data_3NPD # _entry.id 3NPD # _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 3NPD pdb_00003npd 10.2210/pdb3npd/pdb RCSB RCSB060112 ? ? WWPDB D_1000060112 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 416819 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3NPD _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-06-28 _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.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family.' _citation.journal_abbrev Proteins _citation.journal_volume 82 _citation.page_first 1086 _citation.page_last 1092 _citation.year 2014 _citation.journal_id_ASTM PSFGEY _citation.country US _citation.journal_id_ISSN 0887-3585 _citation.journal_id_CSD 0867 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24174223 _citation.pdbx_database_id_DOI 10.1002/prot.24455 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Das, D.' 1 ? primary 'Chiu, H.J.' 2 ? primary 'Farr, C.L.' 3 ? primary 'Grant, J.C.' 4 ? primary 'Jaroszewski, L.' 5 ? primary 'Knuth, M.W.' 6 ? primary 'Miller, M.D.' 7 ? primary 'Tien, H.J.' 8 ? primary 'Elsliger, M.A.' 9 ? primary 'Deacon, A.M.' 10 ? primary 'Godzik, A.' 11 ? primary 'Lesley, S.A.' 12 ? primary 'Wilson, I.A.' 13 ? # _cell.entry_id 3NPD _cell.length_a 34.989 _cell.length_b 51.317 _cell.length_c 56.898 _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 3NPD _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 'putative secreted protein' 13122.354 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 3 non-polymer syn '3-CYCLOHEXYL-1-PROPYLSULFONIC ACID' 221.317 4 ? ? ? ? 4 non-polymer syn 1,2-ETHANEDIOL 62.068 2 ? ? ? ? 5 water nat water 18.015 124 ? ? ? ? # _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 ;GASLKDFELSK(MSE)LEKVAKESSVGTPRAINEDILDQGYTVEGNQLINHLSVRASHAER(MSE)RSNPDSVRSQLGDS VCSNTGYRQLLARGAILTYSFTEYKTNQPVATERFDAGSCRIQGKK ; _entity_poly.pdbx_seq_one_letter_code_can ;GASLKDFELSKMLEKVAKESSVGTPRAINEDILDQGYTVEGNQLINHLSVRASHAERMRSNPDSVRSQLGDSVCSNTGYR QLLARGAILTYSFTEYKTNQPVATERFDAGSCRIQGKK ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 416819 # 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 SER n 1 4 LEU n 1 5 LYS n 1 6 ASP n 1 7 PHE n 1 8 GLU n 1 9 LEU n 1 10 SER n 1 11 LYS n 1 12 MSE n 1 13 LEU n 1 14 GLU n 1 15 LYS n 1 16 VAL n 1 17 ALA n 1 18 LYS n 1 19 GLU n 1 20 SER n 1 21 SER n 1 22 VAL n 1 23 GLY n 1 24 THR n 1 25 PRO n 1 26 ARG n 1 27 ALA n 1 28 ILE n 1 29 ASN n 1 30 GLU n 1 31 ASP n 1 32 ILE n 1 33 LEU n 1 34 ASP n 1 35 GLN n 1 36 GLY n 1 37 TYR n 1 38 THR n 1 39 VAL n 1 40 GLU n 1 41 GLY n 1 42 ASN n 1 43 GLN n 1 44 LEU n 1 45 ILE n 1 46 ASN n 1 47 HIS n 1 48 LEU n 1 49 SER n 1 50 VAL n 1 51 ARG n 1 52 ALA n 1 53 SER n 1 54 HIS n 1 55 ALA n 1 56 GLU n 1 57 ARG n 1 58 MSE n 1 59 ARG n 1 60 SER n 1 61 ASN n 1 62 PRO n 1 63 ASP n 1 64 SER n 1 65 VAL n 1 66 ARG n 1 67 SER n 1 68 GLN n 1 69 LEU n 1 70 GLY n 1 71 ASP n 1 72 SER n 1 73 VAL n 1 74 CYS n 1 75 SER n 1 76 ASN n 1 77 THR n 1 78 GLY n 1 79 TYR n 1 80 ARG n 1 81 GLN n 1 82 LEU n 1 83 LEU n 1 84 ALA n 1 85 ARG n 1 86 GLY n 1 87 ALA n 1 88 ILE n 1 89 LEU n 1 90 THR n 1 91 TYR n 1 92 SER n 1 93 PHE n 1 94 THR n 1 95 GLU n 1 96 TYR n 1 97 LYS n 1 98 THR n 1 99 ASN n 1 100 GLN n 1 101 PRO n 1 102 VAL n 1 103 ALA n 1 104 THR n 1 105 GLU n 1 106 ARG n 1 107 PHE n 1 108 ASP n 1 109 