data_3IC5 # _entry.id 3IC5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.350 _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 3IC5 pdb_00003ic5 10.2210/pdb3ic5/pdb RCSB RCSB054228 ? ? WWPDB D_1000054228 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id APC63807.2 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3IC5 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-07-17 _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 'Osipiuk, J.' 1 'Tesar, C.' 2 'Freeman, L.' 3 'Joachimiak, A.' 4 'Midwest Center for Structural Genomics (MCSG)' 5 # _citation.id primary _citation.title 'X-ray crystal structure of N-terminal domain of putative saccharopine dehydrogenase from Ruegeria pomeroyi.' _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 'Osipiuk, J.' 1 ? primary 'Tesar, C.' 2 ? primary 'Freeman, L.' 3 ? primary 'Joachimiak, A.' 4 ? # _cell.length_a 54.368 _cell.length_b 57.803 _cell.length_c 73.184 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3IC5 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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.space_group_name_H-M 'P 21 21 21' _symmetry.entry_id 3IC5 _symmetry.Int_Tables_number 19 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _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 'putative saccharopine dehydrogenase' 12301.582 2 ? A110V 'N-terminal domain 1-115' ? 2 water nat water 18.015 118 ? ? ? ? # _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 ;SNA(MSE)RWNICVVGAGKIGQ(MSE)IAALLKTSSNYSVTVADHDLAALAVLNR(MSE)GVATKQVDAKDEAGLAKALG GFDAVISAAPFFLTPIIAKAAKAAGAHYFDLTEDVAATNAVRALVEDSQT ; _entity_poly.pdbx_seq_one_letter_code_can ;SNAMRWNICVVGAGKIGQMIAALLKTSSNYSVTVADHDLAALAVLNRMGVATKQVDAKDEAGLAKALGGFDAVISAAPFF LTPIIAKAAKAAGAHYFDLTEDVAATNAVRALVEDSQT ; _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier APC63807.2 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 ASN n 1 3 ALA n 1 4 MSE n 1 5 ARG n 1 6 TRP n 1 7 ASN n 1 8 ILE n 1 9 CYS n 1 10 VAL n 1 11 VAL n 1 12 GLY n 1 13 ALA n 1 14 GLY n 1 15 LYS n 1 16 ILE n 1 17 GLY n 1 18 GLN n 1 19 MSE n 1 20 ILE n 1 21 ALA n 1 22 ALA n 1 23 LEU n 1 24 LEU n 1 25 LYS n 1 26 THR n 1 27 SER n 1 28 SER n 1 29 ASN n 1 30 TYR n 1 31 SER n 1 32 VAL n 1 33 THR n 1 34 VAL n 1 35 ALA n 1 36 ASP n 1 37 HIS n 1 38 ASP n 1 39 LEU n 1 40 ALA n 1 41 ALA n 1 42 LEU n 1 43 ALA n 1 44 VAL n 1 45 LEU n 1 46 ASN n 1 47 ARG n 1 48 MSE n 1 49 GLY n 1 50 VAL n 1 51 ALA n 1 52 THR n 1 53 LYS n 1 54 GLN n 1 55 VAL n 1 56 ASP n 1 57 ALA n 1 58 LYS n 1 59 ASP n 1 60 GLU n 1 61 ALA n 1 62 GLY n 1 63 LEU n 1 64 ALA n 1 65 LYS n 1 66 ALA n 1 67 LEU n 1 68 GLY n 1 69 GLY n 1 70 PHE n 1 71 ASP n 1 72 ALA n 1 73 VAL n 1 74 ILE n 1 75 SER n 1 76 ALA n 1 77 ALA n 1 78 PRO n 1 79 PHE n 1 80 PHE n 1 81 LEU n 1 82 THR n 1 83 PRO n 1 84 ILE n 1 85 ILE n 1 86 ALA n 1 87 LYS n 1 88 ALA n 1 89 ALA n 1 90 LYS n 1 91 ALA n 1 92 ALA n 1 93 GLY n 1 94 ALA n 1 95 HIS n 1 96 TYR n 1 97 PHE n 1 98 ASP n 1 99 LEU n 1 100 THR n 1 101 GLU n 1 102 ASP n 1 103 VAL n 1 104 ALA n 1 105 ALA n 1 106 THR n 1 107 ASN n 1 108 ALA n 1 109 VAL n 1 110 ARG n 1 111 ALA n 1 112 LEU n 1 113 VAL n 1 114 GLU n 1 115 ASP n 1 116 SER n 1 117 GLN n 1 118 THR 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 ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene SPO0234 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain DSS-3 _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 'Ruegeria pomeroyi' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 89184 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _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)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pMCSG19 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q5LX24_SILPO _struct_ref.pdbx_db_accession Q5LX24 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MRWNICVVGAGKIGQMIAALLKTSSNYSVTVADHDLAALAVLNRMGVATKQVDAKDEAGLAKALGGFDAVISAAPFFLTP IIAKAAKAAGAHYFDLTEDVAATNAVRALAEDSQT ; _struct_ref.pdbx_align_begin 1 _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 3IC5 A 4 ? 118 ? Q5LX24 1 ? 115 ? 1 115 2 1 3IC5 B 4 ? 118 ? Q5LX24 1 ? 115 ? 1 115 # 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 3IC5 SER A 1 ? UNP Q5LX24 ? ? 'expression tag' -2 1 1 3IC5 ASN A 2 ? UNP Q5LX24 ? ? 'expression tag' -1 2 1 3IC5 ALA A 3 ? UNP Q5LX24 ? ? 'expression tag' 0 3 1 3IC5 VAL A 113 ? UNP Q5LX24 ALA 110 'engineered mutation' 110 4 2 3IC5 SER B 1 ? UNP Q5LX24 ? ? 'expression tag' -2 5 2 3IC5 ASN B 2 ? UNP Q5LX24 ? ? 'expression tag' -1 6 2 3IC5 ALA B 3 ? UNP Q5LX24 ? ? 'expression tag' 0 7 2 3IC5 VAL B 113 ? UNP Q5LX24 ALA 110 'engineered mutation' 110 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 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 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 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 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.crystals_number 1 _exptl.entry_id 3IC5 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.34 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 47.37 _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.pH 8.5 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '0.1 M Tris buffer, 20% ethanol, 5% PEG-400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.temp_details ? _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 315' _diffrn_detector.pdbx_collection_date 2009-05-30 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'double crystal monochromator' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9792 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_wavelength_list 0.9792 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID # _reflns.entry_id 3IC5 _reflns.d_resolution_high 2.080 _reflns.d_resolution_low 45.4 _reflns.number_obs 14419 _reflns.pdbx_Rmerge_I_obs 0.085 _reflns.pdbx_netI_over_sigmaI 12.700 _reflns.pdbx_chi_squared 2.457 _reflns.pdbx_redundancy 12.300 _reflns.percent_possible_obs 100.000 _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.number_all 14419 _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate 42.3 _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_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.08 _reflns_shell.d_res_low 2.12 _reflns_shell.number_measured_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs ? _reflns_shell.Rmerge_I_obs 0.786 _reflns_shell.meanI_over_sigI_obs 3.22 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 1.649 _reflns_shell.pdbx_redundancy 7.20 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 691 _reflns_shell.percent_possible_all 100.00 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3IC5 _refine.ls_d_res_high 2.080 _refine.ls_d_res_low 45.360 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.770 _refine.ls_number_reflns_obs 14349 _refine.ls_number_reflns_all 14349 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY' _refine.ls_R_factor_all 0.197 _refine.ls_R_factor_obs 0.197 _refine.ls_R_factor_R_work 0.195 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.251 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 722 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 28.092 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.780 _refine.aniso_B[2][2] 0.080 _refine.aniso_B[3][3] -1.870 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.955 _refine.correlation_coeff_Fo_to_Fc_free 0.928 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.220 _refine.pdbx_overall_ESU_R_Free 0.194 _refine.overall_SU_ML 0.140 _refine.overall_SU_B 11.678 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 59.80 _refine.B_iso_min 15.27 _refine.occupancy_max 1.00 _refine.occupancy_min 0.20 _refine.pdbx_ls_sigma_I 0 _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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 1663 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 118 _refine_hist.number_atoms_total 1781 _refine_hist.d_res_high 2.080 _refine_hist.d_res_low 45.360 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 1724 0.017 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 1087 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2348 1.557 1.949 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 2690 0.951 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 239 6.122 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 62 34.385 25.161 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 281 14.871 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 6 26.981 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 288 0.097 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1960 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 328 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 1157 0.843 1.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 477 0.228 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1835 1.465 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 567 2.408 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 508 3.723 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.080 _refine_ls_shell.d_res_low 2.134 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.130 _refine_ls_shell.number_reflns_R_work 968 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.225 _refine_ls_shell.R_factor_R_free 0.278 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 57 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1025 _refine_ls_shell.number_reflns_obs 1025 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3IC5 _struct.title 'N-terminal domain of putative saccharopine dehydrogenase from Ruegeria pomeroyi.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3IC5 _struct_keywords.text ;structural genomics, APC63807.2, N-terminal domain, saccharopine dehydrogenase, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, unknown function ; _struct_keywords.pdbx_keywords 'structural genomics, unknown function' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_biol.id 1 _struct_biol.details 'putative biological unit is a monomer' # 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 GLY A 14 ? SER A 27 ? GLY A 11 SER A 24 1 ? 14 HELX_P HELX_P2 2 ASP A 38 ? ARG A 47 ? ASP A 35 ARG A 44 1 ? 10 HELX_P HELX_P3 3 ASP A 59 ? LEU A 67 ? ASP A 56 LEU A 64 1 ? 9 HELX_P HELX_P4 4 PRO A 78 ? PHE A 80 ? PRO A 75 PHE A 77 5 ? 3 HELX_P HELX_P5 5 LEU A 81 ? ALA A 92 ? LEU A 78 ALA A 89 1 ? 12 HELX_P HELX_P6 6 ASP A 102 ? ASP A 115 ? ASP A 99 ASP A 112 1 ? 14 HELX_P HELX_P7 7 GLY B 14 ? THR B 26 ? GLY B 11 THR B 23 1 ? 13 HELX_P HELX_P8 8 ALA B 40 ? LEU B 45 ? ALA B 37 LEU B 42 1 ? 6 HELX_P HELX_P9 9 ASP B 59 ? LEU B 67 ? ASP B 56 LEU B 64 1 ? 9 HELX_P HELX_P10 10 PRO B 78 ? PHE B 80 ? PRO B 75 PHE B 77 5 ? 3 HELX_P HELX_P11 11 LEU B 81 ? ALA B 92 ? LEU B 78 ALA B 89 1 ? 12 HELX_P HELX_P12 12 ASP B 102 ? SER B 116 ? ASP B 99 SER B 113 1 ? 15 # _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 ALA 3 C ? ? ? 1_555 A MSE 4 N ? ? A ALA 0 A MSE 1 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale2 covale both ? A MSE 4 C ? ? ? 1_555 A ARG 5 N ? ? A MSE 1 A ARG 2 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale3 covale both ? A GLN 18 C ? ? ? 1_555 A MSE 19 N ? ? A GLN 15 A MSE 16 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale4 covale both ? A MSE 19 C ? ? ? 1_555 A ILE 20 N ? ? A MSE 16 A ILE 17 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale5 covale both ? A ARG 47 C ? ? ? 1_555 A MSE 48 N ? ? A ARG 44 A MSE 45 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale6 covale both ? A MSE 48 C ? ? ? 1_555 A GLY 49 N ? ? A MSE 45 A GLY 46 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale7 covale both ? B MSE 4 C ? ? ? 1_555 B ARG 5 N ? ? B MSE 1 B ARG 2 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale8 covale both ? B GLN 18 C ? ? ? 1_555 B MSE 19 N A ? B GLN 15 B MSE 16 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale9 covale both ? B GLN 18 C ? ? ? 1_555 B MSE 19 N B ? B GLN 15 B MSE 16 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale10 covale both ? B MSE 19 C A ? ? 1_555 B ILE 20 N ? ? B MSE 16 B ILE 17 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale11 covale both ? B MSE 19 C B ? ? 1_555 B ILE 20 N ? ? B MSE 16 B ILE 17 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale12 covale both ? B ARG 47 C A ? ? 1_555 B MSE 48 N A ? B ARG 44 B MSE 45 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale13 covale both ? B MSE 48 C A ? ? 1_555 B GLY 49 N ? ? B MSE 45 B GLY 46 1_555 ? ? ? ? ? ? ? 1.325 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 5 ? # 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 ? parallel A 2 3 ? parallel A 3 4 ? parallel A 4 5 ? parallel B 1 2 ? parallel B 2 3 ? parallel B 3 4 ? parallel B 4 5 ? 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 ALA A 51 ? GLN A 54 ? ALA A 48 GLN A 51 A 2 TYR A 30 ? ASP A 36 ? TYR A 27 ASP A 33 A 3 TRP A 6 ? VAL A 11 ? TRP A 3 VAL A 8 A 4 ALA A 72 ? SER A 75 ? ALA A 69 SER A 72 A 5 HIS A 95 ? PHE A 97 ? HIS A 92 PHE A 94 B 1 ALA B 51 ? GLN B 54 ? ALA B 48 GLN B 51 B 2 TYR B 30 ? ASP B 36 ? TYR B 27 ASP B 33 B 3 TRP B 6 ? VAL B 11 ? TRP B 3 VAL B 8 B 4 ALA B 72 ? SER B 75 ? ALA B 69 SER B 72 B 5 HIS B 95 ? PHE B 97 ? HIS B 92 PHE B 94 # 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 ALA A 51 ? O ALA A 48 N VAL A 34 ? N VAL A 31 A 2 3 O SER A 31 ? O SER A 28 N ILE A 8 ? N ILE A 5 A 3 4 N VAL A 11 ? N VAL A 8 O ILE A 74 ? O ILE A 71 A 4 5 N VAL A 73 ? N VAL A 70 O PHE A 97 ? O PHE A 94 B 1 2 O ALA B 51 ? O ALA B 48 N VAL B 34 ? N VAL B 31 B 2 3 O THR B 33 ? O THR B 30 N VAL B 10 ? N VAL B 7 B 3 4 N VAL B 11 ? N VAL B 8 O ILE B 74 ? O ILE B 71 B 4 5 N VAL B 73 ? N VAL B 70 O HIS B 95 ? O HIS B 92 # _atom_sites.entry_id 3IC5 _atom_sites.fract_transf_matrix[1][1] 0.018393 _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] 0.017300 _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] 0.013664 _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 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 SER 1 -2 ? ? ? A . n A 1 2 ASN 2 -1 -1 ASN ASN A . n A 1 3 ALA 3 0 0 ALA ALA A . n A 1 4 MSE 4 1 1 MSE MSE A . n A 1 5 ARG 5 2 2 ARG ARG A . n A 1 6 TRP 6 3 3 TRP TRP A . n A 1 7 ASN 7 4 4 ASN ASN A . n A 1 8 ILE 8 5 5 ILE ILE A . n A 1 9 CYS 9 6 6 CYS CYS A . n A 1 10 VAL 10 7 7 VAL VAL A . n A 1 11 VAL 11 8 8 VAL VAL A . n A 1 12 GLY 12 9 9 GLY GLY A . n A 1 13 ALA 13 10 10 ALA ALA A . n A 1 14 GLY 14 11 11 GLY GLY A . n A 1 15 LYS 15 12 12 LYS LYS A . n A 1 16 ILE 16 13 13 ILE ILE A . n A 1 17 GLY 17 14 14 GLY GLY A . n A 1 18 GLN 18 15 15 GLN GLN A . n A 1 19 MSE 19 16 16 MSE MSE A . n A 1 20 ILE 20 17 17 ILE ILE A . n A 1 21 ALA 21 18 18 ALA ALA A . n A 1 22 ALA 22 19 19 ALA ALA A . n A 1 23 LEU 23 20 20 LEU LEU A . n A 1 24 LEU 24 21 21 LEU LEU A . n A 1 25 LYS 25 22 22 LYS LYS A . n A 1 26 THR 26 23 23 THR THR A . n A 1 27 SER 27 24 24 SER SER A . n A 1 28 SER 28 25 25 SER SER A . n A 1 29 ASN 29 26 26 ASN ASN A . n A 1 30 TYR 30 27 27 TYR TYR A . n A 1 31 SER 31 28 28 SER SER A . n A 1 32 VAL 32 29 29 VAL VAL A . n A 1 33 THR 33 30 30 THR THR A . n A 1 34 VAL 34 31 31 VAL VAL A . n A 1 35 ALA 35 32 32 ALA ALA A . n A 1 36 ASP 36 33 33 ASP ASP A . n A 1 37 HIS 37 34 34 HIS HIS A . n A 1 38 ASP 38 35 35 ASP ASP A . n A 1 39 LEU 39 36 36 LEU LEU A . n A 1 40 ALA 40 37 37 ALA ALA A . n A 1 41 ALA 41 38 38 ALA ALA A . n A 1 42 LEU 42 39 39 LEU LEU A . n A 1 43 ALA 43 40 40 ALA ALA A . n A 1 44 VAL 44 41 41 VAL VAL A . n A 1 45 LEU 45 42 42 LEU LEU A . n A 1 46 ASN 46 43 43 ASN ASN A . n A 1 47 ARG 47 44 44 ARG ARG A . n A 1 48 MSE 48 45 45 MSE MSE A . n A 1 49 GLY 49 46 46 GLY GLY A . n A 1 50 VAL 50 47 47 VAL VAL A . n A 1 51 ALA 51 48 48 ALA ALA A . n A 1 52 THR 52 49 49 THR THR A . n A 1 53 LYS 53 50 50 LYS LYS A . n A 1 54 GLN 54 51 51 GLN GLN A . n A 1 55 VAL 55 52 52 VAL VAL A . n A 1 56 ASP 56 53 53 ASP ASP A . n A 1 57 ALA 57 54 54 ALA ALA A . n A 1 58 LYS 58 55 55 LYS LYS A . n A 1 59 ASP 59 56 56 ASP ASP A . n A 1 60 GLU 60 57 57 GLU GLU A . n A 1 61 ALA 61 58 58 ALA ALA A . n A 1 62 GLY 62 59 59 GLY GLY A . n A 1 63 LEU 63 60 60 LEU LEU A . n A 1 64 ALA 64 61 61 ALA ALA A . n A 1 65 LYS 65 62 62 LYS LYS A . n A 1 66 ALA 66 63 63 ALA ALA A . n A 1 67 LEU 67 64 64 LEU LEU A . n A 1 68 GLY 68 65 65 GLY GLY A . n A 1 69 GLY 69 66 66 GLY GLY A . n A 1 70 PHE 70 67 67 PHE PHE A . n A 1 71 ASP 71 68 68 ASP ASP A . n A 1 72 ALA 72 69 69 ALA ALA A . n A 1 73 VAL 73 70 70 VAL VAL A . n A 1 74 ILE 74 71 71 ILE ILE A . n A 1 75 SER 75 72 72 SER SER A . n A 1 76 ALA 76 73 73 ALA ALA A . n A 1 77 ALA 77 74 74 ALA ALA A . n A 1 78 PRO 78 75 75 PRO PRO A . n A 1 79 PHE 79 76 76 PHE PHE A . n A 1 80 PHE 80 77 77 PHE PHE A . n A 1 81 LEU 81 78 78 LEU LEU A . n A 1 82 THR 82 79 79 THR THR A . n A 1 83 PRO 83 80 80 PRO PRO A . n A 1 84 ILE 84 81 81 ILE ILE A . n A 1 85 ILE 85 82 82 ILE ILE A . n A 1 86 ALA 86 83 83 ALA ALA A . n A 1 87 LYS 87 84 84 LYS LYS A . n A 1 88 ALA 88 85 85 ALA ALA A . n A 1 89 ALA 89 86 86 ALA ALA A . n A 1 90 LYS 90 87 87 LYS LYS A . n A 1 91 ALA 91 88 88 ALA ALA A . n A 1 92 ALA 92 89 89 ALA ALA A . n A 1 93 GLY 93 90 90 GLY GLY A . n A 1 94 ALA 94 91 91 ALA ALA A . n A 1 95 HIS 95 92 92 HIS HIS A . n A 1 96 TYR 96 93 93 TYR TYR A . n A 1 97 PHE 97 94 94 PHE PHE A . n A 1 98 ASP 98 95 95 ASP ASP A . n A 1 99 LEU 99 96 96 LEU LEU A . n A 1 100 THR 100 97 97 THR THR A . n A 1 101 GLU 101 98 98 GLU GLU A . n A 1 102 ASP 102 99 99 ASP ASP A . n A 1 103 VAL 103 100 100 VAL VAL A . n A 1 104 ALA 104 101 101 ALA ALA A . n A 1 105 ALA 105 102 102 ALA ALA A . n A 1 106 THR 106 103 103 THR THR A . n A 1 107 ASN 107 104 104 ASN ASN A . n A 1 108 ALA 108 105 105 ALA ALA A . n A 1 109 VAL 109 106 106 VAL VAL A . n A 1 110 ARG 110 107 107 ARG ARG A . n A 1 111 ALA 111 108 108 ALA ALA A . n A 1 112 LEU 112 109 109 LEU LEU A . n A 1 113 VAL 113 110 110 VAL VAL A . n A 1 114 GLU 114 111 111 GLU GLU A . n A 1 115 ASP 115 112 112 ASP ASP A . n A 1 116 SER 116 113 113 SER SER A . n A 1 117 GLN 117 114 ? ? ? A . n A 1 118 THR 118 115 ? ? ? A . n B 1 1 SER 1 -2 ? ? ? B . n B 1 2 ASN 2 -1 ? ? ? B . n B 1 3 ALA 3 0 ? ? ? B . n B 1 4 MSE 4 1 1 MSE MSE B . n B 1 5 ARG 5 2 2 ARG ARG B . n B 1 6 TRP 6 3 3 TRP TRP B . n B 1 7 ASN 7 4 4 ASN ASN B . n B 1 8 ILE 8 5 5 ILE ILE B . n B 1 9 CYS 9 6 6 CYS CYS B . n B 1 10 VAL 10 7 7 VAL VAL B . n B 1 11 VAL 11 8 8 VAL VAL B . n B 1 12 GLY 12 9 9 GLY GLY B . n B 1 13 ALA 13 10 10 ALA ALA B . n B 1 14 GLY 14 11 11 GLY GLY B . n B 1 15 LYS 15 12 12 LYS LYS B . n B 1 16 ILE 16 13 13 ILE ILE B . n B 1 17 GLY 17 14 14 GLY GLY B . n B 1 18 GLN 18 15 15 GLN GLN B . n B 1 19 MSE 19 16 16 MSE MSE B . n B 1 20 ILE 20 17 17 ILE ILE B . n B 1 21 ALA 21 18 18 ALA ALA B . n B 1 22 ALA 22 19 19 ALA ALA B . n B 1 23 LEU 23 20 20 LEU LEU B . n B 1 24 LEU 24 21 21 LEU LEU B . n B 1 25 LYS 25 22 22 LYS LYS B . n B 1 26 THR 26 23 23 THR THR B . n B 1 27 SER 27 24 24 SER SER B . n B 1 28 SER 28 25 25 SER SER B . n B 1 29 ASN 29 26 26 ASN ASN B . n B 1 30 TYR 30 27 27 TYR TYR B . n B 1 31 SER 31 28 28 SER SER B . n B 1 32 VAL 32 29 29 VAL VAL B . n B 1 33 THR 33 30 30 THR THR B . n B 1 34 VAL 34 31 31 VAL VAL B . n B 1 35 ALA 35 32 32 ALA ALA B . n B 1 36 ASP 36 33 33 ASP ASP B . n B 1 37 HIS 37 34 34 HIS HIS B . n B 1 38 ASP 38 35 35 ASP ASP B . n B 1 39 LEU 39 36 36 LEU LEU B . n B 1 40 ALA 40 37 37 ALA ALA B . n B 1 41 ALA 41 38 38 ALA ALA B . n B 1 42 LEU 42 39 39 LEU LEU B . n B 1 43 ALA 43 40 40 ALA ALA B . n B 1 44 VAL 44 41 41 VAL VAL B . n B 1 45 LEU 45 42 42 LEU LEU B . n B 1 46 ASN 46 43 43 ASN ASN B . n B 1 47 ARG 47 44 44 ARG ARG B . n B 1 48 MSE 48 45 45 MSE MSE B . n B 1 49 GLY 49 46 46 GLY GLY B . n B 1 50 VAL 50 47 47 VAL VAL B . n B 1 51 ALA 51 48 48 ALA ALA B . n B 1 52 THR 52 49 49 THR THR B . n B 1 53 LYS 53 50 50 LYS LYS B . n B 1 54 GLN 54 51 51 GLN GLN B . n B 1 55 VAL 55 52 52 VAL VAL B . n B 1 56 ASP 56 53 53 ASP ASP B . n B 1 57 ALA 57 54 54 ALA ALA B . n B 1 58 LYS 58 55 55 LYS LYS B . n B 1 59 ASP 59 56 56 ASP ASP B . n B 1 60 GLU 60 57 57 GLU GLU B . n B 1 61 ALA 61 58 58 ALA ALA B . n B 1 62 GLY 62 59 59 GLY GLY B . n B 1 63 LEU 63 60 60 LEU LEU B . n B 1 64 ALA 64 61 61 ALA ALA B . n B 1 65 LYS 65 62 62 LYS LYS B . n B 1 66 ALA 66 63 63 ALA ALA B . n B 1 67 LEU 67 64 64 LEU LEU B . n B 1 68 GLY 68 65 65 GLY GLY B . n B 1 69 GLY 69 66 66 GLY GLY B . n B 1 70 PHE 70 67 67 PHE PHE B . n B 1 71 ASP 71 68 68 ASP ASP B . n B 1 72 ALA 72 69 69 ALA ALA B . n B 1 73 VAL 73 70 70 VAL VAL B . n B 1 74 ILE 74 71 71 ILE ILE B . n B 1 75 SER 75 72 72 SER SER B . n B 1 76 ALA 76 73 73 ALA ALA B . n B 1 77 ALA 77 74 74 ALA ALA B . n B 1 78 PRO 78 75 75 PRO PRO B . n B 1 79 PHE 79 76 76 PHE PHE B . n B 1 80 PHE 80 77 77 PHE PHE B . n B 1 81 LEU 81 78 78 LEU LEU B . n B 1 82 THR 82 79 79 THR THR B . n B 1 83 PRO 83 80 80 PRO PRO B . n B 1 84 ILE 84 81 81 ILE ILE B . n B 1 85 ILE 85 82 82 ILE ILE B . n B 1 86 ALA 86 83 83 ALA ALA B . n B 1 87 LYS 87 84 84 LYS LYS B . n B 1 88 ALA 88 85 85 ALA ALA B . n B 1 89 ALA 89 86 86 ALA ALA B . n B 1 90 LYS 90 87 87 LYS LYS B . n B 1 91 ALA 91 88 88 ALA ALA B . n B 1 92 ALA 92 89 89 ALA ALA B . n B 1 93 GLY 93 90 90 GLY GLY B . n B 1 94 ALA 94 91 91 ALA ALA B . n B 1 95 HIS 95 92 92 HIS HIS B . n B 1 96 TYR 96 93 93 TYR TYR B . n B 1 97 PHE 97 94 94 PHE PHE B . n B 1 98 ASP 98 95 95 ASP ASP B . n B 1 99 LEU 99 96 96 LEU LEU B . n B 1 100 THR 100 97 97 THR THR B . n B 1 101 GLU 101 98 98 GLU GLU B . n B 1 102 ASP 102 99 99 ASP ASP B . n B 1 103 VAL 103 100 100 VAL VAL B . n B 1 104 ALA 104 101 101 ALA ALA B . n B 1 105 ALA 105 102 102 ALA ALA B . n B 1 106 THR 106 103 103 THR THR B . n B 1 107 ASN 107 104 104 ASN ASN B . n B 1 108 ALA 108 105 105 ALA ALA B . n B 1 109 VAL 109 106 106 VAL VAL B . n B 1 110 ARG 110 107 107 ARG ARG B . n B 1 111 ALA 111 108 108 ALA ALA B . n B 1 112 LEU 112 109 109 LEU LEU B . n B 1 113 VAL 113 110 110 VAL VAL B . n B 1 114 GLU 114 111 111 GLU GLU B . n B 1 115 ASP 115 112 112 ASP ASP B . n B 1 116 SER 116 113 113 SER SER B . n B 1 117 GLN 117 114 114 GLN GLN B . n B 1 118 THR 118 115 115 THR THR B . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Midwest Center for Structural Genomics' _pdbx_SG_project.initial_of_center MCSG # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 116 116 HOH HOH A . C 2 HOH 2 117 1 HOH HOH A . C 2 HOH 3 118 4 HOH HOH A . C 2 HOH 4 119 9 HOH HOH A . C 2 HOH 5 120 10 HOH HOH A . C 2 HOH 6 121 11 HOH HOH A . C 2 HOH 7 122 12 HOH HOH A . C 2 HOH 8 123 13 HOH HOH A . C 2 HOH 9 124 14 HOH HOH A . C 2 HOH 10 125 17 HOH HOH A . C 2 HOH 11 126 20 HOH HOH A . C 2 HOH 12 127 22 HOH HOH A . C 2 HOH 13 128 23 HOH HOH A . C 2 HOH 14 129 24 HOH HOH A . C 2 HOH 15 131 33 HOH HOH A . C 2 HOH 16 132 36 HOH HOH A . C 2 HOH 17 133 38 HOH HOH A . C 2 HOH 18 134 41 HOH HOH A . C 2 HOH 19 135 42 HOH HOH A . C 2 HOH 20 136 43 HOH HOH A . C 2 HOH 21 137 44 HOH HOH A . C 2 HOH 22 138 46 HOH HOH A . C 2 HOH 23 139 51 HOH HOH A . C 2 HOH 24 140 56 HOH HOH A . C 2 HOH 25 141 59 HOH HOH A . C 2 HOH 26 142 60 HOH HOH A . C 2 HOH 27 143 62 HOH HOH A . C 2 HOH 28 144 63 HOH HOH A . C 2 HOH 29 145 64 HOH HOH A . C 2 HOH 30 146 67 HOH HOH A . C 2 HOH 31 147 68 HOH HOH A . C 2 HOH 32 148 69 HOH HOH A . C 2 HOH 33 149 72 HOH HOH A . C 2 HOH 34 150 74 HOH HOH A . C 2 HOH 35 151 76 HOH HOH A . C 2 HOH 36 152 77 HOH HOH A . C 2 HOH 37 153 78 HOH HOH A . C 2 HOH 38 154 83 HOH HOH A . C 2 HOH 39 155 85 HOH HOH A . C 2 HOH 40 156 90 HOH HOH A . C 2 HOH 41 157 91 HOH HOH A . C 2 HOH 42 158 93 HOH HOH A . C 2 HOH 43 159 94 HOH HOH A . C 2 HOH 44 160 96 HOH HOH A . C 2 HOH 45 161 99 HOH HOH A . C 2 HOH 46 162 100 HOH HOH A . C 2 HOH 47 163 102 HOH HOH A . C 2 HOH 48 164 104 HOH HOH A . C 2 HOH 49 165 106 HOH HOH A . C 2 HOH 50 166 107 HOH HOH A . C 2 HOH 51 167 108 HOH HOH A . C 2 HOH 52 168 109 HOH HOH A . C 2 HOH 53 169 110 HOH HOH A . C 2 HOH 54 170 111 HOH HOH A . D 2 HOH 1 116 2 HOH HOH B . D 2 HOH 2 117 117 HOH HOH B . D 2 HOH 3 118 118 HOH HOH B . D 2 HOH 4 119 3 HOH HOH B . D 2 HOH 5 120 5 HOH HOH B . D 2 HOH 6 121 6 HOH HOH B . D 2 HOH 7 122 7 HOH HOH B . D 2 HOH 8 123 8 HOH HOH B . D 2 HOH 9 124 15 HOH HOH B . D 2 HOH 10 125 16 HOH HOH B . D 2 HOH 11 126 18 HOH HOH B . D 2 HOH 12 127 19 HOH HOH B . D 2 HOH 13 128 21 HOH HOH B . D 2 HOH 14 129 25 HOH HOH B . D 2 HOH 15 130 26 HOH HOH B . D 2 HOH 16 131 28 HOH HOH B . D 2 HOH 17 132 29 HOH HOH B . D 2 HOH 18 133 30 HOH HOH B . D 2 HOH 19 134 31 HOH HOH B . D 2 HOH 20 135 32 HOH HOH B . D 2 HOH 21 136 34 HOH HOH B . D 2 HOH 22 137 35 HOH HOH B . D 2 HOH 23 138 37 HOH HOH B . D 2 HOH 24 139 39 HOH HOH B . D 2 HOH 25 140 40 HOH HOH B . D 2 HOH 26 141 45 HOH HOH B . D 2 HOH 27 142 47 HOH HOH B . D 2 HOH 28 143 48 HOH HOH B . D 2 HOH 29 144 49 HOH HOH B . D 2 HOH 30 145 50 HOH HOH B . D 2 HOH 31 146 52 HOH HOH B . D 2 HOH 32 147 53 HOH HOH B . D 2 HOH 33 148 54 HOH HOH B . D 2 HOH 34 149 55 HOH HOH B . D 2 HOH 35 150 57 HOH HOH B . D 2 HOH 36 151 58 HOH HOH B . D 2 HOH 37 152 61 HOH HOH B . D 2 HOH 38 153 65 HOH HOH B . D 2 HOH 39 154 66 HOH HOH B . D 2 HOH 40 155 70 HOH HOH B . D 2 HOH 41 156 71 HOH HOH B . D 2 HOH 42 157 73 HOH HOH B . D 2 HOH 43 158 75 HOH HOH B . D 2 HOH 44 159 79 HOH HOH B . D 2 HOH 45 160 80 HOH HOH B . D 2 HOH 46 161 81 HOH HOH B . D 2 HOH 47 162 82 HOH HOH B . D 2 HOH 48 163 84 HOH HOH B . D 2 HOH 49 164 86 HOH HOH B . D 2 HOH 50 165 87 HOH HOH B . D 2 HOH 51 166 88 HOH HOH B . D 2 HOH 52 167 89 HOH HOH B . D 2 HOH 53 168 92 HOH HOH B . D 2 HOH 54 169 95 HOH HOH B . D 2 HOH 55 170 97 HOH HOH B . D 2 HOH 56 171 98 HOH HOH B . D 2 HOH 57 172 101 HOH HOH B . D 2 HOH 58 173 103 HOH HOH B . D 2 HOH 59 174 105 HOH HOH B . D 2 HOH 60 175 112 HOH HOH B . D 2 HOH 61 176 113 HOH HOH B . D 2 HOH 62 177 114 HOH HOH B . D 2 HOH 63 178 115 HOH HOH B . D 2 HOH 64 179 27 HOH HOH B . # 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 4 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 19 A MSE 16 ? MET SELENOMETHIONINE 3 A MSE 48 A MSE 45 ? MET SELENOMETHIONINE 4 B MSE 4 B MSE 1 ? MET SELENOMETHIONINE 5 B MSE 19 B MSE 16 ? MET SELENOMETHIONINE 6 B MSE 48 B MSE 45 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA monomeric 1 2 author_and_software_defined_assembly PISA monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C 2 1 B,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 2009-07-28 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-01 4 'Structure model' 1 3 2021-10-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _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' Advisory 2 2 'Structure model' 'Refinement description' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Refinement description' 5 4 'Structure model' 'Database references' 6 4 '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 3 'Structure model' software 2 4 'Structure model' database_2 3 4 'Structure model' struct_conn 4 4 '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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_ref_seq_dif.details' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 41.4482 18.9182 20.5481 0.0750 0.0285 0.0102 -0.0293 -0.0092 0.0018 2.9514 4.6597 3.3939 -0.3531 -0.6711 1.4906 0.0580 0.0091 -0.0670 -0.1480 0.1013 -0.1487 -0.0192 -0.1206 0.1197 'X-RAY DIFFRACTION' 2 ? refined 24.9882 33.3582 31.3391 0.0323 0.0482 0.0362 -0.0229 0.0002 -0.0008 3.6585 3.2780 3.7402 0.0136 0.9529 0.0816 0.1078 0.1055 -0.2133 -0.2148 -0.2826 0.0329 0.1397 0.1513 0.0065 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 1 A 113 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 B 1 B 115 ? . . . . ? # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 REFMAC 5.5.0054 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.005 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 SBC-Collect . ? ? ? ? 'data collection' ? ? ? 6 HKL-3000 . ? ? ? ? 'data reduction' ? ? ? 7 HKL-3000 . ? ? ? ? 'data scaling' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? 9 MLPHARE . ? ? ? ? phasing ? ? ? 10 DM . ? ? ? ? phasing ? ? ? 11 SOLVE . ? ? ? ? phasing ? ? ? 12 RESOLVE . ? ? ? ? phasing ? ? ? 13 HKL-3000 . ? ? ? ? phasing ? ? ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 144 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 157 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.95 # 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 ALA A 0 ? ? -57.07 19.42 2 1 THR A 97 ? ? 76.94 169.65 3 1 MSE B 45 ? A -90.95 -154.19 4 1 ASP B 95 ? ? -90.21 58.41 5 1 THR B 97 ? ? 71.64 170.01 6 1 ASP B 99 ? ? -162.49 96.62 # 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 SER -2 ? A SER 1 2 1 Y 1 A GLN 114 ? A GLN 117 3 1 Y 1 A THR 115 ? A THR 118 4 1 Y 1 B SER -2 ? B SER 1 5 1 Y 1 B ASN -1 ? B ASN 2 6 1 Y 1 B ALA 0 ? B ALA 3 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #