 5 1_555 0.702 -1.320 2.974 -0.201 8.979 28.577 -4.134 -1.395 2.451 17.647 0.395 29.927 3 AA_DT3DA4:DT5DA6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A DA 4 1_555 B DT 5 1_555 A DT 5 1_555 B DA 4 1_555 0.110 -1.291 2.889 -1.340 0.912 33.506 -2.368 -0.383 2.848 1.581 2.323 33.544 4 AA_DA4DT5:DA4DT5_BB A 4 ? B 5 ? A 5 ? B 4 ? 1 A DT 5 1_555 B DA 4 1_555 A DA 6 1_555 B DT 3 1_555 -1.073 -1.299 2.808 0.237 14.988 29.229 -4.282 1.932 1.923 27.534 -0.436 32.774 5 AA_DT5DA6:DT3DA4_BB A 5 ? B 4 ? A 6 ? B 3 ? 1 A DA 6 1_555 B DT 3 1_555 A DC 7 1_555 B DG 2 1_555 0.772 -1.189 3.099 0.517 0.127 37.412 -1.869 -1.139 3.105 0.198 -0.806 37.415 6 AA_DA6DC7:DG2DT3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A DC 7 1_555 B DG 2 1_555 A DC 8 1_555 B DG 1 1_555 -0.723 -1.834 3.212 -2.101 10.987 30.946 -4.930 0.955 2.477 19.798 3.785 32.859 7 AA_DC7DC8:DG1DG2_BB A 7 ? B 2 ? A 8 ? B 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMINE SPM 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 2PL8 _pdbx_initial_refinement_model.details ? #