data_3ORC # _entry.id 3ORC # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.375 _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 3ORC pdb_00003orc 10.2210/pdb3orc/pdb RCSB PD0022 ? ? WWPDB D_1000179072 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3ORC _pdbx_database_status.recvd_initial_deposition_date 1998-04-23 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Albright, R.A.' 1 'Mossing, M.C.' 2 'Matthews, B.W.' 3 # 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 an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein. ; 'Protein Sci.' 7 1485 1494 1998 PRCIEI US 0961-8368 0795 ? 9684880 ? 1 'Refined Structure of Cro Repressor Protein from Bacteriophage Lambda Suggests Both Flexibility and Plasticity' J.Mol.Biol. 280 129 ? 1998 JMOBAK UK 0022-2836 0070 ? ? ? 2 'Crystal Structure of Lambda-Cro Bound to a Consensus Operator at 3.0 A Resolution' J.Mol.Biol. 280 137 ? 1998 JMOBAK UK 0022-2836 0070 ? ? ? 3 'High-Resolution Structure of an Engineered Cro Monomer Shows Changes in Conformation Relative to the Native Dimer' Biochemistry 35 735 ? 1996 BICHAW US 0006-2960 0033 ? ? ? 4 'Stable, Monomeric Variants of Lambda Cro Obtained by Insertion of a Designed Beta-Hairpin Sequence' Science 250 1712 ? 1990 SCIEAS US 0036-8075 0038 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Albright, R.A.' 1 ? primary 'Mossing, M.C.' 2 ? primary 'Matthews, B.W.' 3 ? 1 'Ohlendorf, D.H.' 4 ? 1 'Tronrud, D.E.' 5 ? 1 'Matthews, B.W.' 6 ? 2 'Albright, R.A.' 7 ? 2 'Matthews, B.W.' 8 ? 3 'Albright, R.A.' 9 ? 3 'Mossing, M.C.' 10 ? 3 'Matthews, B.W.' 11 ? 4 'Mossing, M.C.' 12 ? 4 'Sauer, R.T.' 13 ? # _cell.entry_id 3ORC _cell.length_a 45.720 _cell.length_b 60.660 _cell.length_c 45.720 _cell.angle_alpha 90.00 _cell.angle_beta 112.70 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 3ORC _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting monoclinic _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 ;DNA (5'-D(*TP*AP*TP*CP*GP*AP*TP*A)-3') ; 2425.629 2 ? ? ? '50% OCCUPANCY IN THE OUTERMOST POSITIONS' 2 polymer man 'PROTEIN (CRO REPRESSOR)' 7242.207 1 ? 'INSERTION (K56-DGEVK)' ? ;WILDTYPE CRO DOES NOT FORM STABLE MONOMERS. THE ENGINEERED-MONOMER PRESENTED HERE CONTAINS A 5-RESIDUE INSERTION [DGEVK] FOLLOWING K 56. THE FIRST 2 RESIDUES OF THIS INSERTION ALLOW THE FORMATION OF A BETA-TURN. THE REMAINING 3 RESIDUES MIMIC RESIDUES OF THE WILDTYPE DIMER INTERFACE, ALLOWING STABILIZING INTERACTIONS TO BE MAINTAINED. THE OVERALL STRUCTURE OF THIS MONOMER IS QUITE SIMILAR TO A SUBUNIT OF THE WILDTYPE DIMER. ; 3 water nat water 18.015 3 ? ? ? ? # 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 polydeoxyribonucleotide no no '(DT)(DA)(DT)(DC)(DG)(DA)(DT)(DA)' TATCGATA R,S ? 