data_4ME8 # _entry.id 4ME8 # _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 4ME8 pdb_00004me8 10.2210/pdb4me8/pdb RCSB RCSB081799 ? ? WWPDB D_1000081799 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-389959 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4ME8 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2013-08-25 _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 signal peptidase I (EF3073) from Enterococcus faecalis V583 at 2.27 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 4ME8 _cell.length_a 37.488 _cell.length_b 37.488 _cell.length_c 169.046 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _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.entry_id 4ME8 _symmetry.Int_Tables_number 92 _symmetry.space_group_name_H-M 'P 41 21 2' _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 'Signal peptidase I' 17161.840 1 3.4.21.89 ? ? ? 2 non-polymer syn 1,2-ETHANEDIOL 62.068 2 ? ? ? ? 3 water nat water 18.015 39 ? ? ? ? # _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 ;GAAVNGSS(MSE)EPTLHNNDRLWVTSIKKPQRFDIIAFPSPRNGQRVAKRLIGLPGETVEYRDDTLYINGVSLSEDYLA SAKRNVSKNENYTQDFTLETLEATQSLTVPEG(MSE)YFVLGDNRPRSDDSRYFGFVKQASVEGVLTFRYYPLDKIGFP ; _entity_poly.pdbx_seq_one_letter_code_can ;GAAVNGSSMEPTLHNNDRLWVTSIKKPQRFDIIAFPSPRNGQRVAKRLIGLPGETVEYRDDTLYINGVSLSEDYLASAKR NVSKNENYTQDFTLETLEATQSLTVPEGMYFVLGDNRPRSDDSRYFGFVKQASVEGVLTFRYYPLDKIGFP ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier JCSG-389959 # 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 ALA n 1 4 VAL n 1 5 ASN n 1 6 GLY n 1 7 SER n 1 8 SER n 1 9 MSE n 1 10 GLU n 1 11 PRO n 1 12 THR n 1 13 LEU n 1 14 HIS n 1 15 ASN n 1 16 ASN n 1 17 ASP n 1 18 ARG n 1 19 LEU n 1 20 TRP n 1 21 VAL n 1 22 THR n 1 23 SER n 1 24 ILE n 1 25 LYS n 1 26 LYS n 1 27 PRO n 1 28 GLN n 1 29 ARG n 1 30 PHE n 1 31 ASP n 1 32 ILE n 1 33 ILE n 1 34 ALA n 1 35 PHE n 1 36 PRO n 1 37 SER n 1 38 PRO n 1 39 ARG n 1 40 ASN n 1 41 GLY n 1 42 GLN n 1 43 ARG n 1 44 VAL n 1 45 ALA n 1 46 LYS n 1 47 ARG n 1 48 LEU n 1 49 ILE n 1 50 GLY n 1 51 LEU n 1 52 PRO n 1 53 GLY n 1 54 GLU n 1 55 THR n 1 56 VAL n 1 57 GLU n 1 58 TYR n 1 59 ARG n 1 60 ASP n 1 61 ASP n 1 62 THR n 1 63 LEU n 1 64 TYR n 1 65 ILE n 1 66 ASN n 1 67 GLY n 1 68 VAL n 1 69 SER n 1 70 LEU n 1 71 SER n 1 72 GLU n 1 73 ASP n 1 74 TYR n 1 75 LEU n 1 76 ALA n 1 77 SER n 1 78 ALA n 1 79 LYS n 1 80 ARG n 1 81 ASN n 1 82 VAL n 1 83 SER n 1 84 LYS n 1 85 ASN n 1 86 GLU n 1 87 ASN n 1 88 TYR n 1 89 THR n 1 90 GLN n 1 91 ASP n 1 92 PHE n 1 93 THR n 1 94 LEU n 1 95 GLU n 1 96 THR n 1 97 LEU n 1 98 GLU n 1 99 ALA n 1 100 THR n 1 101 GLN n 1 102 SER n 1 103 LEU n 1 104 THR n 1 105 VAL n 1 106 PRO n 1 107 GLU n 1 108 GLY n 1 109 MSE n 1 110 TYR n 1 111 PHE n 1 112 VAL n 1 113 LEU n 1 114 GLY n 1 115 ASP n 1 116 ASN n 1 117 ARG n 1 118 PRO n 1 119 ARG n 1 120 SER n 1 121 ASP n 1 122 ASP n 1 123 SER n 1 124 ARG n 1 125 TYR n 1 126 PHE n 1 127 GLY n 1 128 PHE n 1 129 VAL n 1 130 LYS n 1 131 GLN n 1 132 ALA n 1 133 SER n 1 134 VAL n 1 135 GLU n 1 136 GLY n 1 137 VAL n 1 138 LEU n 1 139 THR n 1 140 PHE n 1 141 ARG n 1 142 TYR n 1 143 TYR n 1 144 PRO n 1 145 LEU n 1 146 ASP n 1 147 LYS n 1 148 ILE n 1 149 GLY n 1 150 PHE n 1 151 PRO 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 EF_3073 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain V583 _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 'Enterococcus faecalis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 226185 _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 HK100 _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 Q82ZI3_ENTFA _struct_ref.pdbx_db_accession Q82ZI3 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;AAVNGSSMEPTLHNNDRLWVTSIKKPQRFDIIAFPSPRNGQRVAKRLIGLPGETVEYRDDTLYINGVSLSEDYLASAKRN VSKNENYTQDFTLETLEATQSLTVPEGMYFVLGDNRPRSDDSRYFGFVKQASVEGVLTFRYYPLDKIGFP ; _struct_ref.pdbx_align_begin 29 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4ME8 _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 151 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q82ZI3 _struct_ref_seq.db_align_beg 29 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 178 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 29 _struct_ref_seq.pdbx_auth_seq_align_end 178 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4ME8 _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 Q82ZI3 _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 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 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.method 'X-RAY DIFFRACTION' _exptl.entry_id 4ME8 # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.73 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 28.92 _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 6.2 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details ;20.00% polyethylene glycol 3350, 0.200M ammonium fluoride, No Buffer pH 6.2, Additive: 0.001 M leupeptin, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K ; _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 'MARMOSAIC 325 mm CCD' _diffrn_detector.details 'Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)' _diffrn_detector.pdbx_collection_date 2011-01-26 # _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 0.91837 1.0 2 0.97944 1.0 3 0.97894 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 0.91837,0.97944,0.97894 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 4ME8 _reflns.d_resolution_high 2.27 _reflns.d_resolution_low 28.174 _reflns.number_obs 6200 _reflns.pdbx_Rmerge_I_obs 0.077 _reflns.pdbx_netI_over_sigmaI 11.930 _reflns.percent_possible_obs 99.400 _reflns.B_iso_Wilson_estimate 47.346 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? _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_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 2.270 2.350 3675 ? 1057 0.777 1.7 ? ? ? ? ? 99.100 1 1 2.350 2.440 4016 ? 998 0.610 2.3 ? ? ? ? ? 100.000 2 1 2.440 2.560 4566 ? 1156 0.535 2.5 ? ? ? ? ? 99.700 3 1 2.560 2.690 4143 ? 1046 0.378 3.7 ? ? ? ? ? 99.800 4 1 2.690 2.860 4149 ? 1069 0.215 5.9 ? ? ? ? ? 99.600 5 1 2.860 3.080 3803 ? 1056 0.132 8.8 ? ? ? ? ? 99.200 6 1 3.080 3.390 4319 ? 1070 0.091 13.9 ? ? ? ? ? 99.900 7 1 3.390 3.870 4127 ? 1043 0.054 21.6 ? ? ? ? ? 99.900 8 1 3.870 4.870 3894 ? 1065 0.037 27.8 ? ? ? ? ? 98.600 9 1 4.870 ? 4212 ? 1094 0.033 30.8 ? ? ? ? ? 98.300 10 1 # _refine.entry_id 4ME8 _refine.ls_d_res_high 2.2700 _refine.ls_d_res_low 28.174 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.5300 _refine.ls_number_reflns_obs 6146 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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 CRYOPROTECTION SOLUTION ARE MODELED. 7. ELECTRON DENSITY IS DISORDERED AROUND RAMACHANDRAN OUTLIER RESIDUE A109. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2162 _refine.ls_R_factor_R_work 0.2124 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2580 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 7.9000 _refine.ls_number_reflns_R_free 486 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 61.7506 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.9100 _refine.aniso_B[2][2] 1.9100 _refine.aniso_B[3][3] -3.8200 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] -0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9480 _refine.correlation_coeff_Fo_to_Fc_free 0.9260 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.3590 _refine.pdbx_overall_ESU_R_Free 0.2480 _refine.overall_SU_ML 0.2280 _refine.overall_SU_B 18.1920 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 160.680 _refine.B_iso_min 28.240 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.500 _refine.pdbx_ls_sigma_I ? _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_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 904 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 39 _refine_hist.number_atoms_total 951 _refine_hist.d_res_high 2.2700 _refine_hist.d_res_low 28.174 # 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 933 0.007 0.020 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 858 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1265 1.229 1.970 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 1961 0.786 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 118 6.606 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 46 28.677 23.478 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 141 15.055 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 9 11.706 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 141 0.076 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 1082 0.005 0.021 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 223 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 469 1.172 2.906 ? ? 'X-RAY DIFFRACTION' r_mcbond_other 468 1.173 2.906 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 585 1.935 5.429 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 2.2700 _refine_ls_shell.d_res_low 2.3290 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.5600 _refine_ls_shell.number_reflns_R_work 408 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2830 _refine_ls_shell.R_factor_R_free 0.3220 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 40 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 448 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 4ME8 _struct.title 'Crystal structure of a signal peptidase I (EF3073) from Enterococcus faecalis V583 at 2.27 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;PF00717 family, Peptidase_S24, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, HYDROLASE ; _struct_keywords.pdbx_keywords HYDROLASE _struct_keywords.entry_id 4ME8 # 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 ? # 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 78 ? VAL A 82 ? ALA A 105 VAL A 109 5 ? 5 HELX_P HELX_P2 2 ASN A 116 ? SER A 120 ? ASN A 143 SER A 147 5 ? 5 HELX_P HELX_P3 3 ASP A 122 ? GLY A 127 ? ASP A 149 GLY A 154 1 ? 6 HELX_P HELX_P4 4 ALA A 132 ? VAL A 134 ? ALA A 159 VAL A 161 5 ? 3 # _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 108 C ? ? ? 1_555 A MSE 109 N ? ? A GLY 135 A MSE 136 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale2 covale both ? A MSE 109 C ? ? ? 1_555 A TYR 110 N ? ? A MSE 136 A TYR 137 1_555 ? ? ? ? ? ? ? 1.335 ? ? # _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 ? 4 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 VAL A 129 ? LYS A 130 ? VAL A 156 LYS A 157 A 2 MSE A 109 ? LEU A 113 ? MSE A 136 LEU A 140 A 3 ARG A 43 ? GLY A 50 ? ARG A 70 GLY A 77 A 4 ILE A 32 ? PRO A 36 ? ILE A 59 PRO A 63 A 5 GLY A 136 ? VAL A 137 ? GLY A 163 VAL A 164 B 1 VAL A 68 ? LEU A 70 ? VAL A 95 LEU A 97 B 2 THR A 62 ? ILE A 65 ? THR A 89 ILE A 92 B 3 VAL A 56 ? ARG A 59 ? VAL A 83 ARG A 86 B 4 PHE A 92 ? THR A 93 ? PHE A 119 THR A 120 # 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 VAL A 129 ? O VAL A 156 N TYR A 110 ? N TYR A 137 A 2 3 O PHE A 111 ? O PHE A 138 N GLY A 50 ? N GLY A 77 A 3 4 O LYS A 46 ? O LYS A 73 N ILE A 33 ? N ILE A 60 A 4 5 N ALA A 34 ? N ALA A 61 O GLY A 136 ? O GLY A 163 B 1 2 O LEU A 70 ? O LEU A 97 N LEU A 63 ? N LEU A 90 B 2 3 O TYR A 64 ? O TYR A 91 N GLU A 57 ? N GLU A 84 B 3 4 N TYR A 58 ? N TYR A 85 O PHE A 92 ? O PHE A 119 # 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 ARG A 39 ? ARG A 66 . ? 6_455 ? 2 AC1 5 ALA A 45 ? ALA A 72 . ? 1_555 ? 3 AC1 5 GLY A 114 ? GLY A 141 . ? 1_555 ? 4 AC1 5 ASP A 115 ? ASP A 142 . ? 1_555 ? 5 AC1 5 TYR A 125 ? TYR A 152 . ? 6_455 ? 6 AC2 4 ARG A 43 ? ARG A 70 . ? 6_555 ? 7 AC2 4 GLU A 98 ? GLU A 125 . ? 1_555 ? 8 AC2 4 ALA A 99 ? ALA A 126 . ? 1_555 ? 9 AC2 4 ARG A 124 ? ARG A 151 . ? 1_555 ? # _atom_sites.entry_id 4ME8 _atom_sites.fract_transf_matrix[1][1] 0.026675 _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] 0.026675 _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] 0.005916 _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 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 ? ? ? A . n A 1 2 ALA 2 29 ? ? ? A . n A 1 3 ALA 3 30 ? ? ? A . n A 1 4 VAL 4 31 ? ? ? A . n A 1 5 ASN 5 32 ? ? ? A . n A 1 6 GLY 6 33 ? ? ? A . n A 1 7 SER 7 34 ? ? ? A . n A 1 8 SER 8 35 ? ? ? A . n A 1 9 MSE 9 36 ? ? ? A . n A 1 10 GLU 10 37 ? ? ? A . n A 1 11 PRO 11 38 ? ? ? A . n A 1 12 THR 12 39 ? ? ? A . n A 1 13 LEU 13 40 ? ? ? A . n A 1 14 HIS 14 41 ? ? ? A . n A 1 15 ASN 15 42 ? ? ? A . n A 1 16 ASN 16 43 ? ? ? A . n A 1 17 ASP 17 44 ? ? ? A . n A 1 18 ARG 18 45 ? ? ? A . n A 1 19 LEU 19 46 ? ? ? A . n A 1 20 TRP 20 47 ? ? ? A . n A 1 21 VAL 21 48 ? ? ? A . n A 1 22 THR 22 49 ? ? ? A . n A 1 23 SER 23 50 50 SER SER A . n A 1 24 ILE 24 51 51 ILE ILE A . n A 1 25 LYS 25 52 52 LYS LYS A . n A 1 26 LYS 26 53 53 LYS LYS A . n A 1 27 PRO 27 54 54 PRO PRO A . n A 1 28 GLN 28 55 55 GLN GLN A . n A 1 29 ARG 29 56 56 ARG ARG A . n A 1 30 PHE 30 57 57 PHE PHE A . n A 1 31 ASP 31 58 58 ASP ASP A . n A 1 32 ILE 32 59 59 ILE ILE A . n A 1 33 ILE 33 60 60 ILE ILE A . n A 1 34 ALA 34 61 61 ALA ALA A . n A 1 35 PHE 35 62 62 PHE PHE A . n A 1 36 PRO 36 63 63 PRO PRO A . n A 1 37 SER 37 64 64 SER SER A . n A 1 38 PRO 38 65 65 PRO PRO A . n A 1 39 ARG 39 66 66 ARG ARG A . n A 1 40 ASN 40 67 67 ASN ASN A . n A 1 41 GLY 41 68 68 GLY GLY A . n A 1 42 GLN 42 69 69 GLN GLN A . n A 1 43 ARG 43 70 70 ARG ARG A . n A 1 44 VAL 44 71 71 VAL VAL A . n A 1 45 ALA 45 72 72 ALA ALA A . n A 1 46 LYS 46 73 73 LYS LYS A . n A 1 47 ARG 47 74 74 ARG ARG A . n A 1 48 LEU 48 75 75 LEU LEU A . n A 1 49 ILE 49 76 76 ILE ILE A . n A 1 50 GLY 50 77 77 GLY GLY A . n A 1 51 LEU 51 78 78 LEU LEU A . n A 1 52 PRO 52 79 79 PRO PRO A . n A 1 53 GLY 53 80 80 GLY GLY A . n A 1 54 GLU 54 81 81 GLU GLU A . n A 1 55 THR 55 82 82 THR THR A . n A 1 56 VAL 56 83 83 VAL VAL A . n A 1 57 GLU 57 84 84 GLU GLU A . n A 1 58 TYR 58 85 85 TYR TYR A . n A 1 59 ARG 59 86 86 ARG ARG A . n A 1 60 ASP 60 87 87 ASP ASP A . n A 1 61 ASP 61 88 88 ASP ASP A . n A 1 62 THR 62 89 89 THR THR A . n A 1 63 LEU 63 90 90 LEU LEU A . n A 1 64 TYR 64 91 91 TYR TYR A . n A 1 65 ILE 65 92 92 ILE ILE A . n A 1 66 ASN 66 93 93 ASN ASN A . n A 1 67 GLY 67 94 94 GLY GLY A . n A 1 68 VAL 68 95 95 VAL VAL A . n A 1 69 SER 69 96 96 SER SER A . n A 1 70 LEU 70 97 97 LEU LEU A . n A 1 71 SER 71 98 98 SER SER A . n A 1 72 GLU 72 99 99 GLU GLU A . n A 1 73 ASP 73 100 100 ASP ASP A . n A 1 74 TYR 74 101 101 TYR TYR A . n A 1 75 LEU 75 102 102 LEU LEU A . n A 1 76 ALA 76 103 103 ALA ALA A . n A 1 77 SER 77 104 104 SER SER A . n A 1 78 ALA 78 105 105 ALA ALA A . n A 1 79 LYS 79 106 106 LYS LYS A . n A 1 80 ARG 80 107 107 ARG ARG A . n A 1 81 ASN 81 108 108 ASN ASN A . n A 1 82 VAL 82 109 109 VAL VAL A . n A 1 83 SER 83 110 110 SER SER A . n A 1 84 LYS 84 111 111 LYS LYS A . n A 1 85 ASN 85 112 112 ASN ASN A . n A 1 86 GLU 86 113 113 GLU GLU A . n A 1 87 ASN 87 114 114 ASN ASN A . n A 1 88 TYR 88 115 115 TYR TYR A . n A 1 89 THR 89 116 116 THR THR A . n A 1 90 GLN 90 117 117 GLN GLN A . n A 1 91 ASP 91 118 118 ASP ASP A . n A 1 92 PHE 92 119 119 PHE PHE A . n A 1 93 THR 93 120 120 THR THR A . n A 1 94 LEU 94 121 121 LEU LEU A . n A 1 95 GLU 95 122 122 GLU GLU A . n A 1 96 THR 96 123 123 THR THR A . n A 1 97 LEU 97 124 124 LEU LEU A . n A 1 98 GLU 98 125 125 GLU GLU A . n A 1 99 ALA 99 126 126 ALA ALA A . n A 1 100 THR 100 127 127 THR THR A . n A 1 101 GLN 101 128 128 GLN GLN A . n A 1 102 SER 102 129 129 SER SER A . n A 1 103 LEU 103 130 130 LEU LEU A . n A 1 104 THR 104 131 131 THR THR A . n A 1 105 VAL 105 132 132 VAL VAL A . n A 1 106 PRO 106 133 133 PRO PRO A . n A 1 107 GLU 107 134 134 GLU GLU A . n A 1 108 GLY 108 135 135 GLY GLY A . n A 1 109 MSE 109 136 136 MSE MSE A . n A 1 110 TYR 110 137 137 TYR TYR A . n A 1 111 PHE 111 138 138 PHE PHE A . n A 1 112 VAL 112 139 139 VAL VAL A . n A 1 113 LEU 113 140 140 LEU LEU A . n A 1 114 GLY 114 141 141 GLY GLY A . n A 1 115 ASP 115 142 142 ASP ASP A . n A 1 116 ASN 116 143 143 ASN ASN A . n A 1 117 ARG 117 144 144 ARG ARG A . n A 1 118 PRO 118 145 145 PRO PRO A . n A 1 119 ARG 119 146 146 ARG ARG A . n A 1 120 SER 120 147 147 SER SER A . n A 1 121 ASP 121 148 148 ASP ASP A . n A 1 122 ASP 122 149 149 ASP ASP A . n A 1 123 SER 123 150 150 SER SER A . n A 1 124 ARG 124 151 151 ARG ARG A . n A 1 125 TYR 125 152 152 TYR TYR A . n A 1 126 PHE 126 153 153 PHE PHE A . n A 1 127 GLY 127 154 154 GLY GLY A . n A 1 128 PHE 128 155 155 PHE PHE A . n A 1 129 VAL 129 156 156 VAL VAL A . n A 1 130 LYS 130 157 157 LYS LYS A . n A 1 131 GLN 131 158 158 GLN GLN A . n A 1 132 ALA 132 159 159 ALA ALA A . n A 1 133 SER 133 160 160 SER SER A . n A 1 134 VAL 134 161 161 VAL VAL A . n A 1 135 GLU 135 162 162 GLU GLU A . n A 1 136 GLY 136 163 163 GLY GLY A . n A 1 137 VAL 137 164 164 VAL VAL A . n A 1 138 LEU 138 165 165 LEU LEU A . n A 1 139 THR 139 166 166 THR THR A . n A 1 140 PHE 140 167 ? ? ? A . n A 1 141 ARG 141 168 ? ? ? A . n A 1 142 TYR 142 169 ? ? ? A . n A 1 143 TYR 143 170 ? ? ? A . n A 1 144 PRO 144 171 ? ? ? A . n A 1 145 LEU 145 172 ? ? ? A . n A 1 146 ASP 146 173 ? ? ? A . n A 1 147 LYS 147 174 ? ? ? A . n A 1 148 ILE 148 175 ? ? ? A . n A 1 149 GLY 149 176 ? ? ? A . n A 1 150 PHE 150 177 ? ? ? A . n A 1 151 PRO 151 178 ? ? ? A . n # _pdbx_SG_project.project_name PSI:Biology _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # 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 . # _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 109 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MSE _pdbx_struct_mod_residue.auth_seq_id 136 _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 2013-09-11 2 'Structure model' 1 1 2017-11-15 3 'Structure model' 1 2 2018-01-24 4 'Structure model' 1 3 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' 'Refinement description' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Database references' 4 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 2 'Structure model' software 2 3 'Structure model' citation_author 3 4 'Structure model' database_2 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_ref_seq_dif 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_software.classification' 2 2 'Structure model' '_software.name' 3 3 'Structure model' '_citation_author.name' 4 4 'Structure model' '_database_2.pdbx_DOI' 5 4 'Structure model' '_database_2.pdbx_database_accession' 6 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 4 'Structure model' '_struct_ref_seq_dif.details' 8 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 9 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 10 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 22.4540 _pdbx_refine_tls.origin_y 14.3200 _pdbx_refine_tls.origin_z 71.1660 _pdbx_refine_tls.T[1][1] 0.2055 _pdbx_refine_tls.T[2][2] 0.5159 _pdbx_refine_tls.T[3][3] 0.3219 _pdbx_refine_tls.T[1][2] 0.0222 _pdbx_refine_tls.T[1][3] 0.0097 _pdbx_refine_tls.T[2][3] 0.0253 _pdbx_refine_tls.L[1][1] 5.9487 _pdbx_refine_tls.L[2][2] 4.3238 _pdbx_refine_tls.L[3][3] 8.0962 _pdbx_refine_tls.L[1][2] 0.2463 _pdbx_refine_tls.L[1][3] -0.3727 _pdbx_refine_tls.L[2][3] 4.7130 _pdbx_refine_tls.S[1][1] -0.3141 _pdbx_refine_tls.S[2][2] 0.3688 _pdbx_refine_tls.S[3][3] -0.0547 _pdbx_refine_tls.S[1][2] 0.5820 _pdbx_refine_tls.S[1][3] -0.0731 _pdbx_refine_tls.S[2][3] 0.0375 _pdbx_refine_tls.S[2][1] 0.3409 _pdbx_refine_tls.S[3][1] 0.4117 _pdbx_refine_tls.S[3][2] 0.6341 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 50 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 166 _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 ? # _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 REFMAC 5.7.0032 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 6 XDS . ? ? ? ? 'data reduction' ? ? ? 7 XSCALE . ? ? ? ? 'data scaling' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.entry_id 4ME8 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_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 29-178 OF THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # 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 PHE A 57 ? ? 79.04 -0.84 2 1 VAL A 109 ? ? -103.92 -111.77 3 1 GLN A 128 ? ? 39.25 68.70 4 1 ASP A 149 ? ? -144.63 -159.90 # 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 52 ? CG ? A LYS 25 CG 2 1 Y 1 A LYS 52 ? CD ? A LYS 25 CD 3 1 Y 1 A LYS 52 ? CE ? A LYS 25 CE 4 1 Y 1 A LYS 52 ? NZ ? A LYS 25 NZ 5 1 Y 1 A LYS 53 ? CE ? A LYS 26 CE 6 1 Y 1 A LYS 53 ? NZ ? A LYS 26 NZ 7 1 Y 1 A LYS 106 ? CG ? A LYS 79 CG 8 1 Y 1 A LYS 106 ? CD ? A LYS 79 CD 9 1 Y 1 A LYS 106 ? CE ? A LYS 79 CE 10 1 Y 1 A LYS 106 ? NZ ? A LYS 79 NZ 11 1 Y 1 A LYS 111 ? CG ? A LYS 84 CG 12 1 Y 1 A LYS 111 ? CD ? A LYS 84 CD 13 1 Y 1 A LYS 111 ? CE ? A LYS 84 CE 14 1 Y 1 A LYS 111 ? NZ ? A LYS 84 NZ 15 1 Y 1 A ASN 112 ? CG ? A ASN 85 CG 16 1 Y 1 A ASN 112 ? OD1 ? A ASN 85 OD1 17 1 Y 1 A ASN 112 ? ND2 ? A ASN 85 ND2 18 1 Y 1 A GLU 113 ? CG ? A GLU 86 CG 19 1 Y 1 A GLU 113 ? CD ? A GLU 86 CD 20 1 Y 1 A GLU 113 ? OE1 ? A GLU 86 OE1 21 1 Y 1 A GLU 113 ? OE2 ? A GLU 86 OE2 22 1 Y 1 A LEU 130 ? CG ? A LEU 103 CG 23 1 Y 1 A LEU 130 ? CD1 ? A LEU 103 CD1 24 1 Y 1 A LEU 130 ? CD2 ? A LEU 103 CD2 25 1 Y 1 A GLU 134 ? CD ? A GLU 107 CD 26 1 Y 1 A GLU 134 ? OE1 ? A GLU 107 OE1 27 1 Y 1 A GLU 134 ? OE2 ? A GLU 107 OE2 # 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 GLY 0 ? A GLY 1 2 1 Y 1 A ALA 29 ? A ALA 2 3 1 Y 1 A ALA 30 ? A ALA 3 4 1 Y 1 A VAL 31 ? A VAL 4 5 1 Y 1 A ASN 32 ? A ASN 5 6 1 Y 1 A GLY 33 ? A GLY 6 7 1 Y 1 A SER 34 ? A SER 7 8 1 Y 1 A SER 35 ? A SER 8 9 1 Y 1 A MSE 36 ? A MSE 9 10 1 Y 1 A GLU 37 ? A GLU 10 11 1 Y 1 A PRO 38 ? A PRO 11 12 1 Y 1 A THR 39 ? A THR 12 13 1 Y 1 A LEU 40 ? A LEU 13 14 1 Y 1 A HIS 41 ? A HIS 14 15 1 Y 1 A ASN 42 ? A ASN 15 16 1 Y 1 A ASN 43 ? A ASN 16 17 1 Y 1 A ASP 44 ? A ASP 17 18 1 Y 1 A ARG 45 ? A ARG 18 19 1 Y 1 A LEU 46 ? A LEU 19 20 1 Y 1 A TRP 47 ? A TRP 20 21 1 Y 1 A VAL 48 ? A VAL 21 22 1 Y 1 A THR 49 ? A THR 22 23 1 Y 1 A PHE 167 ? A PHE 140 24 1 Y 1 A ARG 168 ? A ARG 141 25 1 Y 1 A TYR 169 ? A TYR 142 26 1 Y 1 A TYR 170 ? A TYR 143 27 1 Y 1 A PRO 171 ? A PRO 144 28 1 Y 1 A LEU 172 ? A LEU 145 29 1 Y 1 A ASP 173 ? A ASP 146 30 1 Y 1 A LYS 174 ? A LYS 147 31 1 Y 1 A ILE 175 ? A ILE 148 32 1 Y 1 A GLY 176 ? A GLY 149 33 1 Y 1 A PHE 177 ? A PHE 150 34 1 Y 1 A PRO 178 ? A PRO 151 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-ETHANEDIOL EDO 3 water HOH #