ALA n 1 110 GLY n 1 111 SER n 1 112 CYS n 1 113 ARG n 1 114 ILE n 1 115 GLN n 1 116 GLY n 1 117 LYS n 1 118 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 PA3611 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Pseudomonas aeruginosa' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 287 _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 Q9HY15_PSEAE _struct_ref.pdbx_db_accession Q9HY15 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ASLKDFELSKMLEKVAKESSVGTPRAINEDILDQGYTVEGNQLINHLSVRASHAERMRSNPDSVRSQLGDSVCSNTGYRQ LLARGAILTYSFTEYKTNQPVATERFDAGSCRIQGKK ; _struct_ref.pdbx_align_begin 20 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3NPD _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 118 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9HY15 _struct_ref_seq.db_align_beg 20 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 136 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 20 _struct_ref_seq.pdbx_auth_seq_align_end 136 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3NPD _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 Q9HY15 _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 CXS non-polymer . '3-CYCLOHEXYL-1-PROPYLSULFONIC ACID' ? 'C9 H19 N O3 S' 221.317 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 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 3NPD # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.95 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 36.80 _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 10.5 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '2.000000000M (NH4)2SO4, 0.200000000M Li2SO4, 0.1M CAPS pH 10.5, NANODROP, 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 'MARMOSAIC 325 mm CCD' _diffrn_detector.details ? _diffrn_detector.pdbx_collection_date 2010-05-12 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _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 0.97941 1.0 3 0.97925 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL9-2 _diffrn_source.type 'SSRL BEAMLINE BL9-2' _diffrn_source.pdbx_wavelength_list 0.91837,0.97941,0.97925 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3NPD _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 28.909 _reflns.number_obs 14032 _reflns.pdbx_Rmerge_I_obs 0.060 _reflns.pdbx_netI_over_sigmaI 7.970 _reflns.percent_possible_obs 98.500 _reflns.B_iso_Wilson_estimate 17.794 _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 1.600 1.660 4974 ? 2635 0.473 1.5 ? ? ? ? ? 96.100 1 1 1.660 1.720 4428 ? 2341 0.346 2.0 ? ? ? ? ? 99.500 2 1 1.720 1.800 5028 ? 2664 0.266 2.7 ? ? ? ? ? 99.300 3 1 1.800 1.900 5212 ? 2747 0.210 3.5 ? ? ? ? ? 99.500 4 1 1.900 2.020 5004 ? 2627 0.138 5.0 ? ? ? ? ? 99.300 5 1 2.020 2.170 4776 ? 2487 0.088 7.6 ? ? ? ? ? 99.200 6 1 2.170 2.390 5005 ? 2616 0.066 9.7 ? ? ? ? ? 99.200 7 1 2.390 2.730 4979 ? 2571 0.056 11.7 ? ? ? ? ? 99.100 8 1 2.730 3.440 4972 ? 2582 0.042 15.8 ? ? ? ? ? 98.100 9 1 3.440 28.909 4949 ? 2551 0.033 20.4 ? ? ? ? ? 96.000 10 1 # _refine.entry_id 3NPD _refine.ls_d_res_high 1.6000 _refine.ls_d_res_low 28.909 _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 13997 _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.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. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.SULFATE (SO4) AND N-CYCLOHEXYL-3-AMINOPROPANESULFONIC ACID (CAPS) FROM THE CRYSTALLIZATION SOLUTION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1623 _refine.ls_R_factor_R_work 0.1602 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2046 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.0000 _refine.ls_number_reflns_R_free 700 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 22.6714 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -1.4900 _refine.aniso_B[2][2] 0.2900 _refine.aniso_B[3][3] 1.2000 _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 0.9670 _refine.correlation_coeff_Fo_to_Fc_free 0.9480 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free 0.0960 _refine.overall_SU_ML 0.0630 _refine.overall_SU_B 3.6140 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.4000 _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 72.200 _refine.B_iso_min 10.840 _refine.occupancy_max 1.000 _refine.occupancy_min 0.400 _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 868 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 69 _refine_hist.number_atoms_solvent 124 _refine_hist.number_atoms_total 1061 _refine_hist.d_res_high 1.6000 _refine_hist.d_res_low 28.909 # 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 989 0.016 0.021 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 717 0.004 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1336 1.696 2.024 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1750 1.305 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 125 4.978 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 47 32.205 23.830 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 166 12.195 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 10 16.090 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 148 0.097 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1071 0.007 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 195 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 588 1.798 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 241 0.557 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 948 2.988 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 401 5.402 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 381 8.324 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.6000 _refine_ls_shell.d_res_low 1.6420 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.2100 _refine_ls_shell.number_reflns_R_work 957 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2610 _refine_ls_shell.R_factor_R_free 0.2950 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 52 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1009 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3NPD _struct.title 'Crystal structure of a putative secreted protein (PA3611) from PSEUDOMONAS AERUGINOSA at 1.60 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag Y _struct.pdbx_model_type_details ? # _struct_keywords.text 'Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, UNKNOWN FUNCTION' _struct_keywords.pdbx_keywords 'UNKNOWN FUNCTION' _struct_keywords.entry_id 3NPD # 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 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 4 ? I N N 4 ? J N N 5 ? # _struct_biol.id 1 _struct_biol.details 'CRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.' # 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 SER A 3 ? VAL A 22 ? SER A 21 VAL A 40 1 ? 20 HELX_P HELX_P2 2 ARG A 51 ? ASN A 61 ? ARG A 69 ASN A 79 1 ? 11 HELX_P HELX_P3 3 ASN A 61 ? SER A 75 ? ASN A 79 SER A 93 1 ? 15 HELX_P HELX_P4 4 ASN A 76 ? ALA A 84 ? ASN A 94 ALA A 102 1 ? 9 HELX_P HELX_P5 5 ASP A 108 ? ARG A 113 ? ASP A 126 ARG A 131 1 ? 6 # _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 disulf1 disulf ? ? A CYS 74 SG ? ? ? 1_555 A CYS 112 SG ? ? A CYS 92 A CYS 130 1_555 ? ? ? ? ? ? ? 2.025 ? ? covale1 covale both ? A LYS 11 C ? ? ? 1_555 A MSE 12 N ? ? A LYS 29 A MSE 30 1_555 ? ? ? ? ? ? ? 1.319 ? ? covale2 covale both ? A MSE 12 C ? ? ? 1_555 A LEU 13 N ? ? A MSE 30 A LEU 31 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale3 covale both ? A ARG 57 C ? ? ? 1_555 A MSE 58 N ? ? A ARG 75 A MSE 76 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale4 covale both ? A MSE 58 C ? ? ? 1_555 A ARG 59 N ? ? A MSE 76 A ARG 77 1_555 ? ? ? ? ? ? ? 1.311 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id THR _struct_mon_prot_cis.label_seq_id 24 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id THR _struct_mon_prot_cis.auth_seq_id 42 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 25 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 43 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -2.32 # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? parallel A 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ARG A 26 ? ALA A 27 ? ARG A 44 ALA A 45 A 2 ILE A 32 ? GLU A 40 ? ILE A 50 GLU A 58 A 3 GLN A 43 ? VAL A 50 ? GLN A 61 VAL A 68 A 4 ILE A 88 ? GLU A 95 ? ILE A 106 GLU A 113 A 5 PRO A 101 ? PHE A 107 ? PRO A 119 PHE A 125 # 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 ARG A 26 ? N ARG A 44 O ASP A 34 ? O ASP A 52 A 2 3 N THR A 38 ? N THR A 56 O ILE A 45 ? O ILE A 63 A 3 4 N LEU A 44 ? N LEU A 62 O ILE A 88 ? O ILE A 106 A 4 5 N PHE A 93 ? N PHE A 111 O ALA A 103 ? O ALA A 121 # 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 SO4 1 ? 6 'BINDING SITE FOR RESIDUE SO4 A 1' AC2 Software A SO4 2 ? 8 'BINDING SITE FOR RESIDUE SO4 A 2' AC3 Software A CXS 3 ? 9 'BINDING SITE FOR RESIDUE CXS A 3' AC4 Software A CXS 4 ? 11 'BINDING SITE FOR RESIDUE CXS A 4' AC5 Software A CXS 5 ? 5 'BINDING SITE FOR RESIDUE CXS A 5' AC6 Software A CXS 6 ? 2 'BINDING SITE FOR RESIDUE CXS A 6' AC7 Software A EDO 7 ? 5 'BINDING SITE FOR RESIDUE EDO A 7' AC8 Software A EDO 8 ? 4 'BINDING SITE FOR RESIDUE EDO A 8' # 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 6 ARG A 51 ? ARG A 69 . ? 1_555 ? 2 AC1 6 ALA A 52 ? ALA A 70 . ? 1_555 ? 3 AC1 6 LYS A 97 ? LYS A 115 . ? 1_555 ? 4 AC1 6 HOH J . ? HOH A 163 . ? 1_555 ? 5 AC1 6 HOH J . ? HOH A 210 . ? 1_555 ? 6 AC1 6 HOH J . ? HOH A 211 . ? 1_555 ? 7 AC2 8 GLY A 1 ? GLY A 0 . ? 1_555 ? 8 AC2 8 CXS D . ? CXS A 3 . ? 4_555 ? 9 AC2 8 HOH J . ? HOH A 19 . ? 4_555 ? 10 AC2 8 ALA A 2 ? ALA A 20 . ? 1_555 ? 11 AC2 8 PHE A 7 ? PHE A 25 . ? 1_555 ? 12 AC2 8 ARG A 106 ? ARG A 124 . ? 4_555 ? 13 AC2 8 HOH J . ? HOH A 226 . ? 1_555 ? 14 AC2 8 HOH J . ? HOH A 227 . ? 1_555 ? 15 AC3 9 SO4 C . ? SO4 A 2 . ? 4_455 ? 16 AC3 9 EDO H . ? EDO A 7 . ? 1_555 ? 17 AC3 9 HOH J . ? HOH A 13 . ? 1_555 ? 18 AC3 9 ARG A 66 ? ARG A 84 . ? 1_555 ? 19 AC3 9 THR A 98 ? THR A 116 . ? 2_564 ? 20 AC3 9 ARG A 106 ? ARG A 124 . ? 1_555 ? 21 AC3 9 ASP A 108 ? ASP A 126 . ? 1_555 ? 22 AC3 9 HOH J . ? HOH A 192 . ? 1_455 ? 23 AC3 9 HOH J . ? HOH A 228 . ? 1_555 ? 24 AC4 11 ASN A 29 ? ASN A 47 . ? 4_565 ? 25 AC4 11 GLU A 30 ? GLU A 48 . ? 4_565 ? 26 AC4 11 GLY A 78 ? GLY A 96 . ? 1_555 ? 27 AC4 11 GLN A 81 ? GLN A 99 . ? 1_555 ? 28 AC4 11 ARG A 85 ? ARG A 103 . ? 1_555 ? 29 AC4 11 TYR A 96 ? TYR A 114 . ? 2_664 ? 30 AC4 11 LYS A 97 ? LYS A 115 . ? 2_664 ? 31 AC4 11 THR A 98 ? THR A 116 . ? 2_664 ? 32 AC4 11 HOH J . ? HOH A 204 . ? 4_565 ? 33 AC4 11 HOH J . ? HOH A 239 . ? 1_555 ? 34 AC4 11 HOH J . ? HOH A 240 . ? 1_555 ? 35 AC5 5 ARG A 57 ? ARG A 75 . ? 4_565 ? 36 AC5 5 ASN A 76 ? ASN A 94 . ? 1_555 ? 37 AC5 5 TYR A 79 ? TYR A 97 . ? 1_555 ? 38 AC5 5 TYR A 91 ? TYR A 109 . ? 1_555 ? 39 AC5 5 HOH J . ? HOH A 146 . ? 1_555 ? 40 AC6 2 HIS A 54 ? HIS A 72 . ? 1_555 ? 41 AC6 2 GLN A 68 ? GLN A 86 . ? 1_555 ? 42 AC7 5 CXS D . ? CXS A 3 . ? 1_555 ? 43 AC7 5 ARG A 66 ? ARG A 84 . ? 1_555 ? 44 AC7 5 GLN A 100 ? GLN A 118 . ? 2_564 ? 45 AC7 5 SER A 111 ? SER A 129 . ? 1_555 ? 46 AC7 5 HOH J . ? HOH A 139 . ? 1_555 ? 47 AC8 4 LYS A 5 ? LYS A 23 . ? 1_555 ? 48 AC8 4 GLU A 8 ? GLU A 26 . ? 1_555 ? 49 AC8 4 GLU A 40 ? GLU A 58 . ? 4_555 ? 50 AC8 4 HOH J . ? HOH A 142 . ? 1_555 ? # _atom_sites.entry_id 3NPD _atom_sites.fract_transf_matrix[1][1] 0.028580 _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] 0.019487 _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] 0.017575 _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 20 20 ALA ALA A . n A 1 3 SER 3 21 21 SER SER A . n A 1 4 LEU 4 22 22 LEU LEU A . n A 1 5 LYS 5 23 23 LYS LYS A . n A 1 6 ASP 6 24 24 ASP ASP A . n A 1 7 PHE 7 25 25 PHE PHE A . n A 1 8 GLU 8 26 26 GLU GLU A . n A 1 9 LEU 9 27 27 LEU LEU A . n A 1 10 SER 10 28 28 SER SER A . n A 1 11 LYS 11 29 29 LYS LYS A . n A 1 12 MSE 12 30 30 MSE MSE A . n A 1 13 LEU 13 31 31 LEU LEU A . n A 1 14 GLU 14 32 32 GLU GLU A . n A 1 15 LYS 15 33 33 LYS LYS A . n A 1 16 VAL 16 34 34 VAL VAL A . n A 1 17 ALA 17 35 35 ALA ALA A . n A 1 18 LYS 18 36 36 LYS LYS A . n A 1 19 GLU 19 37 37 GLU GLU A . n A 1 20 SER 20 38 38 SER SER A . n A 1 21 SER 21 39 39 SER SER A . n A 1 22 VAL 22 40 40 VAL VAL A . n A 1 23 GLY 23 41 41 GLY GLY A . n A 1 24 THR 24 42 42 THR THR A . n A 1 25 PRO 25 43 43 PRO PRO A . n A 1 26 ARG 26 44 44 ARG ARG A . n A 1 27 ALA 27 45 45 ALA ALA A . n A 1 28 ILE 28 46 46 ILE ILE A . n A 1 29 ASN 29 47 47 ASN ASN A . n A 1 30 GLU 30 48 48 GLU GLU A . n A 1 31 ASP 31 49 49 ASP ASP A . n A 1 32 ILE 32 50 50 ILE ILE A . n A 1 33 LEU 33 51 51 LEU LEU A . n A 1 34 ASP 34 52 52 ASP ASP A . n A 1 35 GLN 35 53 53 GLN GLN A . n A 1 36 GLY 36 54 54 GLY GLY A . n A 1 37 TYR 37 55 55 TYR TYR A . n A 1 38 THR 38 56 56 THR THR A . n A 1 39 VAL 39 57 57 VAL VAL A . n A 1 40 GLU 40 58 58 GLU GLU A . n A 1 41 GLY 41 59 59 GLY GLY A . n A 1 42 ASN 42 60 60 ASN ASN A . n A 1 43 GLN 43 61 61 GLN GLN A . n A 1 44 LEU 44 62 62 LEU LEU A . n A 1 45 ILE 45 63 63 ILE ILE A . n A 1 46 ASN 46 64 64 ASN ASN A . n A 1 47 HIS 47 65 65 HIS HIS A . n A 1 48 LEU 48 66 66 LEU LEU A . n A 1 49 SER 49 67 67 SER SER A . n A 1 50 VAL 50 68 68 VAL VAL A . n A 1 51 ARG 51 69 69 ARG ARG A . n A 1 52 ALA 52 70 70 ALA ALA A . n A 1 53 SER 53 71 71 SER SER A . n A 1 54 HIS 54 72 72 HIS HIS A . n A 1 55 ALA 55 73 73 ALA ALA A . n A 1 56 GLU 56 74 74 GLU GLU A . n A 1 57 ARG 57 75 75 ARG ARG A . n A 1 58 MSE 58 76 76 MSE MSE A . n A 1 59 ARG 59 77 77 ARG ARG A . n A 1 60 SER 60 78 78 SER SER A . n A 1 61 ASN 61 79 79 ASN ASN A . n A 1 62 PRO 62 80 80 PRO PRO A . n A 1 63 ASP 63 81 81 ASP ASP A . n A 1 64 SER 64 82 82 SER SER A . n A 1 65 VAL 65 83 83 VAL VAL A . n A 1 66 ARG 66 84 84 ARG ARG A . n A 1 67 SER 67 85 85 SER SER A . n A 1 68 GLN 68 86 86 GLN GLN A . n A 1 69 LEU 69 87 87 LEU LEU A . n A 1 70 GLY 70 88 88 GLY GLY A . n A 1 71 ASP 71 89 89 ASP ASP A . n A 1 72 SER 72 90 90 SER SER A . n A 1 73 VAL 73 91 91 VAL VAL A . n A 1 74 CYS 74 92 92 CYS CYS A . n A 1 75 SER 75 93 93 SER SER A . n A 1 76 ASN 76 94 94 ASN ASN A . n A 1 77 THR 77 95 95 THR THR A . n A 1 78 GLY 78 96 96 GLY GLY A . n A 1 79 TYR 79 97 97 TYR TYR A . n A 1 80 ARG 80 98 98 ARG ARG A . n A 1 81 GLN 81 99 99 GLN GLN A . n A 1 82 LEU 82 100 100 LEU LEU A . n A 1 83 LEU 83 101 101 LEU LEU A . n A 1 84 ALA 84 102 102 ALA ALA A . n A 1 85 ARG 85 103 103 ARG ARG A . n A 1 86 GLY 86 104 104 GLY GLY A . n A 1 87 ALA 87 105 105 ALA ALA A . n A 1 88 ILE 88 106 106 ILE ILE A . n A 1 89 LEU 89 107 107 LEU LEU A . n A 1 90 THR 90 108 108 THR THR A . n A 1 91 TYR 91 109 109 TYR TYR A . n A 1 92 SER 92 110 110 SER SER A . n A 1 93 PHE 93 111 111 PHE PHE A . n A 1 94 THR 94 112 112 THR THR A . n A 1 95 GLU 95 113 113 GLU GLU A . n A 1 96 TYR 96 114 114 TYR TYR A . n A 1 97 LYS 97 115 115 LYS LYS A . n A 1 98 THR 98 116 116 THR THR A . n A 1 99 ASN 99 117 117 ASN ASN A . n A 1 100 GLN 100 118 118 GLN GLN A . n A 1 101 PRO 101 119 119 PRO PRO A . n A 1 102 VAL 102 120 120 VAL VAL A . n A 1 103 ALA 103 121 121 ALA ALA A . n A 1 104 THR 104 122 122 THR THR A . n A 1 105 GLU 105 123 123 GLU GLU A . n A 1 106 ARG 106 124 124 ARG ARG A . n A 1 107 PHE 107 125 125 PHE PHE A . n A 1 108 ASP 108 126 126 ASP ASP A . n A 1 109 ALA 109 127 127 ALA ALA A . n A 1 110 GLY 110 128 128 GLY GLY A . n A 1 111 SER 111 129 129 SER SER A . n A 1 112 CYS 112 130 130 CYS CYS A . n A 1 113 ARG 113 131 131 ARG ARG A . n A 1 114 ILE 114 132 ? ? ? A . n A 1 115 GLN 115 133 ? ? ? A . n A 1 116 GLY 116 134 ? ? ? A . n A 1 117 LYS 117 135 ? ? ? A . n A 1 118 LYS 118 136 ? ? ? A . n # _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _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 SO4 1 1 1 SO4 SO4 A . C 2 SO4 1 2 2 SO4 SO4 A . D 3 CXS 1 3 3 CXS CXS A . E 3 CXS 1 4 4 CXS CXS A . F 3 CXS 1 5 5 CXS CXS A . G 3 CXS 1 6 6 CXS CXS A . H 4 EDO 1 7 7 EDO EDO A . I 4 EDO 1 8 8 EDO EDO A . J 5 HOH 1 9 9 HOH HOH A . J 5 HOH 2 10 10 HOH HOH A . J 5 HOH 3 11 11 HOH HOH A . J 5 HOH 4 12 12 HOH HOH A . J 5 HOH 5 13 13 HOH HOH A . J 5 HOH 6 14 14 HOH HOH A . J 5 HOH 7 15 15 HOH HOH A . J 5 HOH 8 16 16 HOH HOH A . J 5 HOH 9 17 17 HOH HOH A . J 5 HOH 10 18 18 HOH HOH A . J 5 HOH 11 19 19 HOH HOH A . J 5 HOH 12 137 20 HOH HOH A . J 5 HOH 13 138 21 HOH HOH A . J 5 HOH 14 139 22 HOH HOH A . J 5 HOH 15 140 23 HOH HOH A . J 5 HOH 16 141 24 HOH HOH A . J 5 HOH 17 142 25 HOH HOH A . J 5 HOH 18 143 26 HOH HOH A . J 5 HOH 19 144 27 HOH HOH A . J 5 HOH 20 145 28 HOH HOH A . J 5 HOH 21 146 29 HOH HOH A . J 5 HOH 22 147 30 HOH HOH A . J 5 HOH 23 148 31 HOH HOH A . J 5 HOH 24 149 32 HOH HOH A . J 5 HOH 25 150 33 HOH HOH A . J 5 HOH 26 151 34 HOH HOH A . J 5 HOH 27 152 35 HOH HOH A . J 5 HOH 28 153 36 HOH HOH A . J 5 HOH 29 154 37 HOH HOH A . J 5 HOH 30 155 38 HOH HOH A . J 5 HOH 31 156 39 HOH HOH A . J 5 HOH 32 157 40 HOH HOH A . J 5 HOH 33 158 41 HOH HOH A . J 5 HOH 34 159 42 HOH HOH A . J 5 HOH 35 160 43 HOH HOH A . J 5 HOH 36 161 44 HOH HOH A . J 5 HOH 37 162 45 HOH HOH A . J 5 HOH 38 163 46 HOH HOH A . J 5 HOH 39 164 47 HOH HOH A . J 5 HOH 40 165 48 HOH HOH A . J 5 HOH 41 166 49 HOH HOH A . J 5 HOH 42 167 50 HOH HOH A . J 5 HOH 43 168 51 HOH HOH A . J 5 HOH 44 169 52 HOH HOH A . J 5 HOH 45 170 53 HOH HOH A . J 5 HOH 46 171 54 HOH HOH A . J 5 HOH 47 172 55 HOH HOH A . J 5 HOH 48 173 56 HOH HOH A . J 5 HOH 49 174 57 HOH HOH A . J 5 HOH 50 175 58 HOH HOH A . J 5 HOH 51 176 59 HOH HOH A . J 5 HOH 52 177 60 HOH HOH A . J 5 HOH 53 178 61 HOH HOH A . J 5 HOH 54 179 62 HOH HOH A . J 5 HOH 55 180 63 HOH HOH A . J 5 HOH 56 181 64 HOH HOH A . J 5 HOH 57 182 65 HOH HOH A . J 5 HOH 58 183 66 HOH HOH A . J 5 HOH 59 184 67 HOH HOH A . J 5 HOH 60 185 68 HOH HOH A . J 5 HOH 61 186 69 HOH HOH A . J 5 HOH 62 187 70 HOH HOH A . J 5 HOH 63 188 71 HOH HOH A . J 5 HOH 64 189 72 HOH HOH A . J 5 HOH 65 190 73 HOH HOH A . J 5 HOH 66 191 74 HOH HOH A . J 5 HOH 67 192 75 HOH HOH A . J 5 HOH 68 193 76 HOH HOH A . J 5 HOH 69 194 77 HOH HOH A . J 5 HOH 70 195 78 HOH HOH A . J 5 HOH 71 196 79 HOH HOH A . J 5 HOH 72 197 80 HOH HOH A . J 5 HOH 73 198 81 HOH HOH A . J 5 HOH 74 199 82 HOH HOH A . J 5 HOH 75 200 83 HOH HOH A . J 5 HOH 76 201 84 HOH HOH A . J 5 HOH 77 202 85 HOH HOH A . J 5 HOH 78 203 86 HOH HOH A . J 5 HOH 79 204 87 HOH HOH A . J 5 HOH 80 205 88 HOH HOH A . J 5 HOH 81 206 89 HOH HOH A . J 5 HOH 82 207 90 HOH HOH A . J 5 HOH 83 208 91 HOH HOH A . J 5 HOH 84 209 92 HOH HOH A . J 5 HOH 85 210 93 HOH HOH A . J 5 HOH 86 211 94 HOH HOH A . J 5 HOH 87 212 95 HOH HOH A . J 5 HOH 88 213 96 HOH HOH A . J 5 HOH 89 214 97 HOH HOH A . J 5 HOH 90 215 98 HOH HOH A . J 5 HOH 91 216 99 HOH HOH A . J 5 HOH 92 217 100 HOH HOH A . J 5 HOH 93 218 101 HOH HOH A . J 5 HOH 94 219 102 HOH HOH A . J 5 HOH 95 220 103 HOH HOH A . J 5 HOH 96 221 104 HOH HOH A . J 5 HOH 97 222 105 HOH HOH A . J 5 HOH 98 223 106 HOH HOH A . J 5 HOH 99 224 107 HOH HOH A . J 5 HOH 100 225 108 HOH HOH A . J 5 HOH 101 226 109 HOH HOH A . J 5 HOH 102 227 110 HOH HOH A . J 5 HOH 103 228 111 HOH HOH A . J 5 HOH 104 229 112 HOH HOH A . J 5 HOH 105 230 113 HOH HOH A . J 5 HOH 106 231 114 HOH HOH A . J 5 HOH 107 232 115 HOH HOH A . J 5 HOH 108 233 116 HOH HOH A . J 5 HOH 109 234 117 HOH HOH A . J 5 HOH 110 235 118 HOH HOH A . J 5 HOH 111 236 119 HOH HOH A . J 5 HOH 112 237 120 HOH HOH A . J 5 HOH 113 238 121 HOH HOH A . J 5 HOH 114 239 122 HOH HOH A . J 5 HOH 115 240 123 HOH HOH A . J 5 HOH 116 241 124 HOH HOH A . J 5 HOH 117 242 125 HOH HOH A . J 5 HOH 118 243 126 HOH HOH A . J 5 HOH 119 244 127 HOH HOH A . J 5 HOH 120 245 128 HOH HOH A . J 5 HOH 121 246 129 HOH HOH A . J 5 HOH 122 247 130 HOH HOH A . J 5 HOH 123 248 131 HOH HOH A . J 5 HOH 124 249 132 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 12 A MSE 30 ? MET SELENOMETHIONINE 2 A MSE 58 A MSE 76 ? MET 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,E,F,G,H,I,J # _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 2010-07-28 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2014-09-24 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' 'Version format compliance' 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 4 'Structure model' database_2 2 4 'Structure model' struct_conn 3 4 'Structure model' struct_ref_seq_dif 4 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 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' 5 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 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 21.1461 _pdbx_refine_tls.origin_y 27.0064 _pdbx_refine_tls.origin_z 0.7537 _pdbx_refine_tls.T[1][1] 0.0233 _pdbx_refine_tls.T[2][2] 0.0172 _pdbx_refine_tls.T[3][3] 0.0104 _pdbx_refine_tls.T[1][2] -0.0037 _pdbx_refine_tls.T[1][3] -0.0020 _pdbx_refine_tls.T[2][3] -0.0001 _pdbx_refine_tls.L[1][1] 0.6927 _pdbx_refine_tls.L[2][2] 0.5397 _pdbx_refine_tls.L[3][3] 0.6132 _pdbx_refine_tls.L[1][2] -0.1365 _pdbx_refine_tls.L[1][3] -0.1554 _pdbx_refine_tls.L[2][3] 0.0943 _pdbx_refine_tls.S[1][1] 0.0349 _pdbx_refine_tls.S[2][2] -0.0318 _pdbx_refine_tls.S[3][3] -0.0031 _pdbx_refine_tls.S[1][2] 0.0185 _pdbx_refine_tls.S[1][3] 0.0617 _pdbx_refine_tls.S[2][3] -0.0377 _pdbx_refine_tls.S[2][1] -0.0242 _pdbx_refine_tls.S[3][1] 0.0014 _pdbx_refine_tls.S[3][2] -0.0217 # _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 0 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 131 _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 SOLVE . ? program 'Tom Terwilliger' terwilliger@LANL.gov phasing http://www.solve.lanl.gov/ ? ? 2 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 ? 3 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 XDS . ? ? ? ? 'data reduction' ? ? ? # _pdbx_entry_details.entry_id 3NPD _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THIS CONSTRUCT (RESIDUES 20-136) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 NE _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 ARG _pdbx_validate_rmsd_angle.auth_seq_id_1 131 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 A _pdbx_validate_rmsd_angle.auth_atom_id_2 CZ _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 ARG _pdbx_validate_rmsd_angle.auth_seq_id_2 131 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 A _pdbx_validate_rmsd_angle.auth_atom_id_3 NH2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 ARG _pdbx_validate_rmsd_angle.auth_seq_id_3 131 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 A _pdbx_validate_rmsd_angle.angle_value 115.90 _pdbx_validate_rmsd_angle.angle_target_value 120.30 _pdbx_validate_rmsd_angle.angle_deviation -4.40 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # 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 33 ? CE ? A LYS 15 CE 2 1 Y 1 A LYS 33 ? NZ ? A LYS 15 NZ 3 1 Y 1 A LYS 36 ? CE ? A LYS 18 CE 4 1 Y 1 A LYS 36 ? NZ ? A LYS 18 NZ 5 1 N 1 A CXS 6 ? S ? G CXS 1 S 6 1 N 1 A CXS 6 ? O1 ? G CXS 1 O1 7 1 N 1 A CXS 6 ? O2 ? G CXS 1 O2 8 1 N 1 A CXS 6 ? O3 ? G CXS 1 O3 9 1 N 1 A CXS 6 ? C1 ? G CXS 1 C1 # 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 ILE 132 ? A ILE 114 2 1 Y 1 A GLN 133 ? A GLN 115 3 1 Y 1 A GLY 134 ? A GLY 116 4 1 Y 1 A LYS 135 ? A LYS 117 5 1 Y 1 A LYS 136 ? A LYS 118 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 '3-CYCLOHEXYL-1-PROPYLSULFONIC ACID' CXS 4 1,2-ETHANEDIOL EDO 5 water HOH #