2 'polypeptide(L)' no no EQRITLKDYAMRFGQTKTAKDLGVYQSAINKAIHAGRKIFLTINADGSVYAEEVKDGEVKPFPSN EQRITLKDYAMRFGQTKTAKDLGVYQSAINKAIHAGRKIFLTINADGSVYAEEVKDGEVKPFPSN A ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DA n 1 3 DT n 1 4 DC n 1 5 DG n 1 6 DA n 1 7 DT n 1 8 DA n 2 1 GLU n 2 2 GLN n 2 3 ARG n 2 4 ILE n 2 5 THR n 2 6 LEU n 2 7 LYS n 2 8 ASP n 2 9 TYR n 2 10 ALA n 2 11 MET n 2 12 ARG n 2 13 PHE n 2 14 GLY n 2 15 GLN n 2 16 THR n 2 17 LYS n 2 18 THR n 2 19 ALA n 2 20 LYS n 2 21 ASP n 2 22 LEU n 2 23 GLY n 2 24 VAL n 2 25 TYR n 2 26 GLN n 2 27 SER n 2 28 ALA n 2 29 ILE n 2 30 ASN n 2 31 LYS n 2 32 ALA n 2 33 ILE n 2 34 HIS n 2 35 ALA n 2 36 GLY n 2 37 ARG n 2 38 LYS n 2 39 ILE n 2 40 PHE n 2 41 LEU n 2 42 THR n 2 43 ILE n 2 44 ASN n 2 45 ALA n 2 46 ASP n 2 47 GLY n 2 48 SER n 2 49 VAL n 2 50 TYR n 2 51 ALA n 2 52 GLU n 2 53 GLU n 2 54 VAL n 2 55 LYS n 2 56 ASP n 2 57 GLY n 2 58 GLU n 2 59 VAL n 2 60 LYS n 2 61 PRO n 2 62 PHE n 2 63 PRO n 2 64 SER n 2 65 ASN 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 ? _entity_src_gen.gene_src_genus 'Lambda-like viruses' _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Enterobacteria phage lambda' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10710 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene 'CRO MUTANT K56-[DGEVK]' _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain X90 _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PUCRO.MDG _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 UNP RCRO_LAMBD 2 ? ? P03040 ? 2 PDB 3ORC 1 ? ? 3ORC ? # 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 3ORC A 1 ? 65 ? P03040 2 ? 61 ? 2 66 2 2 3ORC R 1 ? 8 ? 3ORC 1 ? 8 ? 1 8 3 2 3ORC S 1 ? 8 ? 3ORC 1 ? 8 ? 1 8 # 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 3ORC ASP A 56 ? UNP P03040 ASP ? 'SEE REMARK 999' 57 1 1 3ORC GLY A 57 ? UNP P03040 GLY ? 'SEE REMARK 999' 58 2 1 3ORC GLU A 58 ? UNP P03040 GLU 54 'SEE REMARK 999' 59 3 1 3ORC VAL A 59 ? UNP P03040 VAL 55 'SEE REMARK 999' 60 4 1 3ORC LYS A 60 ? UNP P03040 LYS 56 'SEE REMARK 999' 61 5 1 3ORC PRO A 61 ? UNP P03040 PRO 57 'SEE REMARK 999' 62 6 1 3ORC PHE A 62 ? UNP P03040 PHE 58 'SEE REMARK 999' 63 7 1 3ORC PRO A 63 ? UNP P03040 PRO 59 'SEE REMARK 999' 64 8 1 3ORC SER A 64 ? UNP P03040 SER 60 'SEE REMARK 999' 65 9 1 3ORC ASN A 65 ? UNP P03040 ASN 61 'SEE REMARK 999' 66 10 # 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 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 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 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 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 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3ORC _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.0 _exptl_crystal.density_percent_sol 48.45 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _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 4.6 _exptl_crystal_grow.pdbx_details ;COCRYSTALS WERE OBTAINED BY MIXING A 1.5 MOLAR EXCESS OF THE 7BP DNA FRAGMENT WITH CRO K56-[DGEVK], COMBINING WITH AN EQUAL VOLUME OF PRECIPITANT BUFFER (140MM AMMONIUM ACETATE, 31% PEG 3350, 100MM ACETATE BUFFER PH 4.6), THEN EQUILIBRATING AGAINST THE PRECIPITANT BUFFER VIA THE HANGING-DROP METHOD AT ROOM TEMPERATURE., 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 'AMMONIUM ACETATE' ? ? ? 