data_1YDL # _entry.id 1YDL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.351 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1YDL pdb_00001ydl 10.2210/pdb1ydl/pdb RCSB RCSB031407 ? ? WWPDB D_1000031407 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id HR2045 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YDL _pdbx_database_status.recvd_initial_deposition_date 2004-12-24 _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 Y _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 'Forouhar, F.' 1 'Edstrom, W.' 2 'Xiao, R.' 3 'Acton, T.B.' 4 'Montelione, G.T.' 5 'Tong, L.' 6 'Hunt, J.F.' 7 'Northeast Structural Genomics Consortium (NESG)' 8 # _citation.id primary _citation.title 'Crystal Structure of the Human TFIIH, Northeast Structural Genomics Target HR2045.' _citation.journal_abbrev 'To be Published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Forouhar, F.' 1 ? primary 'Edstrom, W.' 2 ? primary 'Xiao, R.' 3 ? primary 'Acton, T.B.' 4 ? primary 'Montelione, G.T.' 5 ? primary 'Tong, L.' 6 ? primary 'Hunt, J.F.' 7 ? # _cell.entry_id 1YDL _cell.length_a 41.412 _cell.length_b 53.922 _cell.length_c 34.818 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YDL _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _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 man 'general transcription factor IIH, polypeptide 5' 9234.096 1 ? ? ? ? 2 water nat water 18.015 35 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name TFIIH # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;MGHHHHHHSHGTRKG(MSE)LIECDPA(MSE)KQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGEL (MSE)DQNAFSLTQK ; _entity_poly.pdbx_seq_one_letter_code_can MGHHHHHHSHGTRKGMLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQK _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier HR2045 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 GLY n 1 3 HIS n 1 4 HIS n 1 5 HIS n 1 6 HIS n 1 7 HIS n 1 8 HIS n 1 9 SER n 1 10 HIS n 1 11 GLY n 1 12 THR n 1 13 ARG n 1 14 LYS n 1 15 GLY n 1 16 MSE n 1 17 LEU n 1 18 ILE n 1 19 GLU n 1 20 CYS n 1 21 ASP n 1 22 PRO n 1 23 ALA n 1 24 MSE n 1 25 LYS n 1 26 GLN n 1 27 PHE n 1 28 LEU n 1 29 LEU n 1 30 TYR n 1 31 LEU n 1 32 ASP n 1 33 GLU n 1 34 SER n 1 35 ASN n 1 36 ALA n 1 37 LEU n 1 38 GLY n 1 39 LYS n 1 40 LYS n 1 41 PHE n 1 42 ILE n 1 43 ILE n 1 44 GLN n 1 45 ASP n 1 46 ILE n 1 47 ASP n 1 48 ASP n 1 49 THR n 1 50 HIS n 1 51 VAL n 1 52 PHE n 1 53 VAL n 1 54 ILE n 1 55 ALA n 1 56 GLU n 1 57 LEU n 1 58 VAL n 1 59 ASN n 1 60 VAL n 1 61 LEU n 1 62 GLN n 1 63 GLU n 1 64 ARG n 1 65 VAL n 1 66 GLY n 1 67 GLU n 1 68 LEU n 1 69 MSE n 1 70 ASP n 1 71 GLN n 1 72 ASN n 1 73 ALA n 1 74 PHE n 1 75 SER n 1 76 LEU n 1 77 THR n 1 78 GLN n 1 79 LYS n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene C6orf175 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)+Magic' _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 pET21 _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name BL21 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TF2H5_HUMAN _struct_ref.pdbx_db_accession Q6ZYL4 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQK _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1YDL _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 79 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q6ZYL4 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 71 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg -7 _struct_ref_seq.pdbx_auth_seq_align_end 71 # 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 1YDL GLY A 2 ? UNP Q6ZYL4 ? ? 'cloning artifact' -6 1 1 1YDL HIS A 3 ? UNP Q6ZYL4 ? ? 'cloning artifact' -5 2 1 1YDL HIS A 4 ? UNP Q6ZYL4 ? ? 'expression tag' -4 3 1 1YDL HIS A 5 ? UNP Q6ZYL4 ? ? 'expression tag' -3 4 1 1YDL HIS A 6 ? UNP Q6ZYL4 ? ? 'expression tag' -2 5 1 1YDL HIS A 7 ? UNP Q6ZYL4 ? ? 