data_3F7S # _entry.id 3F7S # _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 3F7S pdb_00003f7s 10.2210/pdb3f7s/pdb RCSB RCSB050253 ? ? WWPDB D_1000050253 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 391198 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3F7S _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-11-10 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of NTF2-like protein of unknown function (NP_746665.1) from PSEUDOMONAS PUTIDA KT2440 at 2.11 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 3F7S _cell.length_a 65.920 _cell.length_b 65.920 _cell.length_c 89.390 _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 3F7S _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 'uncharacterized NTF2-like protein' 16310.308 1 ? ? ? ? 2 non-polymer syn 'UNKNOWN LIGAND' ? 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 4 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 5 water nat water 18.015 65 ? ? ? ? # _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 ;G(MSE)STAAESEIRQLIERW(MSE)QAVRDRDIPGIIAPYADDIVAFDAIQALQFKGKSAYTAHWE(MSE)C(MSE)G (MSE)CTGP(MSE)VFELAQLTVHAAGDLALAHWLNRCGPGDDESQCGF(MSE)RATVGYRRQGGQWQVIHEHWSAPFD (MSE)ETQKALFDLKP ; _entity_poly.pdbx_seq_one_letter_code_can ;GMSTAAESEIRQLIERWMQAVRDRDIPGIIAPYADDIVAFDAIQALQFKGKSAYTAHWEMCMGMCTGPMVFELAQLTVHA AGDLALAHWLNRCGPGDDESQCGFMRATVGYRRQGGQWQVIHEHWSAPFDMETQKALFDLKP ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 391198 # 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 MSE n 1 3 SER n 1 4 THR n 1 5 ALA n 1 6 ALA n 1 7 GLU n 1 8 SER n 1 9 GLU n 1 10 ILE n 1 11 ARG n 1 12 GLN n 1 13 LEU n 1 14 ILE n 1 15 GLU n 1 16 ARG n 1 17 TRP n 1 18 MSE n 1 19 GLN n 1 20 ALA n 1 21 VAL n 1 22 ARG n 1 23 ASP n 1 24 ARG n 1 25 ASP n 1 26 ILE n 1 27 PRO n 1 28 GLY n 1 29 ILE n 1 30 ILE n 1 31 ALA n 1 32 PRO n 1 33 TYR n 1 34 ALA n 1 35 ASP n 1 36 ASP n 1 37 ILE n 1 38 VAL n 1 39 ALA n 1 40 PHE n 1 41 ASP n 1 42 ALA n 1 43 ILE n 1 44 GLN n 1 45 ALA n 1 46 LEU n 1 47 GLN n 1 48 PHE n 1 49 LYS n 1 50 GLY n 1 51 LYS n 1 52 SER n 1 53 ALA n 1 54 TYR n 1 55 THR n 1 56 ALA n 1 57 HIS n 1 58 TRP n 1 59 GLU n 1 60 MSE n 1 61 CYS n 1 62 MSE n 1 63 GLY n 1 64 MSE n 1 65 CYS n 1 66 THR n 1 67 GLY n 1 68 PRO n 1 69 MSE n 1 70 VAL n 1 71 PHE n 1 72 GLU n 1 73 LEU n 1 74 ALA n 1 75 GLN n 1 76 LEU n 1 77 THR n 1 78 VAL n 1 79 HIS n 1 80 ALA n 1 81 ALA n 1 82 GLY n 1 83 ASP n 1 84 LEU n 1 85 ALA n 1 86 LEU n 1 87 ALA n 1 88 HIS n 1 89 TRP n 1 90 LEU n 1 91 ASN n 1 92 ARG n 1 93 CYS n 1 94 GLY n 1 95 PRO n 1 96 GLY n 1 97 ASP n 1 98 ASP n 1 99 GLU n 1 100 SER n 1 101 GLN n 1 102 CYS n 1 103 GLY n 1 104 PHE n 1 105 MSE n 1 106 ARG n 1 107 ALA n 1 108 THR n 1 109 VAL n 1 110 GLY n 1 111 TYR n 1 112 ARG n 1 113 ARG n 1 114 GLN n 1 115 GLY n 1 116 GLY n 1 117 GLN n 1 118 TRP n 1 119 GLN n 1 120 VAL n 1 121 ILE n 1 122 HIS n 1 123 GLU n 1 124 HIS n 1 125 TRP n 1 126 SER n 1 127 ALA n 1 128 PRO n 1 129 PHE n 1 130 ASP n 1 131 MSE n 1 132 GLU n 1 133 THR n 1 134 GLN n 1 135 LYS n 1 136 ALA n 1 137 LEU n 1 138 PHE n 1 139 ASP n 1 140 LEU n 1 141 LYS n 1 142 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 'NP_746665.1, PP4556, PP_4556' _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 putida KT2440' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 160488 _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 Q88EB0_PSEPK _struct_ref.pdbx_db_accession Q88EB0 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSTAAESEIRQLIERWMQAVRDRDIPGIIAPYADDIVAFDAIQALQFKGKSAYTAHWEMCMGMCTGPMVFELAQLTVHAA GDLALAHWLNRCGPGDDESQCGFMRATVGYRRQGGQWQVIHEHWSAPFDMETQKALFDLKP ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3F7S _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 142 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q88EB0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 141 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 141 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3F7S _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 Q88EB0 _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 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 UNL non-polymer . 'UNKNOWN LIGAND' ? ? ? VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 3F7S # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.98 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 58.68 _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 '0.8000M K2HPO4, 0.2000M Li2SO4, 1.2000M NaH2PO4, 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 300 mm CCD' _diffrn_detector.details 'Adjustable focusing mirrors in K-B geometry' _diffrn_detector.pdbx_collection_date 2008-10-13 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111) Double Crystal Monochrometer' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97948 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline 23-ID-B _diffrn_source.type 'APS BEAMLINE 23-ID-B' _diffrn_source.pdbx_wavelength 0.97948 _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site APS # _reflns.entry_id 3F7S _reflns.d_resolution_high 2.11 _reflns.d_resolution_low 29.476 _reflns.number_obs 11917 _reflns.pdbx_Rmerge_I_obs 0.120 _reflns.percent_possible_obs 99.900 _reflns.B_iso_Wilson_estimate 31.836 _reflns.observed_criterion_sigma_I -3.00 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 9.680 _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 2.11 2.19 11570 ? 2296 0.986 1.6 ? ? ? ? ? 99.90 1 1 2.19 2.27 10090 ? 1995 0.751 2.1 ? ? ? ? ? 99.90 2 1 2.27 2.38 11511 ? 2268 0.654 2.5 ? ? ? ? ? 99.80 3 1 2.38 2.50 10517 ? 2066 0.566 2.9 ? ? ? ? ? 100.00 4 1 2.50 2.66 11360 ? 2219 0.398 4.0 ? ? ? ? ? 100.00 5 1 2.66 2.86 10904 ? 2132 0.256 6.1 ? ? ? ? ? 100.00 6 1 2.86 3.15 11134 ? 2179 0.161 9.3 ? ? ? ? ? 100.00 7 1 3.15 3.60 11056 ? 2155 0.086 16.0 ? ? ? ? ? 100.00 8 1 3.60 4.53 11125 ? 2172 0.053 23.9 ? ? ? ? ? 100.00 9 1 4.53 29.476 11294 ? 2204 0.041 28.2 ? ? ? ? ? 99.50 10 1 # _refine.entry_id 3F7S _refine.ls_d_res_high 2.110 _refine.ls_d_res_low 29.476 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.910 _refine.ls_number_reflns_obs 11874 _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 RESIDUAL B FACTORS ONLY. 4. GLYCEROL (PRESENT IN THE CRYOPROTECTION CONDITIONS) AND SULFATE (PRESENT IN THE CRYSTALLIZATION SOLUTION) ARE MODELED. THE ASSIGNMENT OF SULFATE IS TENTATIVE AS PHOSPHATE IS ALSO PRESENT IN THE CRYSTALLIZATION SOLUTION. 5. AN UNKNOWN LIGAND (UNL) WAS MODELED INTO THE PUTATVE ACTIVE SITE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.179 _refine.ls_R_factor_R_work 0.177 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.217 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.700 _refine.ls_number_reflns_R_free 564 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 33.633 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.050 _refine.aniso_B[2][2] -0.050 _refine.aniso_B[3][3] 0.110 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.956 _refine.correlation_coeff_Fo_to_Fc_free 0.938 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.161 _refine.pdbx_overall_ESU_R_Free 0.150 _refine.overall_SU_ML 0.099 _refine.overall_SU_B 8.412 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_method_to_determine_struct SAD _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 96.63 _refine.B_iso_min 13.02 _refine.occupancy_max 1.00 _refine.occupancy_min 0.50 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 1091 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 65 _refine_hist.number_atoms_total 1171 _refine_hist.d_res_high 2.110 _refine_hist.d_res_low 29.476 # loop_ _refine_ls_restr.type _refine_ls_restr.pdbx_refine_id _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 r_bond_refined_d 'X-RAY DIFFRACTION' 1138 0.016 0.021 ? ? r_bond_other_d 'X-RAY DIFFRACTION' 761 0.001 0.020 ? ? r_angle_refined_deg 'X-RAY DIFFRACTION' 1543 1.517 1.931 ? ? r_angle_other_deg 'X-RAY DIFFRACTION' 1839 0.928 3.000 ? ? r_dihedral_angle_1_deg 'X-RAY DIFFRACTION' 143 6.192 5.000 ? ? r_dihedral_angle_2_deg 'X-RAY DIFFRACTION' 52 35.877 23.654 ? ? r_dihedral_angle_3_deg 'X-RAY DIFFRACTION' 177 16.121 15.000 ? ? r_dihedral_angle_4_deg 'X-RAY DIFFRACTION' 7 4.955 15.000 ? ? r_chiral_restr 'X-RAY DIFFRACTION' 159 0.094 0.200 ? ? r_gen_planes_refined 'X-RAY DIFFRACTION' 1289 0.008 0.021 ? ? r_gen_planes_other 'X-RAY DIFFRACTION' 241 0.001 0.020 ? ? r_mcbond_it 'X-RAY DIFFRACTION' 707 2.121 3.000 ? ? r_mcbond_other 'X-RAY DIFFRACTION' 290 0.498 3.000 ? ? r_mcangle_it 'X-RAY DIFFRACTION' 1118 3.785 5.000 ? ? r_scbond_it 'X-RAY DIFFRACTION' 431 6.370 8.000 ? ? r_scangle_it 'X-RAY DIFFRACTION' 424 8.957 11.000 ? ? # _refine_ls_shell.d_res_high 2.110 _refine_ls_shell.d_res_low 2.165 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 100.000 _refine_ls_shell.number_reflns_R_work 801 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.220 _refine_ls_shell.R_factor_R_free 0.273 _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 841 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3F7S _struct.title 'CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (PP_4556) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.11 A RESOLUTION' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;NTF2-LIKE PROTEIN, 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 3F7S # 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 3 ? D N N 4 ? E N N 5 ? # _struct_biol.id 1 # 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 ? ASP A 23 ? SER A 2 ASP A 22 1 ? 21 HELX_P HELX_P2 2 ASP A 25 ? ALA A 31 ? ASP A 24 ALA A 30 1 ? 7 HELX_P HELX_P3 3 GLY A 50 ? MSE A 64 ? GLY A 49 MSE A 63 1 ? 15 HELX_P HELX_P4 4 ASP A 98 ? CYS A 102 ? ASP A 97 CYS A 101 5 ? 5 # _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 1 C ? ? ? 1_555 A MSE 2 N ? ? A GLY 0 A MSE 1 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale2 covale both ? A MSE 2 C ? ? ? 1_555 A SER 3 N ? ? A MSE 1 A SER 2 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale3 covale both ? A TRP 17 C ? ? ? 1_555 A MSE 18 N ? ? A TRP 16 A MSE 17 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale4 covale both ? A MSE 18 C ? ? ? 1_555 A GLN 19 N ? ? A MSE 17 A GLN 18 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale5 covale both ? A GLU 59 C ? ? ? 1_555 A MSE 60 N ? ? A GLU 58 A MSE 59 1_555 ? ? ? ? ? ? ? 1.322 ? ? covale6 covale both ? A MSE 60 C ? ? ? 1_555 A CYS 61 N ? ? A MSE 59 A CYS 60 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale7 covale both ? A CYS 61 C ? ? ? 1_555 A MSE 62 N ? ? A CYS 60 A MSE 61 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale8 covale both ? A MSE 62 C ? ? ? 1_555 A GLY 63 N ? ? A MSE 61 A GLY 62 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale9 covale both ? A GLY 63 C ? ? ? 1_555 A MSE 64 N ? ? A GLY 62 A MSE 63 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale10 covale both ? A MSE 64 C ? ? ? 1_555 A CYS 65 N ? ? A MSE 63 A CYS 64 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale11 covale both ? A PRO 68 C ? ? ? 1_555 A MSE 69 N ? ? A PRO 67 A MSE 68 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale12 covale both ? A MSE 69 C ? ? ? 1_555 A VAL 70 N ? ? A MSE 68 A VAL 69 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale13 covale both ? A PHE 104 C ? ? ? 1_555 A MSE 105 N ? ? A PHE 103 A MSE 104 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale14 covale both ? A MSE 105 C ? ? ? 1_555 A ARG 106 N ? ? A MSE 104 A ARG 105 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale15 covale both ? A ASP 130 C ? ? ? 1_555 A MSE 131 N ? ? A ASP 129 A MSE 130 1_555 ? ? ? ? ? ? ? 1.316 ? ? covale16 covale both ? A MSE 131 C ? ? ? 1_555 A GLU 132 N ? ? A MSE 130 A GLU 131 1_555 ? ? ? ? ? ? ? 1.325 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _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 ? parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? 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 PHE A 48 ? LYS A 49 ? PHE A 47 LYS A 48 A 2 TYR A 33 ? PHE A 40 ? TYR A 32 PHE A 39 A 3 GLN A 117 ? SER A 126 ? GLN A 116 SER A 125 A 4 GLY A 103 ? GLN A 114 ? GLY A 102 GLN A 113 A 5 LEU A 84 ? PRO A 95 ? LEU A 83 PRO A 94 A 6 MSE A 69 ? ALA A 81 ? MSE A 68 ALA A 80 # 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 PHE A 48 ? O PHE A 47 N ALA A 39 ? N ALA A 38 A 2 3 N PHE A 40 ? N PHE A 39 O GLU A 123 ? O GLU A 122 A 3 4 O GLN A 117 ? O GLN A 116 N GLN A 114 ? N GLN A 113 A 4 5 O MSE A 105 ? O MSE A 104 N ASN A 91 ? N ASN A 90 A 5 6 O GLY A 94 ? O GLY A 93 N VAL A 70 ? N VAL A 69 # 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 UNL 142 ? 2 'BINDING SITE FOR RESIDUE UNL A 142' AC2 Software A SO4 143 ? 3 'BINDING SITE FOR RESIDUE SO4 A 143' AC3 Software A GOL 144 ? 5 'BINDING SITE FOR RESIDUE GOL A 144' # 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 2 ASP A 41 ? ASP A 40 . ? 1_555 ? 2 AC1 2 TRP A 58 ? TRP A 57 . ? 1_555 ? 3 AC2 3 ARG A 16 ? ARG A 15 . ? 4_454 ? 4 AC2 3 SER A 52 ? SER A 51 . ? 1_555 ? 5 AC2 3 HOH E . ? HOH A 152 . ? 1_555 ? 6 AC3 5 ASP A 36 ? ASP A 35 . ? 1_555 ? 7 AC3 5 THR A 77 ? THR A 76 . ? 7_556 ? 8 AC3 5 HIS A 79 ? HIS A 78 . ? 7_556 ? 9 AC3 5 HIS A 88 ? HIS A 87 . ? 7_556 ? 10 AC3 5 ILE A 121 ? ILE A 120 . ? 1_555 ? # _atom_sites.entry_id 3F7S _atom_sites.fract_transf_matrix[1][1] 0.015170 _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] 0.015170 _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] 0.011187 _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 MSE 2 1 1 MSE MSE A . n A 1 3 SER 3 2 2 SER SER A . n A 1 4 THR 4 3 3 THR THR A . n A 1 5 ALA 5 4 4 ALA ALA A . n A 1 6 ALA 6 5 5 ALA ALA A . n A 1 7 GLU 7 6 6 GLU GLU A . n A 1 8 SER 8 7 7 SER SER A . n A 1 9 GLU 9 8 8 GLU GLU A . n A 1 10 ILE 10 9 9 ILE ILE A . n A 1 11 ARG 11 10 10 ARG ARG A . n A 1 12 GLN 12 11 11 GLN GLN A . n A 1 13 LEU 13 12 12 LEU LEU A . n A 1 14 ILE 14 13 13 ILE ILE A . n A 1 15 GLU 15 14 14 GLU GLU A . n A 1 16 ARG 16 15 15 ARG ARG A . n A 1 17 TRP 17 16 16 TRP TRP A . n A 1 18 MSE 18 17 17 MSE MSE A . n A 1 19 GLN 19 18 18 GLN GLN A . n A 1 20 ALA 20 19 19 ALA ALA A . n A 1 21 VAL 21 20 20 VAL VAL A . n A 1 22 ARG 22 21 21 ARG ARG A . n A 1 23 ASP 23 22 22 ASP ASP A . n A 1 24 ARG 24 23 23 ARG ARG A . n A 1 25 ASP 25 24 24 ASP ASP A . n A 1 26 ILE 26 25 25 ILE ILE A . n A 1 27 PRO 27 26 26 PRO PRO A . n A 1 28 GLY 28 27 27 GLY GLY A . n A 1 29 ILE 29 28 28 ILE ILE A . n A 1 30 ILE 30 29 29 ILE ILE A . n A 1 31 ALA 31 30 30 ALA ALA A . n A 1 32 PRO 32 31 31 PRO PRO A . n A 1 33 TYR 33 32 32 TYR TYR A . n A 1 34 ALA 34 33 33 ALA ALA A . n A 1 35 ASP 35 34 34 ASP ASP A . n A 1 36 ASP 36 35 35 ASP ASP A . n A 1 37 ILE 37 36 36 ILE ILE A . n A 1 38 VAL 38 37 37 VAL VAL A . n A 1 39 ALA 39 38 38 ALA ALA A . n A 1 40 PHE 40 39 39 PHE PHE A . n A 1 41 ASP 41 40 40 ASP ASP A . n A 1 42 ALA 42 41 41 ALA ALA A . n A 1 43 ILE 43 42 42 ILE ILE A . n A 1 44 GLN 44 43 43 GLN GLN A . n A 1 45 ALA 45 44 44 ALA ALA A . n A 1 46 LEU 46 45 45 LEU LEU A . n A 1 47 GLN 47 46 46 GLN GLN A . n A 1 48 PHE 48 47 47 PHE PHE A . n A 1 49 LYS 49 48 48 LYS LYS A . n A 1 50 GLY 50 49 49 GLY GLY A . n A 1 51 LYS 51 50 50 LYS LYS A . n A 1 52 SER 52 51 51 SER SER A . n A 1 53 ALA 53 52 52 ALA ALA A . n A 1 54 TYR 54 53 53 TYR TYR A . n A 1 55 THR 55 54 54 THR THR A . n A 1 56 ALA 56 55 55 ALA ALA A . n A 1 57 HIS 57 56 56 HIS HIS A . n A 1 58 TRP 58 57 57 TRP TRP A . n A 1 59 GLU 59 58 58 GLU GLU A . n A 1 60 MSE 60 59 59 MSE MSE A . n A 1 61 CYS 61 60 60 CYS CYS A . n A 1 62 MSE 62 61 61 MSE MSE A . n A 1 63 GLY 63 62 62 GLY GLY A . n A 1 64 MSE 64 63 63 MSE MSE A . n A 1 65 CYS 65 64 64 CYS CYS A . n A 1 66 THR 66 65 65 THR THR A . n A 1 67 GLY 67 66 66 GLY GLY A . n A 1 68 PRO 68 67 67 PRO PRO A . n A 1 69 MSE 69 68 68 MSE MSE A . n A 1 70 VAL 70 69 69 VAL VAL A . n A 1 71 PHE 71 70 70 PHE PHE A . n A 1 72 GLU 72 71 71 GLU GLU A . n A 1 73 LEU 73 72 72 LEU LEU A . n A 1 74 ALA 74 73 73 ALA ALA A . n A 1 75 GLN 75 74 74 GLN GLN A . n A 1 76 LEU 76 75 75 LEU LEU A . n A 1 77 THR 77 76 76 THR THR A . n A 1 78 VAL 78 77 77 VAL VAL A . n A 1 79 HIS 79 78 78 HIS HIS A . n A 1 80 ALA 80 79 79 ALA ALA A . n A 1 81 ALA 81 80 80 ALA ALA A . n A 1 82 GLY 82 81 81 GLY GLY A . n A 1 83 ASP 83 82 82 ASP ASP A . n A 1 84 LEU 84 83 83 LEU LEU A . n A 1 85 ALA 85 84 84 ALA ALA A . n A 1 86 LEU 86 85 85 LEU LEU A . n A 1 87 ALA 87 86 86 ALA ALA A . n A 1 88 HIS 88 87 87 HIS HIS A . n A 1 89 TRP 89 88 88 TRP TRP A . n A 1 90 LEU 90 89 89 LEU LEU A . n A 1 91 ASN 91 90 90 ASN ASN A . n A 1 92 ARG 92 91 91 ARG ARG A . n A 1 93 CYS 93 92 92 CYS CYS A . n A 1 94 GLY 94 93 93 GLY GLY A . n A 1 95 PRO 95 94 94 PRO PRO A . n A 1 96 GLY 96 95 95 GLY GLY A . n A 1 97 ASP 97 96 96 ASP ASP A . n A 1 98 ASP 98 97 97 ASP ASP A . n A 1 99 GLU 99 98 98 GLU GLU A . n A 1 100 SER 100 99 99 SER SER A . n A 1 101 GLN 101 100 100 GLN GLN A . n A 1 102 CYS 102 101 101 CYS CYS A . n A 1 103 GLY 103 102 102 GLY GLY A . n A 1 104 PHE 104 103 103 PHE PHE A . n A 1 105 MSE 105 104 104 MSE MSE A . n A 1 106 ARG 106 105 105 ARG ARG A . n A 1 107 ALA 107 106 106 ALA ALA A . n A 1 108 THR 108 107 107 THR THR A . n A 1 109 VAL 109 108 108 VAL VAL A . n A 1 110 GLY 110 109 109 GLY GLY A . n A 1 111 TYR 111 110 110 TYR TYR A . n A 1 112 ARG 112 111 111 ARG ARG A . n A 1 113 ARG 113 112 112 ARG ARG A . n A 1 114 GLN 114 113 113 GLN GLN A . n A 1 115 GLY 115 114 114 GLY GLY A . n A 1 116 GLY 116 115 115 GLY GLY A . n A 1 117 GLN 117 116 116 GLN GLN A . n A 1 118 TRP 118 117 117 TRP TRP A . n A 1 119 GLN 119 118 118 GLN GLN A . n A 1 120 VAL 120 119 119 VAL VAL A . n A 1 121 ILE 121 120 120 ILE ILE A . n A 1 122 HIS 122 121 121 HIS HIS A . n A 1 123 GLU 123 122 122 GLU GLU A . n A 1 124 HIS 124 123 123 HIS HIS A . n A 1 125 TRP 125 124 124 TRP TRP A . n A 1 126 SER 126 125 125 SER SER A . n A 1 127 ALA 127 126 126 ALA ALA A . n A 1 128 PRO 128 127 127 PRO PRO A . n A 1 129 PHE 129 128 128 PHE PHE A . n A 1 130 ASP 130 129 129 ASP ASP A . n A 1 131 MSE 131 130 130 MSE MSE A . n A 1 132 GLU 132 131 131 GLU GLU A . n A 1 133 THR 133 132 132 THR THR A . n A 1 134 GLN 134 133 133 GLN GLN A . n A 1 135 LYS 135 134 134 LYS LYS A . n A 1 136 ALA 136 135 135 ALA ALA A . n A 1 137 LEU 137 136 136 LEU LEU A . n A 1 138 PHE 138 137 137 PHE PHE A . n A 1 139 ASP 139 138 138 ASP ASP A . n A 1 140 LEU 140 139 139 LEU LEU A . n A 1 141 LYS 141 140 140 LYS LYS A . n A 1 142 PRO 142 141 141 PRO PRO 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 UNL 1 142 1 UNL UNL A . C 3 SO4 1 143 2 SO4 SO4 A . D 4 GOL 1 144 3 GOL GOL A . E 5 HOH 1 145 4 HOH HOH A . E 5 HOH 2 146 5 HOH HOH A . E 5 HOH 3 147 6 HOH HOH A . E 5 HOH 4 148 7 HOH HOH A . E 5 HOH 5 149 8 HOH HOH A . E 5 HOH 6 150 9 HOH HOH A . E 5 HOH 7 151 10 HOH HOH A . E 5 HOH 8 152 11 HOH HOH A . E 5 HOH 9 153 12 HOH HOH A . E 5 HOH 10 154 13 HOH HOH A . E 5 HOH 11 155 14 HOH HOH A . E 5 HOH 12 156 15 HOH HOH A . E 5 HOH 13 157 16 HOH HOH A . E 5 HOH 14 158 17 HOH HOH A . E 5 HOH 15 159 18 HOH HOH A . E 5 HOH 16 160 19 HOH HOH A . E 5 HOH 17 161 20 HOH HOH A . E 5 HOH 18 162 21 HOH HOH A . E 5 HOH 19 163 22 HOH HOH A . E 5 HOH 20 164 23 HOH HOH A . E 5 HOH 21 165 24 HOH HOH A . E 5 HOH 22 166 25 HOH HOH A . E 5 HOH 23 167 26 HOH HOH A . E 5 HOH 24 168 27 HOH HOH A . E 5 HOH 25 169 28 HOH HOH A . E 5 HOH 26 170 29 HOH HOH A . E 5 HOH 27 171 30 HOH HOH A . E 5 HOH 28 172 31 HOH HOH A . E 5 HOH 29 173 32 HOH HOH A . E 5 HOH 30 174 33 HOH HOH A . E 5 HOH 31 175 34 HOH HOH A . E 5 HOH 32 176 35 HOH HOH A . E 5 HOH 33 177 36 HOH HOH A . E 5 HOH 34 178 37 HOH HOH A . E 5 HOH 35 179 38 HOH HOH A . E 5 HOH 36 180 39 HOH HOH A . E 5 HOH 37 181 40 HOH HOH A . E 5 HOH 38 182 41 HOH HOH A . E 5 HOH 39 183 42 HOH HOH A . E 5 HOH 40 184 43 HOH HOH A . E 5 HOH 41 185 44 HOH HOH A . E 5 HOH 42 186 45 HOH HOH A . E 5 HOH 43 187 46 HOH HOH A . E 5 HOH 44 188 47 HOH HOH A . E 5 HOH 45 189 48 HOH HOH A . E 5 HOH 46 190 49 HOH HOH A . E 5 HOH 47 191 50 HOH HOH A . E 5 HOH 48 192 51 HOH HOH A . E 5 HOH 49 193 52 HOH HOH A . E 5 HOH 50 194 53 HOH HOH A . E 5 HOH 51 195 54 HOH HOH A . E 5 HOH 52 196 55 HOH HOH A . E 5 HOH 53 197 56 HOH HOH A . E 5 HOH 54 198 57 HOH HOH A . E 5 HOH 55 199 58 HOH HOH A . E 5 HOH 56 200 59 HOH HOH A . E 5 HOH 57 201 60 HOH HOH A . E 5 HOH 58 202 61 HOH HOH A . E 5 HOH 59 203 62 HOH HOH A . E 5 HOH 60 204 63 HOH HOH A . E 5 HOH 61 205 64 HOH HOH A . E 5 HOH 62 206 65 HOH HOH A . E 5 HOH 63 207 66 HOH HOH A . E 5 HOH 64 208 67 HOH HOH A . E 5 HOH 65 209 68 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 2 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 18 A MSE 17 ? MET SELENOMETHIONINE 3 A MSE 60 A MSE 59 ? MET SELENOMETHIONINE 4 A MSE 62 A MSE 61 ? MET SELENOMETHIONINE 5 A MSE 64 A MSE 63 ? MET SELENOMETHIONINE 6 A MSE 69 A MSE 68 ? MET SELENOMETHIONINE 7 A MSE 105 A MSE 104 ? MET SELENOMETHIONINE 8 A MSE 131 A MSE 130 ? 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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 5740 ? 1 MORE -48 ? 1 'SSA (A^2)' 12280 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 7_556 y,x,-z+1 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 89.3900000000 # 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 2008-11-25 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2019-07-24 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' Advisory 2 2 'Structure model' 'Refinement description' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Refinement description' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Refinement description' 8 5 'Structure model' 'Database references' 9 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' software 3 4 'Structure model' struct_conn 4 5 'Structure model' database_2 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' '_software.classification' 4 4 'Structure model' '_software.contact_author' 5 4 'Structure model' '_software.contact_author_email' 6 4 'Structure model' '_software.language' 7 4 'Structure model' '_software.location' 8 4 'Structure model' '_software.name' 9 4 'Structure model' '_software.type' 10 4 'Structure model' '_software.version' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 5 'Structure model' '_database_2.pdbx_DOI' 13 5 'Structure model' '_database_2.pdbx_database_accession' 14 5 'Structure model' '_struct_ref_seq_dif.details' 15 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 5 '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 11.5692 _pdbx_refine_tls.origin_y 25.3864 _pdbx_refine_tls.origin_z 45.0636 _pdbx_refine_tls.T[1][1] 0.0213 _pdbx_refine_tls.T[2][2] 0.0265 _pdbx_refine_tls.T[3][3] 0.0364 _pdbx_refine_tls.T[1][2] -0.0099 _pdbx_refine_tls.T[1][3] 0.0038 _pdbx_refine_tls.T[2][3] -0.0036 _pdbx_refine_tls.L[1][1] 1.0035 _pdbx_refine_tls.L[2][2] 1.3020 _pdbx_refine_tls.L[3][3] 0.8997 _pdbx_refine_tls.L[1][2] -0.4466 _pdbx_refine_tls.L[1][3] 0.1268 _pdbx_refine_tls.L[2][3] 0.1552 _pdbx_refine_tls.S[1][1] 0.0029 _pdbx_refine_tls.S[2][2] 0.0137 _pdbx_refine_tls.S[3][3] -0.0166 _pdbx_refine_tls.S[1][2] -0.0811 _pdbx_refine_tls.S[1][3] 0.0463 _pdbx_refine_tls.S[2][3] 0.1617 _pdbx_refine_tls.S[2][1] -0.0010 _pdbx_refine_tls.S[3][1] -0.0276 _pdbx_refine_tls.S[3][2] -0.0940 # _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 141 _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 SAD # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal REFMAC 5.5.0053 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 3 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 4 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 5 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 XDS . ? ? ? ? 'data reduction' ? ? ? 7 SHELXD . ? ? ? ? phasing ? ? ? 8 autoSHARP . ? ? ? ? phasing ? ? ? 9 # _pdbx_entry_details.entry_id 3F7S _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT 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 ? # 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 GLN A 43 ? ? 79.19 -45.28 2 1 MSE A 63 ? ? -102.96 49.63 3 1 CYS A 64 ? ? -161.02 102.43 4 1 GLN A 133 ? ? 46.20 28.33 # 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 ARG 23 ? CZ ? A ARG 24 CZ 2 1 Y 1 A ARG 23 ? NH1 ? A ARG 24 NH1 3 1 Y 1 A ARG 23 ? NH2 ? A ARG 24 NH2 4 1 Y 1 A THR 65 ? OG1 ? A THR 66 OG1 5 1 Y 1 A THR 65 ? CG2 ? A THR 66 CG2 6 1 Y 1 A ASP 96 ? CG ? A ASP 97 CG 7 1 Y 1 A ASP 96 ? OD1 ? A ASP 97 OD1 8 1 Y 1 A ASP 96 ? OD2 ? A ASP 97 OD2 9 1 Y 1 A SER 99 ? OG ? A SER 100 OG 10 1 Y 1 A GLN 100 ? CG ? A GLN 101 CG 11 1 Y 1 A GLN 100 ? CD ? A GLN 101 CD 12 1 Y 1 A GLN 100 ? OE1 ? A GLN 101 OE1 13 1 Y 1 A GLN 100 ? NE2 ? A GLN 101 NE2 14 1 Y 1 A ARG 112 ? CZ ? A ARG 113 CZ 15 1 Y 1 A ARG 112 ? NH1 ? A ARG 113 NH1 16 1 Y 1 A ARG 112 ? NH2 ? A ARG 113 NH2 17 1 Y 1 A GLU 131 ? CG ? A GLU 132 CG 18 1 Y 1 A GLU 131 ? CD ? A GLU 132 CD 19 1 Y 1 A GLU 131 ? OE1 ? A GLU 132 OE1 20 1 Y 1 A GLU 131 ? OE2 ? A GLU 132 OE2 21 1 Y 1 A LYS 140 ? CG ? A LYS 141 CG 22 1 Y 1 A LYS 140 ? CD ? A LYS 141 CD 23 1 Y 1 A LYS 140 ? CE ? A LYS 141 CE 24 1 Y 1 A LYS 140 ? NZ ? A LYS 141 NZ # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'UNKNOWN LIGAND' UNL 3 'SULFATE ION' SO4 4 GLYCEROL GOL 5 water HOH #