1 2 1 'PEG 3350' ? ? ? 1 3 1 'ACETATE BUFFER' ? ? ? 1 4 2 'AMMONIUM ACETATE' ? ? ? 1 5 2 'PEG 3350' ? ? ? 1 6 2 'ACETATE BUFFER' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 295 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type SDMS _diffrn_detector.pdbx_collection_date 1993-02 _diffrn_detector.details COLLIMATOR # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'GRAPHITE CRYSTAL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 3ORC _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 3.0 _reflns.number_obs 2452 _reflns.number_all ? _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.0530000 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate 51.1 _reflns.pdbx_redundancy 5.3 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 3ORC _refine.ls_number_reflns_obs 2452 _refine.ls_number_reflns_all 13041 _refine.pdbx_ls_sigma_I 13041 _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 20.0 _refine.ls_d_res_high 3.0 _refine.ls_percent_reflns_obs 99.7 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _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 ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _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 BABINET _refine.solvent_model_param_ksol 0.60 _refine.solvent_model_param_bsol 160 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 1ORC' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model 'TNT BCORREL (MODIFIED TO INCLUDE DNA)' _refine.pdbx_stereochemistry_target_values 'TNT PROTGEO (MODIFIED TO INCLUDE DNA)' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _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.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_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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 501 _refine_hist.pdbx_number_atoms_nucleic_acid 322 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 826 _refine_hist.d_res_high 3.0 _refine_hist.d_res_low 20.0 # 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 t_bond_d 0.015 ? 0.380 689 'X-RAY DIFFRACTION' ? t_angle_deg 2.656 ? 0.660 959 'X-RAY DIFFRACTION' ? t_dihedral_angle_d 19.550 ? 0.700 399 'X-RAY DIFFRACTION' ? t_incorr_chiral_ct 0 ? ? ? 'X-RAY DIFFRACTION' ? t_pseud_angle ? ? ? ? 'X-RAY DIFFRACTION' ? t_trig_c_planes 0.006 ? 1.500 13 'X-RAY DIFFRACTION' ? t_gen_planes 0.013 ? 2.000 82 'X-RAY DIFFRACTION' ? t_it 2.548 ? 4.00 707 'X-RAY DIFFRACTION' ? t_nbd 0.018 ? 10.00 51 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 3ORC _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.2240000 _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 ? _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 ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 3ORC _struct.title 'CRYSTAL STRUCTURE OF AN ENGINEERED CRO MONOMER BOUND NONSPECIFICALLY TO DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3ORC _struct_keywords.pdbx_keywords 'GENE REGULATION/DNA' _struct_keywords.text ;CRO, PROTEIN-DNA INTERACTION, BACTERIOPHAGE LAMBDA, REPRESSOR, MONOMER-DIMER, HELIX-TURN-HELIX, COMPLEX (GENE REGULATING PROTEIN-DNA), GENE REGULATION-DNA 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 1 ? C N N 2 ? D N N 3 ? # _struct_biol.id 1 _struct_biol.details ;WILDTYPE CRO DOES NOT FORM STABLE MONOMERS. THE ENGINEERED MONOMER PRESENTED HERE CONTAINS A 5-RESIDUE INSERTION [DGEVK] FOLLOWING K 56. THE FIRST 2 RESIDUES OF THIS INSERTION ALLOW THE FORMATION OF A BETA-TURN. THE REMAINING 3 RESIDUES MIMIC RESIDUES OF THE WILDTYPE DIMER INTERFACE, ALLOWING STABILIZING INTERACTIONS TO BE MAINTAINED. THE OVERALL STRUCTURE OF THIS MONOMER IS QUITE SIMILAR TO A SUBUNIT OF THE WILDTYPE DIMER. ; _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 LEU C 6 ? LEU C 22 ? LEU A 7 LEU A 23 1 ? 17 HELX_P HELX_P2 2 GLN C 26 ? ALA C 35 ? GLN A 27 ALA A 36 1 ? 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DT 1 N3 ? ? ? 1_555 B DA 8 N1 ? ? R DT 1 S DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 B DA 8 N6 ? ? R DT 1 S DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 7 N3 ? ? R DA 2 S DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 7 O4 ? ? R DA 2 S DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 6 N1 ? ? R DT 3 S DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 6 N6 ? ? R DT 3 S DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 5 N1 ? ? R DC 4 S DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 5 O6 ? ? R DC 4 S DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 5 N2 ? ? R DC 4 S DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 4 N3 ? ? R DG 5 S DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 4 O2 ? ? R DG 5 S DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 4 N4 ? ? R DG 5 S DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 3 N3 ? ? R DA 6 S DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 3 O4 ? ? R DA 6 S DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 2 N1 ? ? R DT 7 S DA 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 2 N6 ? ? R DT 7 S DA 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 1 N3 ? ? R DA 8 S DT 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 1 O4 ? ? R DA 8 S DT 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id PHE _struct_mon_prot_cis.label_seq_id 62 _struct_mon_prot_cis.label_asym_id C _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id PHE _struct_mon_prot_cis.auth_seq_id 63 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 63 _struct_mon_prot_cis.pdbx_label_asym_id_2 C _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 64 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -2.22 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 4 _struct_sheet.details ? # 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 # 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 ARG C 3 ? THR C 5 ? ARG A 4 THR A 6 A 2 ILE C 39 ? ASN C 44 ? ILE A 40 ASN A 45 A 3 SER C 48 ? ASP C 56 ? SER A 49 ASP A 57 A 4 GLU C 58 ? PHE C 62 ? GLU A 59 PHE A 63 # 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 O ILE C 4 ? O ILE A 5 N LEU C 41 ? N LEU A 42 A 2 3 O PHE C 40 ? O PHE A 41 N GLU C 52 ? N GLU A 53 A 3 4 O ALA C 51 ? O ALA A 52 N PHE C 62 ? N PHE A 63 # _database_PDB_matrix.entry_id 3ORC _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 3ORC _atom_sites.fract_transf_matrix[1][1] 0.021872 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.009149 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.016485 _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] 0.023709 _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 # 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 DT 1 1 1 DT T R . n A 1 2 DA 2 2 2 DA A R . n A 1 3 DT 3 3 3 DT T R . n A 1 4 DC 4 4 4 DC C R . n A 1 5 DG 5 5 5 DG G R . n A 1 6 DA 6 6 6 DA A R . n A 1 7 DT 7 7 7 DT T R . n A 1 8 DA 8 8 8 DA A R . n B 1 1 DT 1 1 1 DT T S . n B 1 2 DA 2 2 2 DA A S . n B 1 3 DT 3 3 3 DT T S . n B 1 4 DC 4 4 4 DC C S . n B 1 5 DG 5 5 5 DG G S . n B 1 6 DA 6 6 6 DA A S . n B 1 7 DT 7 7 7 DT T S . n B 1 8 DA 8 8 8 DA A S . n C 2 1 GLU 1 2 2 GLU GLU A . n C 2 2 GLN 2 3 3 GLN GLN A . n C 2 3 ARG 3 4 4 ARG ARG A . n C 2 4 ILE 4 5 5 ILE ILE A . n C 2 5 THR 5 6 6 THR THR A . n C 2 6 LEU 6 7 7 LEU LEU A . n C 2 7 LYS 7 8 8 LYS LYS A . n C 2 8 ASP 8 9 9 ASP ASP A . n C 2 9 TYR 9 10 10 TYR TYR A . n C 2 10 ALA 10 11 11 ALA ALA A . n C 2 11 MET 11 12 12 MET MET A . n C 2 12 ARG 12 13 13 ARG ARG A . n C 2 13 PHE 13 14 14 PHE PHE A . n C 2 14 GLY 14 15 15 GLY GLY A . n C 2 15 GLN 15 16 16 GLN GLN A . n C 2 16 THR 16 17 17 THR THR A . n C 2 17 LYS 17 18 18 LYS LYS A . n C 2 18 THR 18 19 19 THR THR A . n C 2 19 ALA 19 20 20 ALA ALA A . n C 2 20 LYS 20 21 21 LYS LYS A . n C 2 21 ASP 21 22 22 ASP ASP A . n C 2 22 LEU 22 23 23 LEU LEU A . n C 2 23 GLY 23 24 24 GLY GLY A . n C 2 24 VAL 24 25 25 VAL VAL A . n C 2 25 TYR 25 26 26 TYR TYR A . n C 2 26 GLN 26 27 27 GLN GLN A . n C 2 27 SER 27 28 28 SER SER A . n C 2 28 ALA 28 29 29 ALA ALA A . n C 2 29 ILE 29 30 30 ILE ILE A . n C 2 30 ASN 30 31 31 ASN ASN A . n C 2 31 LYS 31 32 32 LYS LYS A . n C 2 32 ALA 32 33 33 ALA ALA A . n C 2 33 ILE 33 34 34 ILE ILE A . n C 2 34 HIS 34 35 35 HIS HIS A . n C 2 35 ALA 35 36 36 ALA ALA A . n C 2 36 GLY 36 37 37 GLY GLY A . n C 2 37 ARG 37 38 38 ARG ARG A . n C 2 38 LYS 38 39 39 LYS LYS A . n C 2 39 ILE 39 40 40 ILE ILE A . n C 2 40 PHE 40 41 41 PHE PHE A . n C 2 41 LEU 41 42 42 LEU LEU A . n C 2 42 THR 42 43 43 THR THR A . n C 2 43 ILE 43 44 44 ILE ILE A . n C 2 44 ASN 44 45 45 ASN ASN A . n C 2 45 ALA 45 46 46 ALA ALA A . n C 2 46 ASP 46 47 47 ASP ASP A . n C 2 47 GLY 47 48 48 GLY GLY A . n C 2 48 SER 48 49 49 SER SER A . n C 2 49 VAL 49 50 50 VAL VAL A . n C 2 50 TYR 50 51 51 TYR TYR A . n C 2 51 ALA 51 52 52 ALA ALA A . n C 2 52 GLU 52 53 53 GLU GLU A . n C 2 53 GLU 53 54 54 GLU GLU A . n C 2 54 VAL 54 55 55 VAL VAL A . n C 2 55 LYS 55 56 56 LYS LYS A . n C 2 56 ASP 56 57 57 ASP ASP A . n C 2 57 GLY 57 58 58 GLY GLY A . n C 2 58 GLU 58 59 59 GLU GLU A . n C 2 59 VAL 59 60 60 VAL VAL A . n C 2 60 LYS 60 61 61 LYS LYS A . n C 2 61 PRO 61 62 62 PRO PRO A . n C 2 62 PHE 62 63 63 PHE PHE A . n C 2 63 PRO 63 64 64 PRO PRO A . n C 2 64 SER 64 65 65 SER SER A . n C 2 65 ASN 65 66 66 ASN ASN A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 3 HOH 1 401 401 HOH HOH A . D 3 HOH 2 402 402 HOH HOH A . D 3 HOH 3 403 403 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _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 # _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 1998-12-02 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-11-29 5 'Structure model' 1 4 2023-08-02 # _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' 'Derived calculations' 4 5 'Structure model' 'Database references' 5 5 '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' struct_conf 2 4 'Structure model' struct_conf_type 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_initial_refinement_model # 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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal EDPDB 'model building' '(ZHANG)' ? 1 TNT refinement 5EB ? 2 SDMS 'data reduction' . ? 3 SDMS 'data scaling' . ? 4 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" R DA 2 ? ? "C3'" R DA 2 ? ? 1.515 1.435 0.080 0.013 N 2 1 "O3'" R DC 4 ? ? "C3'" R DC 4 ? ? 1.516 1.435 0.081 0.013 N 3 1 "O3'" S DA 2 ? ? "C3'" S DA 2 ? ? 1.515 1.435 0.080 0.013 N 4 1 "O3'" S DC 4 ? ? "C3'" S DC 4 ? ? 1.516 1.435 0.081 0.013 N 5 1 CD A GLU 54 ? ? OE2 A GLU 54 ? ? 1.321 1.252 0.069 0.011 N 6 1 CD A GLU 59 ? ? OE2 A GLU 59 ? ? 1.324 1.252 0.072 0.011 N # 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 "C3'" R DA 2 ? ? "O3'" R DA 2 ? ? P R DT 3 ? ? 132.24 119.70 12.54 1.20 Y 2 1 "O4'" R DC 4 ? ? "C1'" R DC 4 ? ? N1 R DC 4 ? ? 102.30 108.00 -5.70 0.70 N 3 1 P R DA 6 ? ? "O5'" R DA 6 ? ? "C5'" R DA 6 ? ? 110.77 120.90 -10.13 1.60 N 4 1 "O4'" R DT 7 ? ? "C4'" R DT 7 ? ? "C3'" R DT 7 ? ? 100.82 104.50 -3.68 0.40 N 5 1 "C3'" S DA 2 ? ? "O3'" S DA 2 ? ? P S DT 3 ? ? 132.24 119.70 12.54 1.20 Y 6 1 "O4'" S DC 4 ? ? "C1'" S DC 4 ? ? N1 S DC 4 ? ? 102.30 108.00 -5.70 0.70 N 7 1 P S DA 6 ? ? "O5'" S DA 6 ? ? "C5'" S DA 6 ? ? 110.77 120.90 -10.13 1.60 N 8 1 "O4'" S DT 7 ? ? "C4'" S DT 7 ? ? "C3'" S DT 7 ? ? 100.82 104.50 -3.68 0.40 N 9 1 NE A ARG 4 ? ? CZ A ARG 4 ? ? NH1 A ARG 4 ? ? 123.62 120.30 3.32 0.50 N 10 1 CB A ILE 5 ? ? CA A ILE 5 ? ? C A ILE 5 ? ? 99.30 111.60 -12.30 2.00 N 11 1 CB A ASP 9 ? ? CG A ASP 9 ? ? OD2 A ASP 9 ? ? 112.69 118.30 -5.61 0.90 N 12 1 CB A ASP 22 ? ? CG A ASP 22 ? ? OD1 A ASP 22 ? ? 124.72 118.30 6.42 0.90 N 13 1 CB A ASP 22 ? ? CG A ASP 22 ? ? OD2 A ASP 22 ? ? 111.56 118.30 -6.74 0.90 N 14 1 C A LYS 61 ? ? N A PRO 62 ? ? CD A PRO 62 ? ? 108.77 128.40 -19.63 2.10 Y # 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 GLN A 3 ? ? -158.13 -21.79 2 1 ARG A 4 ? ? -161.97 114.08 3 1 ARG A 13 ? ? -66.21 -76.50 4 1 ILE A 30 ? ? -62.43 -71.52 5 1 ALA A 46 ? ? -32.64 -31.18 6 1 LYS A 56 ? ? -58.58 -82.79 7 1 PHE A 63 ? ? -161.93 112.81 # 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 GLU 2 ? CG ? C GLU 1 CG 2 1 Y 1 A GLU 2 ? CD ? C GLU 1 CD 3 1 Y 1 A GLU 2 ? OE1 ? C GLU 1 OE1 4 1 Y 1 A GLU 2 ? OE2 ? C GLU 1 OE2 5 1 Y 1 A LYS 21 ? CG ? C LYS 20 CG 6 1 Y 1 A LYS 21 ? CD ? C LYS 20 CD 7 1 Y 1 A LYS 21 ? CE ? C LYS 20 CE 8 1 Y 1 A LYS 21 ? NZ ? C LYS 20 NZ # _ndb_struct_conf_na.entry_id 3ORC _ndb_struct_conf_na.feature 'b-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 DT 1 1_555 B DA 8 1_555 -0.935 -0.528 0.409 -27.799 7.739 1.556 1 R_DT1:DA8_S R 1 ? S 8 ? 20 1 1 A DA 2 1_555 B DT 7 1_555 0.981 -0.798 -0.591 6.870 -4.013 1.786 2 R_DA2:DT7_S R 2 ? S 7 ? 20 1 1 A DT 3 1_555 B DA 6 1_555 -0.379 -0.863 -0.591 -2.513 -19.862 -0.100 3 R_DT3:DA6_S R 3 ? S 6 ? 20 1 1 A DC 4 1_555 B DG 5 1_555 -0.417 -0.350 0.557 -9.287 -7.121 -10.217 4 R_DC4:DG5_S R 4 ? S 5 ? 19 1 1 A DG 5 1_555 B DC 4 1_555 0.417 -0.350 0.557 9.289 -7.120 -10.211 5 R_DG5:DC4_S R 5 ? S 4 ? 19 1 1 A DA 6 1_555 B DT 3 1_555 0.379 -0.862 -0.591 2.512 -19.863 -0.091 6 R_DA6:DT3_S R 6 ? S 3 ? 20 1 1 A DT 7 1_555 B DA 2 1_555 -0.980 -0.797 -0.591 -6.870 -4.012 1.791 7 R_DT7:DA2_S R 7 ? S 2 ? 20 1 1 A DA 8 1_555 B DT 1 1_555 0.936 -0.528 0.409 27.800 7.739 1.549 8 R_DA8:DT1_S R 8 ? S 1 ? 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 DT 1 1_555 B DA 8 1_555 A DA 2 1_555 B DT 7 1_555 -0.490 0.597 2.789 6.330 -0.615 42.320 0.870 1.204 2.683 -0.846 -8.709 42.774 1 RR_DT1DA2:DT7DA8_SS R 1 ? S 8 ? R 2 ? S 7 ? 1 A DA 2 1_555 B DT 7 1_555 A DT 3 1_555 B DA 6 1_555 -0.741 -0.250 3.481 -0.654 10.165 31.087 -2.305 1.197 3.255 18.359 1.181 32.674 2 RR_DA2DT3:DA6DT7_SS R 2 ? S 7 ? R 3 ? S 6 ? 1 A DT 3 1_555 B DA 6 1_555 A DC 4 1_555 B DG 5 1_555 -0.691 0.147 3.712 -9.553 1.449 31.751 -0.027 -0.665 3.760 2.574 16.976 33.152 3 RR_DT3DC4:DG5DA6_SS R 3 ? S 6 ? R 4 ? S 5 ? 1 A DC 4 1_555 B DG 5 1_555 A DG 5 1_555 B DC 4 1_555 0.000 0.879 3.161 0.000 -13.505 44.092 2.208 0.000 2.790 -17.508 0.000 46.015 4 RR_DC4DG5:DC4DG5_SS R 4 ? S 5 ? R 5 ? S 4 ? 1 A DG 5 1_555 B DC 4 1_555 A DA 6 1_555 B DT 3 1_555 0.691 0.147 3.712 9.552 1.447 31.753 -0.026 0.665 3.760 2.571 -16.974 33.154 5 RR_DG5DA6:DT3DC4_SS R 5 ? S 4 ? R 6 ? S 3 ? 1 A DA 6 1_555 B DT 3 1_555 A DT 7 1_555 B DA 2 1_555 0.741 -0.250 3.481 0.655 10.166 31.085 -2.305 -1.197 3.255 18.361 -1.182 32.672 6 RR_DA6DT7:DA2DT3_SS R 6 ? S 3 ? R 7 ? S 2 ? 1 A DT 7 1_555 B DA 2 1_555 A DA 8 1_555 B DT 1 1_555 0.489 0.597 2.789 -6.331 -0.616 42.321 0.870 -1.203 2.683 -0.847 8.709 42.775 7 RR_DT7DA8:DT1DA2_SS R 7 ? S 2 ? R 8 ? S 1 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 1ORC _pdbx_initial_refinement_model.details 'PDB ENTRY 1ORC' #