'expression tag' -1 6 1 1YDL HIS A 8 ? UNP Q6ZYL4 ? ? 'expression tag' 0 7 1 1YDL SER A 9 ? UNP Q6ZYL4 MET ? 'SEE REMARK 999' 1 8 1 1YDL HIS A 10 ? UNP Q6ZYL4 VAL 2 'SEE REMARK 999' 2 9 1 1YDL GLY A 11 ? UNP Q6ZYL4 ASN 3 'SEE REMARK 999' 3 10 1 1YDL THR A 12 ? UNP Q6ZYL4 VAL 4 'SEE REMARK 999' 4 11 1 1YDL ARG A 13 ? UNP Q6ZYL4 LEU 5 'SEE REMARK 999' 5 12 1 1YDL MSE A 16 ? UNP Q6ZYL4 VAL 8 'engineered mutation' 8 13 1 1YDL MSE A 24 ? UNP Q6ZYL4 MET 16 'modified residue' 16 14 1 1YDL MSE A 69 ? UNP Q6ZYL4 MET 61 'modified residue' 61 15 # 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 1YDL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.2 _exptl_crystal.density_percent_sol 50 _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 7.5 _exptl_crystal_grow.pdbx_details '22% PEG 3350, 100 mM MgCl2, and 10 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2004-11-07 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si 111 CHANNEL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.979 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X4A' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X4A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.979 # _reflns.entry_id 1YDL _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 29.25 _reflns.d_resolution_high 2.3 _reflns.number_obs 6602 _reflns.number_all ? _reflns.percent_possible_obs 97.8 _reflns.pdbx_Rmerge_I_obs 0.09 _reflns.pdbx_Rsym_value 0.083 _reflns.pdbx_netI_over_sigmaI 22.23 _reflns.B_iso_Wilson_estimate 19.6 _reflns.pdbx_redundancy 7.4 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.3 _reflns_shell.d_res_low 2.38 _reflns_shell.percent_possible_all 93.5 _reflns_shell.Rmerge_I_obs 0.302 _reflns_shell.pdbx_Rsym_value 0.316 _reflns_shell.meanI_over_sigI_obs 5.1 _reflns_shell.pdbx_redundancy 5.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 633 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1YDL _refine.ls_number_reflns_obs 5916 _refine.ls_number_reflns_all 6601 _refine.pdbx_ls_sigma_I 2.0 _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF 444155.03 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.25 _refine.ls_d_res_high 2.30 _refine.ls_percent_reflns_obs 88.4 _refine.ls_R_factor_obs 0.236 _refine.ls_R_factor_all 0.239 _refine.ls_R_factor_R_work 0.236 _refine.ls_R_factor_R_free 0.297 _refine.ls_R_factor_R_free_error 0.012 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.7 _refine.ls_number_reflns_R_free 634 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 35.9 _refine.aniso_B[1][1] -12.97 _refine.aniso_B[2][2] -7.05 _refine.aniso_B[3][3] 20.02 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.35852 _refine.solvent_model_param_bsol 51.8039 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model OVERALL _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_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 1YDL _refine_analyze.Luzzati_coordinate_error_obs 0.28 _refine_analyze.Luzzati_sigma_a_obs 0.11 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.39 _refine_analyze.Luzzati_sigma_a_free 0.16 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _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 565 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 35 _refine_hist.number_atoms_total 600 _refine_hist.d_res_high 2.30 _refine_hist.d_res_low 29.25 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.0 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 21.9 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.60 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.30 _refine_ls_shell.d_res_low 2.44 _refine_ls_shell.number_reflns_R_work 715 _refine_ls_shell.R_factor_R_work 0.211 _refine_ls_shell.percent_reflns_obs 70.5 _refine_ls_shell.R_factor_R_free 0.282 _refine_ls_shell.R_factor_R_free_error 0.034 _refine_ls_shell.percent_reflns_R_free 8.9 _refine_ls_shell.number_reflns_R_free 70 _refine_ls_shell.number_reflns_obs 634 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # _struct.entry_id 1YDL _struct.title 'Crystal Structure of the Human TFIIH, Northeast Structural Genomics Target HR2045.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YDL _struct_keywords.pdbx_keywords TRANSCRIPTION _struct_keywords.text ;alpha-beta protein, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, TRANSCRIPTION ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_biol.id 1 _struct_biol.details 'possibly 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 ASP A 21 ? SER A 34 ? ASP A 13 SER A 26 1 ? 14 HELX_P HELX_P2 2 GLU A 56 ? LEU A 68 ? GLU A 48 LEU A 60 1 ? 13 # _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 covale1 covale both ? A GLY 15 C ? ? ? 1_555 A MSE 16 N ? ? A GLY 7 A MSE 8 1_555 ? ? ? ? ? ? ? 1.322 ? ? covale2 covale both ? A MSE 16 C ? ? ? 1_555 A LEU 17 N ? ? A MSE 8 A LEU 9 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale3 covale both ? A ALA 23 C ? ? ? 1_555 A MSE 24 N ? ? A ALA 15 A MSE 16 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale4 covale both ? A MSE 24 C ? ? ? 1_555 A LYS 25 N ? ? A MSE 16 A LYS 17 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale5 covale both ? A LEU 68 C ? ? ? 1_555 A MSE 69 N ? ? A LEU 60 A MSE 61 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale6 covale both ? A MSE 69 C ? ? ? 1_555 A ASP 70 N ? ? A MSE 61 A ASP 62 1_555 ? ? ? ? ? ? ? 1.330 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 3 _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 # 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 MSE A 16 ? GLU A 19 ? MSE A 8 GLU A 11 A 2 HIS A 50 ? VAL A 53 ? HIS A 42 VAL A 45 A 3 ILE A 42 ? ASP A 45 ? ILE A 34 ASP A 37 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N MSE A 16 ? N MSE A 8 O VAL A 53 ? O VAL A 45 A 2 3 O PHE A 52 ? O PHE A 44 N GLN A 44 ? N GLN A 36 # _database_PDB_matrix.entry_id 1YDL _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 1YDL _atom_sites.fract_transf_matrix[1][1] 0.024148 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.018545 _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] 0.028721 _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 S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 -7 ? ? ? A . n A 1 2 GLY 2 -6 ? ? ? A . n A 1 3 HIS 3 -5 ? ? ? A . n A 1 4 HIS 4 -4 ? ? ? A . n A 1 5 HIS 5 -3 ? ? ? A . n A 1 6 HIS 6 -2 ? ? ? A . n A 1 7 HIS 7 -1 ? ? ? A . n A 1 8 HIS 8 0 ? ? ? A . n A 1 9 SER 9 1 1 SER SER A . n A 1 10 HIS 10 2 2 HIS HIS A . n A 1 11 GLY 11 3 3 GLY GLY A . n A 1 12 THR 12 4 4 THR THR A . n A 1 13 ARG 13 5 5 ARG ARG A . n A 1 14 LYS 14 6 6 LYS LYS A . n A 1 15 GLY 15 7 7 GLY GLY A . n A 1 16 MSE 16 8 8 MSE MSE A . n A 1 17 LEU 17 9 9 LEU LEU A . n A 1 18 ILE 18 10 10 ILE ILE A . n A 1 19 GLU 19 11 11 GLU GLU A . n A 1 20 CYS 20 12 12 CYS CYS A . n A 1 21 ASP 21 13 13 ASP ASP A . n A 1 22 PRO 22 14 14 PRO PRO A . n A 1 23 ALA 23 15 15 ALA ALA A . n A 1 24 MSE 24 16 16 MSE MSE A . n A 1 25 LYS 25 17 17 LYS LYS A . n A 1 26 GLN 26 18 18 GLN GLN A . n A 1 27 PHE 27 19 19 PHE PHE A . n A 1 28 LEU 28 20 20 LEU LEU A . n A 1 29 LEU 29 21 21 LEU LEU A . n A 1 30 TYR 30 22 22 TYR TYR A . n A 1 31 LEU 31 23 23 LEU LEU A . n A 1 32 ASP 32 24 24 ASP ASP A . n A 1 33 GLU 33 25 25 GLU GLU A . n A 1 34 SER 34 26 26 SER SER A . n A 1 35 ASN 35 27 27 ASN ASN A . n A 1 36 ALA 36 28 28 ALA ALA A . n A 1 37 LEU 37 29 29 LEU LEU A . n A 1 38 GLY 38 30 30 GLY GLY A . n A 1 39 LYS 39 31 31 LYS LYS A . n A 1 40 LYS 40 32 32 LYS LYS A . n A 1 41 PHE 41 33 33 PHE PHE A . n A 1 42 ILE 42 34 34 ILE ILE A . n A 1 43 ILE 43 35 35 ILE ILE A . n A 1 44 GLN 44 36 36 GLN GLN A . n A 1 45 ASP 45 37 37 ASP ASP A . n A 1 46 ILE 46 38 38 ILE ILE A . n A 1 47 ASP 47 39 39 ASP ASP A . n A 1 48 ASP 48 40 40 ASP ASP A . n A 1 49 THR 49 41 41 THR THR A . n A 1 50 HIS 50 42 42 HIS HIS A . n A 1 51 VAL 51 43 43 VAL VAL A . n A 1 52 PHE 52 44 44 PHE PHE A . n A 1 53 VAL 53 45 45 VAL VAL A . n A 1 54 ILE 54 46 46 ILE ILE A . n A 1 55 ALA 55 47 47 ALA ALA A . n A 1 56 GLU 56 48 48 GLU GLU A . n A 1 57 LEU 57 49 49 LEU LEU A . n A 1 58 VAL 58 50 50 VAL VAL A . n A 1 59 ASN 59 51 51 ASN ASN A . n A 1 60 VAL 60 52 52 VAL VAL A . n A 1 61 LEU 61 53 53 LEU LEU A . n A 1 62 GLN 62 54 54 GLN GLN A . n A 1 63 GLU 63 55 55 GLU GLU A . n A 1 64 ARG 64 56 56 ARG ARG A . n A 1 65 VAL 65 57 57 VAL VAL A . n A 1 66 GLY 66 58 58 GLY GLY A . n A 1 67 GLU 67 59 59 GLU GLU A . n A 1 68 LEU 68 60 60 LEU LEU A . n A 1 69 MSE 69 61 61 MSE MSE A . n A 1 70 ASP 70 62 62 ASP ASP A . n A 1 71 GLN 71 63 63 GLN GLN A . n A 1 72 ASN 72 64 64 ASN ASN A . n A 1 73 ALA 73 65 65 ALA ALA A . n A 1 74 PHE 74 66 66 PHE PHE A . n A 1 75 SER 75 67 67 SER SER A . n A 1 76 LEU 76 68 68 LEU LEU A . n A 1 77 THR 77 69 69 THR THR A . n A 1 78 GLN 78 70 70 GLN GLN A . n A 1 79 LYS 79 71 71 LYS LYS A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Northeast Structural Genomics Consortium' _pdbx_SG_project.initial_of_center NESG # 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 B 2 HOH 1 72 1 HOH HOH A . B 2 HOH 2 73 2 HOH HOH A . B 2 HOH 3 74 3 HOH HOH A . B 2 HOH 4 75 4 HOH HOH A . B 2 HOH 5 76 5 HOH HOH A . B 2 HOH 6 77 6 HOH HOH A . B 2 HOH 7 78 7 HOH HOH A . B 2 HOH 8 79 8 HOH HOH A . B 2 HOH 9 80 9 HOH HOH A . B 2 HOH 10 81 10 HOH HOH A . B 2 HOH 11 82 11 HOH HOH A . B 2 HOH 12 83 12 HOH HOH A . B 2 HOH 13 84 13 HOH HOH A . B 2 HOH 14 85 14 HOH HOH A . B 2 HOH 15 86 15 HOH HOH A . B 2 HOH 16 87 16 HOH HOH A . B 2 HOH 17 88 17 HOH HOH A . B 2 HOH 18 89 18 HOH HOH A . B 2 HOH 19 90 19 HOH HOH A . B 2 HOH 20 91 20 HOH HOH A . B 2 HOH 21 92 21 HOH HOH A . B 2 HOH 22 93 22 HOH HOH A . B 2 HOH 23 94 23 HOH HOH A . B 2 HOH 24 95 24 HOH HOH A . B 2 HOH 25 96 25 HOH HOH A . B 2 HOH 26 97 26 HOH HOH A . B 2 HOH 27 98 27 HOH HOH A . B 2 HOH 28 99 28 HOH HOH A . B 2 HOH 29 100 29 HOH HOH A . B 2 HOH 30 101 30 HOH HOH A . B 2 HOH 31 102 31 HOH HOH A . B 2 HOH 32 103 32 HOH HOH A . B 2 HOH 33 104 33 HOH HOH A . B 2 HOH 34 105 34 HOH HOH A . B 2 HOH 35 106 35 HOH HOH A . # 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 MSE 16 A MSE 8 ? MET SELENOMETHIONINE 2 A MSE 24 A MSE 16 ? MET SELENOMETHIONINE 3 A MSE 69 A MSE 61 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 2005-02-08 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 5 'Structure model' 1 4 2021-10-20 # _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' 'Refinement description' 4 5 'Structure model' 'Database references' 5 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' database_2 3 5 'Structure model' struct_conn 4 5 'Structure model' struct_ref_seq_dif # 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' '_software.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 5 'Structure model' '_struct_ref_seq_dif.details' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 SnB phasing . ? 4 SOLVE phasing . ? 5 RESOLVE phasing . ? 6 # _pdbx_database_remark.id 999 _pdbx_database_remark.text ; SEQUENCE THE FIRST FIVE N-TERMINAL RESIDUES OF THE NATIVE PROTEIN, 1-MVNVL-5, WERE SUBSTITUTED BY GTR AND AN N-TAG (MGHHHHHHSH). ; # 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 HIS A 2 ? ? -106.35 -60.50 2 1 ILE A 38 ? ? -128.77 -78.66 3 1 GLU A 48 ? ? -93.04 39.63 # 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 MET -7 ? A MET 1 2 1 Y 1 A GLY -6 ? A GLY 2 3 1 Y 1 A HIS -5 ? A HIS 3 4 1 Y 1 A HIS -4 ? A HIS 4 5 1 Y 1 A HIS -3 ? A HIS 5 6 1 Y 1 A HIS -2 ? A HIS 6 7 1 Y 1 A HIS -1 ? A HIS 7 8 1 Y 1 A HIS 0 ? A HIS 8 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #