data_4JM1 # _entry.id 4JM1 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _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 4JM1 pdb_00004jm1 10.2210/pdb4jm1/pdb RCSB RCSB078215 ? ? WWPDB D_1000078215 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-419124 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4JM1 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-03-13 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of a hypothetical protein (BDI_0842) from Parabacteroides distasonis ATCC 8503 at 1.40 A resolution' _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 ? # _citation_author.citation_id primary _citation_author.name 'Joint Center for Structural Genomics (JCSG)' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # _cell.entry_id 4JM1 _cell.length_a 37.405 _cell.length_b 45.673 _cell.length_c 48.105 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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 4JM1 _symmetry.Int_Tables_number 19 _symmetry.space_group_name_H-M 'P 21 21 21' _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 'hypothetical protein' 8948.997 1 ? ? ? ? 2 non-polymer syn 1,2-ETHANEDIOL 62.068 2 ? ? ? ? 3 water nat water 18.015 148 ? ? ? ? # _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 ;GADKYIDTITGFSCEKAAVTDNGFLVIAIDADSDSGYD(MSE)LASQFLEEAKKEGVSGLKGVLIVDIKNAKFEQGAVVG KRIGKAYK ; _entity_poly.pdbx_seq_one_letter_code_can ;GADKYIDTITGFSCEKAAVTDNGFLVIAIDADSDSGYDMLASQFLEEAKKEGVSGLKGVLIVDIKNAKFEQGAVVGKRIG KAYK ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier JCSG-419124 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 ALA n 1 3 ASP n 1 4 LYS n 1 5 TYR n 1 6 ILE n 1 7 ASP n 1 8 THR n 1 9 ILE n 1 10 THR n 1 11 GLY n 1 12 PHE n 1 13 SER n 1 14 CYS n 1 15 GLU n 1 16 LYS n 1 17 ALA n 1 18 ALA n 1 19 VAL n 1 20 THR n 1 21 ASP n 1 22 ASN n 1 23 GLY n 1 24 PHE n 1 25 LEU n 1 26 VAL n 1 27 ILE n 1 28 ALA n 1 29 ILE n 1 30 ASP n 1 31 ALA n 1 32 ASP n 1 33 SER n 1 34 ASP n 1 35 SER n 1 36 GLY n 1 37 TYR n 1 38 ASP n 1 39 MSE n 1 40 LEU n 1 41 ALA n 1 42 SER n 1 43 GLN n 1 44 PHE n 1 45 LEU n 1 46 GLU n 1 47 GLU n 1 48 ALA n 1 49 LYS n 1 50 LYS n 1 51 GLU n 1 52 GLY n 1 53 VAL n 1 54 SER n 1 55 GLY n 1 56 LEU n 1 57 LYS n 1 58 GLY n 1 59 VAL n 1 60 LEU n 1 61 ILE n 1 62 VAL n 1 63 ASP n 1 64 ILE n 1 65 LYS n 1 66 ASN n 1 67 ALA n 1 68 LYS n 1 69 PHE n 1 70 GLU n 1 71 GLN n 1 72 GLY n 1 73 ALA n 1 74 VAL n 1 75 VAL n 1 76 GLY n 1 77 LYS n 1 78 ARG n 1 79 ILE n 1 80 GLY n 1 81 LYS n 1 82 ALA n 1 83 TYR n 1 84 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 ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'BDI_0842, YP_001302234.1' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 8503' _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 'Parabacteroides distasonis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 435591 _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 ? _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 PB1 _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 SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A6LA98_PARD8 _struct_ref.pdbx_db_accession A6LA98 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ADKYIDTITGFSCEKAAVTDNGFLVIAIDADSDSGYDMLASQFLEEAKKEGVSGLKGVLIVDIKNAKFEQGAVVGKRIGK AYK ; _struct_ref.pdbx_align_begin 26 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4JM1 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 84 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A6LA98 _struct_ref_seq.db_align_beg 26 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 108 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 26 _struct_ref_seq.pdbx_auth_seq_align_end 108 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4JM1 _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code A6LA98 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 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 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 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.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 4JM1 # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.30 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 46.42 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.pdbx_details '8.0% ethylene glycol, 20.0% polyethylene glycol 10000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp 277 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.pH 7.5 # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.details 'Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)' _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2013-02-21 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'single crystal Si(111) bent' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.97917 1.0 2 0.88557 1.0 3 0.97849 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength_list 0.97917,0.88557,0.97849 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.limit_k_max ? _reflns.d_resolution_high 1.40 _reflns.observed_criterion_F_min ? _reflns.pdbx_netI_over_sigmaI 11.890 _reflns.observed_criterion_F_max ? _reflns.pdbx_Rmerge_I_obs 0.045 _reflns.limit_l_max ? _reflns.limit_k_min ? _reflns.entry_id 4JM1 _reflns.B_iso_Wilson_estimate 13.784 _reflns.percent_possible_obs 97.300 _reflns.pdbx_Rsym_value ? _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.limit_l_min ? _reflns.limit_h_min ? _reflns.R_free_details ? _reflns.number_all ? _reflns.d_resolution_low 29.529 _reflns.pdbx_redundancy ? _reflns.number_obs 16677 _reflns.limit_h_max ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.400 1.450 6396 ? 3066 0.513 1.9 ? ? ? ? ? 97.700 1 1 1.450 1.510 6653 ? 3167 0.342 2.9 ? ? ? ? ? 97.700 2 1 1.510 1.580 6184 ? 3077 0.266 3.6 ? ? ? ? ? 97.300 3 1 1.580 1.660 6351 ? 2983 0.184 5.0 ? ? ? ? ? 98.700 4 1 1.660 1.760 6289 ? 2952 0.140 6.5 ? ? ? ? ? 98.200 5 1 1.760 1.900 6453 ? 3167 0.095 8.9 ? ? ? ? ? 97.300 6 1 1.900 2.090 6639 ? 3055 0.056 14.6 ? ? ? ? ? 97.800 7 1 2.090 2.390 6273 ? 2994 0.039 19.4 ? ? ? ? ? 96.200 8 1 2.390 3.010 6763 ? 3077 0.031 24.4 ? ? ? ? ? 97.700 9 1 3.010 ? 6436 ? 3005 0.021 32.3 ? ? ? ? ? 94.900 10 1 # _refine.ls_percent_reflns_R_free 5.1000 _refine.overall_SU_B 1.8530 _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_R_Free_selection_details RANDOM _refine.overall_FOM_free_R_set ? _refine.pdbx_data_cutoff_low_absF ? _refine.entry_id 4JM1 _refine.aniso_B[2][3] 0.0000 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_ML 0.0330 _refine.pdbx_ls_sigma_I ? _refine.aniso_B[1][3] 0.0000 _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.aniso_B[3][3] -0.0400 _refine.occupancy_max 1.000 _refine.ls_number_restraints ? _refine.aniso_B[1][1] 0.5900 _refine.pdbx_overall_ESU_R 0.0580 _refine.ls_R_factor_obs 0.1309 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_starting_model ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_method_to_determine_struct MAD _refine.solvent_model_param_ksol ? _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.correlation_coeff_Fo_to_Fc 0.9790 _refine.ls_number_reflns_R_free 845 _refine.correlation_coeff_Fo_to_Fc_free 0.9720 _refine.pdbx_ls_sigma_F 0.000 _refine.ls_percent_reflns_obs 99.1500 _refine.ls_R_factor_R_work 0.1289 _refine.overall_SU_R_free ? _refine.ls_d_res_high 1.4000 _refine.pdbx_overall_ESU_R_Free 0.0550 _refine.B_iso_min 9.140 _refine.occupancy_min 0.200 _refine.B_iso_mean 18.9160 _refine.pdbx_stereochem_target_val_spec_case ? _refine.ls_R_factor_all ? _refine.aniso_B[2][2] -0.5500 _refine.B_iso_max 55.440 _refine.ls_d_res_low 29.529 _refine.pdbx_overall_phase_error ? _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.aniso_B[1][2] 0.0000 _refine.ls_R_factor_R_free 0.1679 _refine.ls_R_factor_R_free_error ? _refine.ls_number_reflns_obs 16642 _refine.overall_FOM_work_R_set ? _refine.ls_number_parameters ? _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. ; _refine.ls_number_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.solvent_model_param_bsol ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 622 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 148 _refine_hist.number_atoms_total 778 _refine_hist.d_res_high 1.4000 _refine_hist.d_res_low 29.529 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 688 0.013 0.022 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 475 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 928 1.416 1.981 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 1182 0.920 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 97 5.056 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 29 34.919 26.897 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 133 10.302 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 1 20.339 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 104 0.084 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 786 0.006 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 127 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 437 2.359 3.000 ? ? 'X-RAY DIFFRACTION' r_mcbond_other 186 1.222 3.000 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 700 3.512 5.000 ? ? 'X-RAY DIFFRACTION' r_scbond_it 251 4.591 8.000 ? ? 'X-RAY DIFFRACTION' r_scangle_it 221 6.728 11.000 ? ? 'X-RAY DIFFRACTION' r_rigid_bond_restr 1163 1.761 3.000 ? ? 'X-RAY DIFFRACTION' r_sphericity_free 151 6.497 3.000 ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded 1151 3.202 3.000 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 1.4010 _refine_ls_shell.d_res_low 1.4370 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.1900 _refine_ls_shell.number_reflns_R_work 1159 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.1880 _refine_ls_shell.R_factor_R_free 0.2690 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 66 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1225 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.title ;Crystal structure of a protein with alpha-lytic protease prodomain-like fold (BDI_0842) from Parabacteroides distasonis ATCC 8503 at 1.40 A resolution ; _struct.entry_id 4JM1 _struct.pdbx_model_type_details ? _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.pdbx_keywords 'Structural Genomics, Unknown Function' _struct_keywords.text ;ORFan, new alpha/beta fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION ; _struct_keywords.entry_id 4JM1 # 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 ? C N N 2 ? D N N 3 ? # _struct_biol.id 1 _struct_biol.details 'CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.' # 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 ALA A 2 ? THR A 10 ? ALA A 26 THR A 34 1 ? 9 HELX_P HELX_P2 2 TYR A 37 ? GLU A 51 ? TYR A 61 GLU A 75 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 ASP 38 C ? ? ? 1_555 A MSE 39 N ? ? A ASP 62 A MSE 63 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale2 covale both ? A MSE 39 C ? ? ? 1_555 A LEU 40 N ? ? A MSE 63 A LEU 64 1_555 ? ? ? ? ? ? ? 1.320 ? ? # _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 ? 4 ? B ? 2 ? # 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 ? parallel A 3 4 ? anti-parallel B 1 2 ? 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 LYS A 16 ? VAL A 19 ? LYS A 40 VAL A 43 A 2 PHE A 24 ? ILE A 29 ? PHE A 48 ILE A 53 A 3 GLY A 58 ? ASP A 63 ? GLY A 82 ASP A 87 A 4 ARG A 78 ? TYR A 83 ? ARG A 102 TYR A 107 B 1 LYS A 68 ? GLU A 70 ? LYS A 92 GLU A 94 B 2 ALA A 73 ? VAL A 75 ? ALA A 97 VAL A 99 # 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 ALA A 18 ? N ALA A 42 O VAL A 26 ? O VAL A 50 A 2 3 N ILE A 27 ? N ILE A 51 O LEU A 60 ? O LEU A 84 A 3 4 N ILE A 61 ? N ILE A 85 O GLY A 80 ? O GLY A 104 B 1 2 N GLU A 70 ? N GLU A 94 O ALA A 73 ? O ALA A 97 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A EDO 200 ? 5 'BINDING SITE FOR RESIDUE EDO A 200' AC2 Software A EDO 201 ? 4 'BINDING SITE FOR RESIDUE EDO A 201' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 5 ILE A 9 ? ILE A 33 . ? 1_555 ? 2 AC1 5 GLU A 47 ? GLU A 71 . ? 1_555 ? 3 AC1 5 GLU A 51 ? GLU A 75 . ? 1_555 ? 4 AC1 5 HOH D . ? HOH A 324 . ? 1_555 ? 5 AC1 5 HOH D . ? HOH A 415 . ? 1_555 ? 6 AC2 4 GLU A 47 ? GLU A 71 . ? 1_555 ? 7 AC2 4 GLY A 52 ? GLY A 76 . ? 4_555 ? 8 AC2 4 SER A 54 ? SER A 78 . ? 4_555 ? 9 AC2 4 HOH D . ? HOH A 386 . ? 4_555 ? # _atom_sites.entry_id 4JM1 _atom_sites.fract_transf_matrix[1][1] 0.026734 _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] 0.021895 _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] 0.020788 _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 GLY 1 0 0 GLY GLY A . n A 1 2 ALA 2 26 26 ALA ALA A . n A 1 3 ASP 3 27 27 ASP ASP A . n A 1 4 LYS 4 28 28 LYS LYS A . n A 1 5 TYR 5 29 29 TYR TYR A . n A 1 6 ILE 6 30 30 ILE ILE A . n A 1 7 ASP 7 31 31 ASP ASP A . n A 1 8 THR 8 32 32 THR THR A . n A 1 9 ILE 9 33 33 ILE ILE A . n A 1 10 THR 10 34 34 THR THR A . n A 1 11 GLY 11 35 35 GLY GLY A . n A 1 12 PHE 12 36 36 PHE PHE A . n A 1 13 SER 13 37 37 SER SER A . n A 1 14 CYS 14 38 38 CYS CYS A . n A 1 15 GLU 15 39 39 GLU GLU A . n A 1 16 LYS 16 40 40 LYS LYS A . n A 1 17 ALA 17 41 41 ALA ALA A . n A 1 18 ALA 18 42 42 ALA ALA A . n A 1 19 VAL 19 43 43 VAL VAL A . n A 1 20 THR 20 44 44 THR THR A . n A 1 21 ASP 21 45 45 ASP ASP A . n A 1 22 ASN 22 46 46 ASN ASN A . n A 1 23 GLY 23 47 47 GLY GLY A . n A 1 24 PHE 24 48 48 PHE PHE A . n A 1 25 LEU 25 49 49 LEU LEU A . n A 1 26 VAL 26 50 50 VAL VAL A . n A 1 27 ILE 27 51 51 ILE ILE A . n A 1 28 ALA 28 52 52 ALA ALA A . n A 1 29 ILE 29 53 53 ILE ILE A . n A 1 30 ASP 30 54 54 ASP ASP A . n A 1 31 ALA 31 55 55 ALA ALA A . n A 1 32 ASP 32 56 56 ASP ASP A . n A 1 33 SER 33 57 57 SER SER A . n A 1 34 ASP 34 58 58 ASP ASP A . n A 1 35 SER 35 59 59 SER SER A . n A 1 36 GLY 36 60 60 GLY GLY A . n A 1 37 TYR 37 61 61 TYR TYR A . n A 1 38 ASP 38 62 62 ASP ASP A . n A 1 39 MSE 39 63 63 MSE MSE A . n A 1 40 LEU 40 64 64 LEU LEU A . n A 1 41 ALA 41 65 65 ALA ALA A . n A 1 42 SER 42 66 66 SER SER A . n A 1 43 GLN 43 67 67 GLN GLN A . n A 1 44 PHE 44 68 68 PHE PHE A . n A 1 45 LEU 45 69 69 LEU LEU A . n A 1 46 GLU 46 70 70 GLU GLU A . n A 1 47 GLU 47 71 71 GLU GLU A . n A 1 48 ALA 48 72 72 ALA ALA A . n A 1 49 LYS 49 73 73 LYS LYS A . n A 1 50 LYS 50 74 74 LYS LYS A . n A 1 51 GLU 51 75 75 GLU GLU A . n A 1 52 GLY 52 76 76 GLY GLY A . n A 1 53 VAL 53 77 77 VAL VAL A . n A 1 54 SER 54 78 78 SER SER A . n A 1 55 GLY 55 79 79 GLY GLY A . n A 1 56 LEU 56 80 80 LEU LEU A . n A 1 57 LYS 57 81 81 LYS LYS A . n A 1 58 GLY 58 82 82 GLY GLY A . n A 1 59 VAL 59 83 83 VAL VAL A . n A 1 60 LEU 60 84 84 LEU LEU A . n A 1 61 ILE 61 85 85 ILE ILE A . n A 1 62 VAL 62 86 86 VAL VAL A . n A 1 63 ASP 63 87 87 ASP ASP A . n A 1 64 ILE 64 88 88 ILE ILE A . n A 1 65 LYS 65 89 89 LYS LYS A . n A 1 66 ASN 66 90 90 ASN ASN A . n A 1 67 ALA 67 91 91 ALA ALA A . n A 1 68 LYS 68 92 92 LYS LYS A . n A 1 69 PHE 69 93 93 PHE PHE A . n A 1 70 GLU 70 94 94 GLU GLU A . n A 1 71 GLN 71 95 95 GLN GLN A . n A 1 72 GLY 72 96 96 GLY GLY A . n A 1 73 ALA 73 97 97 ALA ALA A . n A 1 74 VAL 74 98 98 VAL VAL A . n A 1 75 VAL 75 99 99 VAL VAL A . n A 1 76 GLY 76 100 100 GLY GLY A . n A 1 77 LYS 77 101 101 LYS LYS A . n A 1 78 ARG 78 102 102 ARG ARG A . n A 1 79 ILE 79 103 103 ILE ILE A . n A 1 80 GLY 80 104 104 GLY GLY A . n A 1 81 LYS 81 105 105 LYS LYS A . n A 1 82 ALA 82 106 106 ALA ALA A . n A 1 83 TYR 83 107 107 TYR TYR A . n A 1 84 LYS 84 108 108 LYS LYS A . n # _pdbx_SG_project.project_name PSI:Biology _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.initial_of_center JCSG _pdbx_SG_project.id 1 # 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 EDO 1 200 200 EDO EDO A . C 2 EDO 1 201 201 EDO EDO A . D 3 HOH 1 301 202 HOH HOH A . D 3 HOH 2 302 203 HOH HOH A . D 3 HOH 3 303 204 HOH HOH A . D 3 HOH 4 304 205 HOH HOH A . D 3 HOH 5 305 206 HOH HOH A . D 3 HOH 6 306 207 HOH HOH A . D 3 HOH 7 307 208 HOH HOH A . D 3 HOH 8 308 209 HOH HOH A . D 3 HOH 9 309 210 HOH HOH A . D 3 HOH 10 310 211 HOH HOH A . D 3 HOH 11 311 212 HOH HOH A . D 3 HOH 12 312 213 HOH HOH A . D 3 HOH 13 313 214 HOH HOH A . D 3 HOH 14 314 215 HOH HOH A . D 3 HOH 15 315 216 HOH HOH A . D 3 HOH 16 316 217 HOH HOH A . D 3 HOH 17 317 218 HOH HOH A . D 3 HOH 18 318 219 HOH HOH A . D 3 HOH 19 319 220 HOH HOH A . D 3 HOH 20 320 221 HOH HOH A . D 3 HOH 21 321 222 HOH HOH A . D 3 HOH 22 322 223 HOH HOH A . D 3 HOH 23 323 224 HOH HOH A . D 3 HOH 24 324 225 HOH HOH A . D 3 HOH 25 325 226 HOH HOH A . D 3 HOH 26 326 227 HOH HOH A . D 3 HOH 27 327 228 HOH HOH A . D 3 HOH 28 328 229 HOH HOH A . D 3 HOH 29 329 230 HOH HOH A . D 3 HOH 30 330 231 HOH HOH A . D 3 HOH 31 331 232 HOH HOH A . D 3 HOH 32 332 233 HOH HOH A . D 3 HOH 33 333 234 HOH HOH A . D 3 HOH 34 334 235 HOH HOH A . D 3 HOH 35 335 236 HOH HOH A . D 3 HOH 36 336 237 HOH HOH A . D 3 HOH 37 337 238 HOH HOH A . D 3 HOH 38 338 239 HOH HOH A . D 3 HOH 39 339 240 HOH HOH A . D 3 HOH 40 340 241 HOH HOH A . D 3 HOH 41 341 242 HOH HOH A . D 3 HOH 42 342 243 HOH HOH A . D 3 HOH 43 343 244 HOH HOH A . D 3 HOH 44 344 245 HOH HOH A . D 3 HOH 45 345 246 HOH HOH A . D 3 HOH 46 346 247 HOH HOH A . D 3 HOH 47 347 248 HOH HOH A . D 3 HOH 48 348 249 HOH HOH A . D 3 HOH 49 349 250 HOH HOH A . D 3 HOH 50 350 251 HOH HOH A . D 3 HOH 51 351 252 HOH HOH A . D 3 HOH 52 352 253 HOH HOH A . D 3 HOH 53 353 254 HOH HOH A . D 3 HOH 54 354 255 HOH HOH A . D 3 HOH 55 355 256 HOH HOH A . D 3 HOH 56 356 257 HOH HOH A . D 3 HOH 57 357 258 HOH HOH A . D 3 HOH 58 358 259 HOH HOH A . D 3 HOH 59 359 260 HOH HOH A . D 3 HOH 60 360 261 HOH HOH A . D 3 HOH 61 361 262 HOH HOH A . D 3 HOH 62 362 263 HOH HOH A . D 3 HOH 63 363 264 HOH HOH A . D 3 HOH 64 364 265 HOH HOH A . D 3 HOH 65 365 266 HOH HOH A . D 3 HOH 66 366 267 HOH HOH A . D 3 HOH 67 367 268 HOH HOH A . D 3 HOH 68 368 269 HOH HOH A . D 3 HOH 69 369 270 HOH HOH A . D 3 HOH 70 370 271 HOH HOH A . D 3 HOH 71 371 272 HOH HOH A . D 3 HOH 72 372 273 HOH HOH A . D 3 HOH 73 373 274 HOH HOH A . D 3 HOH 74 374 275 HOH HOH A . D 3 HOH 75 375 276 HOH HOH A . D 3 HOH 76 376 277 HOH HOH A . D 3 HOH 77 377 278 HOH HOH A . D 3 HOH 78 378 279 HOH HOH A . D 3 HOH 79 379 280 HOH HOH A . D 3 HOH 80 380 281 HOH HOH A . D 3 HOH 81 381 282 HOH HOH A . D 3 HOH 82 382 283 HOH HOH A . D 3 HOH 83 383 284 HOH HOH A . D 3 HOH 84 384 285 HOH HOH A . D 3 HOH 85 385 286 HOH HOH A . D 3 HOH 86 386 287 HOH HOH A . D 3 HOH 87 387 288 HOH HOH A . D 3 HOH 88 388 289 HOH HOH A . D 3 HOH 89 389 290 HOH HOH A . D 3 HOH 90 390 291 HOH HOH A . D 3 HOH 91 391 292 HOH HOH A . D 3 HOH 92 392 293 HOH HOH A . D 3 HOH 93 393 294 HOH HOH A . D 3 HOH 94 394 295 HOH HOH A . D 3 HOH 95 395 296 HOH HOH A . D 3 HOH 96 396 297 HOH HOH A . D 3 HOH 97 397 298 HOH HOH A . D 3 HOH 98 398 299 HOH HOH A . D 3 HOH 99 399 300 HOH HOH A . D 3 HOH 100 400 301 HOH HOH A . D 3 HOH 101 401 302 HOH HOH A . D 3 HOH 102 402 303 HOH HOH A . D 3 HOH 103 403 304 HOH HOH A . D 3 HOH 104 404 305 HOH HOH A . D 3 HOH 105 405 306 HOH HOH A . D 3 HOH 106 406 307 HOH HOH A . D 3 HOH 107 407 308 HOH HOH A . D 3 HOH 108 408 309 HOH HOH A . D 3 HOH 109 409 310 HOH HOH A . D 3 HOH 110 410 311 HOH HOH A . D 3 HOH 111 411 312 HOH HOH A . D 3 HOH 112 412 313 HOH HOH A . D 3 HOH 113 413 314 HOH HOH A . D 3 HOH 114 414 315 HOH HOH A . D 3 HOH 115 415 316 HOH HOH A . D 3 HOH 116 416 317 HOH HOH A . D 3 HOH 117 417 318 HOH HOH A . D 3 HOH 118 418 319 HOH HOH A . D 3 HOH 119 419 320 HOH HOH A . D 3 HOH 120 420 321 HOH HOH A . D 3 HOH 121 421 322 HOH HOH A . D 3 HOH 122 422 323 HOH HOH A . D 3 HOH 123 423 324 HOH HOH A . D 3 HOH 124 424 325 HOH HOH A . D 3 HOH 125 425 326 HOH HOH A . D 3 HOH 126 426 327 HOH HOH A . D 3 HOH 127 427 328 HOH HOH A . D 3 HOH 128 428 329 HOH HOH A . D 3 HOH 129 429 330 HOH HOH A . D 3 HOH 130 430 331 HOH HOH A . D 3 HOH 131 431 332 HOH HOH A . D 3 HOH 132 432 333 HOH HOH A . D 3 HOH 133 433 334 HOH HOH A . D 3 HOH 134 434 335 HOH HOH A . D 3 HOH 135 435 336 HOH HOH A . D 3 HOH 136 436 337 HOH HOH A . D 3 HOH 137 437 338 HOH HOH A . D 3 HOH 138 438 339 HOH HOH A . D 3 HOH 139 439 340 HOH HOH A . D 3 HOH 140 440 341 HOH HOH A . D 3 HOH 141 441 342 HOH HOH A . D 3 HOH 142 442 343 HOH HOH A . D 3 HOH 143 443 344 HOH HOH A . D 3 HOH 144 444 345 HOH HOH A . D 3 HOH 145 445 346 HOH HOH A . D 3 HOH 146 446 347 HOH HOH A . D 3 HOH 147 447 348 HOH HOH A . D 3 HOH 148 448 349 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id MSE _pdbx_struct_mod_residue.label_seq_id 39 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MSE _pdbx_struct_mod_residue.auth_seq_id 63 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id MET _pdbx_struct_mod_residue.details SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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,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 2013-04-03 2 'Structure model' 1 1 2014-12-24 3 'Structure model' 1 2 2017-11-15 4 'Structure model' 1 3 2018-01-24 5 'Structure model' 1 4 2023-02-01 # _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' 'Structure summary' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Database references' 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 3 'Structure model' software 2 4 'Structure model' citation_author 3 5 'Structure model' database_2 4 5 'Structure model' struct_conn 5 5 'Structure model' struct_ref_seq_dif 6 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_citation_author.name' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 5 'Structure model' '_struct_ref_seq_dif.details' 8 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 9 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 10 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _phasing.method MAD # 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 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 4 SHARP . ? package 'Eric de La Fortelle' sharp-develop@globalphasing.com phasing http://www.globalphasing.com/sharp/ ? ? 5 XSCALE 'July 4, 2012' ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 6 REFMAC 5.5.0110 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 7 XDS . ? ? ? ? 'data reduction' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.compound_details ? _pdbx_entry_details.sequence_details ;THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 26-108 OF THE TARGET SEQUENCE. ; _pdbx_entry_details.entry_id 4JM1 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OD1 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 ASP _pdbx_validate_close_contact.auth_seq_id_1 27 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 B _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_2 376 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.18 # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id PHE _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 36 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -109.90 _pdbx_validate_torsion.psi -60.72 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LYS 92 ? CD ? A LYS 68 CD 2 1 Y 1 A LYS 92 ? CE ? A LYS 68 CE 3 1 Y 1 A LYS 92 ? NZ ? A LYS 68 NZ # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-ETHANEDIOL EDO 3 water HOH #