data_4QY7 # _entry.id 4QY7 # _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 4QY7 pdb_00004qy7 10.2210/pdb4qy7/pdb RCSB RCSB086662 ? ? WWPDB D_1000086662 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-418978 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4QY7 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-07-23 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of a hypothetical protein (yobA) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 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 4QY7 _cell.length_a 27.556 _cell.length_b 37.988 _cell.length_c 81.245 _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 4QY7 _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 'Uncharacterized protein YobA' 10690.822 1 ? ? ? ? 2 non-polymer syn 'NONAETHYLENE GLYCOL' 414.488 1 ? ? ? ? 3 water nat water 18.015 89 ? ? ? ? # _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 ;GDETK(MSE)QSLVGYVVLKDNERAILITDTKAPGKEDYNLSEGQL(MSE)NKFKNNIVIVGLSEIDNTDDLKRGEKIKV WFHTRKESNPPSATIQKYELL ; _entity_poly.pdbx_seq_one_letter_code_can ;GDETKMQSLVGYVVLKDNERAILITDTKAPGKEDYNLSEGQLMNKFKNNIVIVGLSEIDNTDDLKRGEKIKVWFHTRKES NPPSATIQKYELL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier JCSG-418978 # 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 ASP n 1 3 GLU n 1 4 THR n 1 5 LYS n 1 6 MSE n 1 7 GLN n 1 8 SER n 1 9 LEU n 1 10 VAL n 1 11 GLY n 1 12 TYR n 1 13 VAL n 1 14 VAL n 1 15 LEU n 1 16 LYS n 1 17 ASP n 1 18 ASN n 1 19 GLU n 1 20 ARG n 1 21 ALA n 1 22 ILE n 1 23 LEU n 1 24 ILE n 1 25 THR n 1 26 ASP n 1 27 THR n 1 28 LYS n 1 29 ALA n 1 30 PRO n 1 31 GLY n 1 32 LYS n 1 33 GLU n 1 34 ASP n 1 35 TYR n 1 36 ASN n 1 37 LEU n 1 38 SER n 1 39 GLU n 1 40 GLY n 1 41 GLN n 1 42 LEU n 1 43 MSE n 1 44 ASN n 1 45 LYS n 1 46 PHE n 1 47 LYS n 1 48 ASN n 1 49 ASN n 1 50 ILE n 1 51 VAL n 1 52 ILE n 1 53 VAL n 1 54 GLY n 1 55 LEU n 1 56 SER n 1 57 GLU n 1 58 ILE n 1 59 ASP n 1 60 ASN n 1 61 THR n 1 62 ASP n 1 63 ASP n 1 64 LEU n 1 65 LYS n 1 66 ARG n 1 67 GLY n 1 68 GLU n 1 69 LYS n 1 70 ILE n 1 71 LYS n 1 72 VAL n 1 73 TRP n 1 74 PHE n 1 75 HIS n 1 76 THR n 1 77 ARG n 1 78 LYS n 1 79 GLU n 1 80 SER n 1 81 ASN n 1 82 PRO n 1 83 PRO n 1 84 SER n 1 85 ALA n 1 86 THR n 1 87 ILE n 1 88 GLN n 1 89 LYS n 1 90 TYR n 1 91 GLU n 1 92 LEU n 1 93 LEU 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 'yobA, BSU18810' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 168 _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 'Bacillus subtilis subsp. subtilis str. 168' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 224308 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia Coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain PB1 _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code YOBA_BACSU _struct_ref.pdbx_db_accession O31835 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;DETKMQSLVGYVVLKDNERAILITDTKAPGKEDYNLSEGQLMNKFKNNIVIVGLSEIDNTDDLKRGEKIKVWFHTRKESN PPSATIQKYELL ; _struct_ref.pdbx_align_begin 29 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4QY7 _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 93 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O31835 _struct_ref_seq.db_align_beg 29 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 120 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 29 _struct_ref_seq.pdbx_auth_seq_align_end 120 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4QY7 _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 O31835 _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 2PE non-polymer . 'NONAETHYLENE GLYCOL' ? 'C18 H38 O10' 414.488 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 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 4QY7 # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.99 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 38.15 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details ;5.00% polyethylene glycol 3000, 40.00% polyethylene glycol 400, 0.1M MES pH 6.0, 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 'Vertical focusing mirror; double crystal Si(111) monochromator' _diffrn_detector.pdbx_collection_date 2014-06-11 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'double crystal Si(111)' _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 0.95369 1.0 2 0.97937 1.0 3 0.97922 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL14-1 _diffrn_source.type 'SSRL BEAMLINE BL14-1' _diffrn_source.pdbx_wavelength_list 0.95369,0.97937,0.97922 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 4QY7 _reflns.d_resolution_high 1.55 _reflns.d_resolution_low 27.746 _reflns.number_obs 12907 _reflns.pdbx_Rmerge_I_obs 0.031 _reflns.pdbx_netI_over_sigmaI 14.830 _reflns.percent_possible_obs 98.300 _reflns.B_iso_Wilson_estimate 21.025 _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 1.550 1.610 4536 ? 2442 0.521 1.6 ? ? ? ? ? 94.500 1 1 1.610 1.670 4093 ? 2183 0.409 2.2 ? ? ? ? ? 99.000 2 1 1.670 1.750 4739 ? 2492 0.288 3.2 ? ? ? ? ? 99.200 3 1 1.750 1.840 4397 ? 2309 0.179 4.9 ? ? ? ? ? 99.100 4 1 1.840 1.950 4318 ? 2275 0.107 8.1 ? ? ? ? ? 99.300 5 1 1.950 2.100 4532 ? 2372 0.067 12.6 ? ? ? ? ? 99.000 6 1 2.100 2.310 4559 ? 2376 0.042 18.4 ? ? ? ? ? 99.400 7 1 2.310 2.650 4580 ? 2401 0.032 21.9 ? ? ? ? ? 98.700 8 1 2.650 3.330 4560 ? 2359 0.020 32.3 ? ? ? ? ? 98.600 9 1 3.330 27.746 4512 ? 2346 0.016 42.8 ? ? ? ? ? 96.400 10 1 # _refine.entry_id 4QY7 _refine.ls_d_res_high 1.5500 _refine.ls_d_res_low 27.746 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.2400 _refine.ls_number_reflns_obs 12850 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. 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. 5. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 6. NONAETHYLENE GLYCOL (2PE) MOLECULE FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1918 _refine.ls_R_factor_R_work 0.1903 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.2232 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.8800 _refine.ls_number_reflns_R_free 627 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 28.8288 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -1.7543 _refine.aniso_B[2][2] -0.8936 _refine.aniso_B[3][3] 2.6479 _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 0.9571 _refine.correlation_coeff_Fo_to_Fc_free 0.9390 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.solvent_model_details ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 97.540 _refine.B_iso_min 11.530 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.260 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 4QY7 _refine_analyze.Luzzati_coordinate_error_obs 0.232 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 730 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 7 _refine_hist.number_atoms_solvent 89 _refine_hist.number_atoms_total 826 _refine_hist.d_res_high 1.5500 _refine_hist.d_res_low 27.746 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id t_dihedral_angle_d 486 ? ? 2.000 SINUSOIDAL 'X-RAY DIFFRACTION' t_trig_c_planes 26 ? ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_gen_planes 243 ? ? 5.000 HARMONIC 'X-RAY DIFFRACTION' t_it 1645 ? ? 20.000 HARMONIC 'X-RAY DIFFRACTION' t_nbd 0 ? ? 5.000 SEMIHARMONIC 'X-RAY DIFFRACTION' t_improper_torsion ? ? ? ? ? 'X-RAY DIFFRACTION' t_pseud_angle ? ? ? ? ? 'X-RAY DIFFRACTION' t_chiral_improper_torsion 110 ? ? 5.000 SEMIHARMONIC 'X-RAY DIFFRACTION' t_sum_occupancies ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_distance ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_angle ? ? ? ? ? 'X-RAY DIFFRACTION' t_utility_torsion ? ? ? ? ? 'X-RAY DIFFRACTION' t_ideal_dist_contact 1872 ? ? 4.000 SEMIHARMONIC 'X-RAY DIFFRACTION' t_bond_d 1645 0.010 ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_angle_deg 3011 1.080 ? 2.000 HARMONIC 'X-RAY DIFFRACTION' t_omega_torsion ? 3.870 ? ? ? 'X-RAY DIFFRACTION' t_other_torsion ? 2.960 ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 1.5500 _refine_ls_shell.d_res_low 1.7000 _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.percent_reflns_obs 99.2400 _refine_ls_shell.number_reflns_R_work 2811 _refine_ls_shell.R_factor_all 0.2085 _refine_ls_shell.R_factor_R_work 0.2077 _refine_ls_shell.R_factor_R_free 0.2232 _refine_ls_shell.percent_reflns_R_free 5.3200 _refine_ls_shell.number_reflns_R_free 158 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 2969 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.title 'Crystal structure of a yobA protein (BSU18810) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 A resolution' _struct.entry_id 4QY7 _struct.pdbx_model_type_details ? _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.text ;PF11518 family protein, DUF3221, OB-fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION ; _struct_keywords.pdbx_keywords 'STRUCTURAL GENOMICS, UNKNOWN FUNCTION' _struct_keywords.entry_id 4QY7 # 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 ? # _struct_biol.id 1 _struct_biol.details 'CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.' # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLY A 31 ? LEU A 37 ? GLY A 58 LEU A 64 5 ? 7 HELX_P HELX_P2 2 SER A 38 ? PHE A 46 ? SER A 65 PHE A 73 1 ? 9 # _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 LYS 5 C ? ? ? 1_555 A MSE 6 N ? ? A LYS 32 A MSE 33 1_555 ? ? ? ? ? ? ? 1.353 ? ? covale2 covale both ? A MSE 6 C ? ? ? 1_555 A GLN 7 N ? ? A MSE 33 A GLN 34 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale3 covale both ? A LEU 42 C ? ? ? 1_555 A MSE 43 N ? ? A LEU 69 A MSE 70 1_555 ? ? ? ? ? ? ? 1.377 ? ? covale4 covale both ? A MSE 43 C ? ? ? 1_555 A ASN 44 N ? ? A MSE 70 A ASN 71 1_555 ? ? ? ? ? ? ? 1.339 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id ASN _struct_mon_prot_cis.label_seq_id 81 _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 ASN _struct_mon_prot_cis.auth_seq_id 108 _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 82 _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_2 109 _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 0.33 # _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 ? parallel A 2 3 ? anti-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 SER A 84 ? THR A 86 ? SER A 111 THR A 113 A 2 ILE A 50 ? GLY A 54 ? ILE A 77 GLY A 81 A 3 ARG A 20 ? ILE A 24 ? ARG A 47 ILE A 51 A 4 GLN A 7 ? LYS A 16 ? GLN A 34 LYS A 43 A 5 LYS A 69 ? PHE A 74 ? LYS A 96 PHE A 101 A 6 LYS A 89 ? LEU A 93 ? LYS A 116 LEU A 120 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O ALA A 85 ? O ALA A 112 N GLY A 54 ? N GLY A 81 A 2 3 O VAL A 51 ? O VAL A 78 N LEU A 23 ? N LEU A 50 A 3 4 O ILE A 22 ? O ILE A 49 N VAL A 14 ? N VAL A 41 A 4 5 N GLY A 11 ? N GLY A 38 O ILE A 70 ? O ILE A 97 A 5 6 N LYS A 69 ? N LYS A 96 O LEU A 93 ? O LEU A 120 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id 2PE _struct_site.pdbx_auth_seq_id 200 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE 2PE A 200' # 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 4 TRP A 73 ? TRP A 100 . ? 1_555 ? 2 AC1 4 LYS A 89 ? LYS A 116 . ? 1_555 ? 3 AC1 4 GLU A 91 ? GLU A 118 . ? 1_555 ? 4 AC1 4 HOH C . ? HOH A 387 . ? 1_555 ? # _atom_sites.entry_id 4QY7 _atom_sites.fract_transf_matrix[1][1] 0.036290 _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] 0.026324 _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] 0.012308 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 0 GLY GLY A . n A 1 2 ASP 2 29 29 ASP ASP A . n A 1 3 GLU 3 30 30 GLU GLU A . n A 1 4 THR 4 31 31 THR THR A . n A 1 5 LYS 5 32 32 LYS LYS A . n A 1 6 MSE 6 33 33 MSE MSE A . n A 1 7 GLN 7 34 34 GLN GLN A . n A 1 8 SER 8 35 35 SER SER A . n A 1 9 LEU 9 36 36 LEU LEU A . n A 1 10 VAL 10 37 37 VAL VAL A . n A 1 11 GLY 11 38 38 GLY GLY A . n A 1 12 TYR 12 39 39 TYR TYR A . n A 1 13 VAL 13 40 40 VAL VAL A . n A 1 14 VAL 14 41 41 VAL VAL A . n A 1 15 LEU 15 42 42 LEU LEU A . n A 1 16 LYS 16 43 43 LYS LYS A . n A 1 17 ASP 17 44 44 ASP ASP A . n A 1 18 ASN 18 45 45 ASN ASN A . n A 1 19 GLU 19 46 46 GLU GLU A . n A 1 20 ARG 20 47 47 ARG ARG A . n A 1 21 ALA 21 48 48 ALA ALA A . n A 1 22 ILE 22 49 49 ILE ILE A . n A 1 23 LEU 23 50 50 LEU LEU A . n A 1 24 ILE 24 51 51 ILE ILE A . n A 1 25 THR 25 52 52 THR THR A . n A 1 26 ASP 26 53 53 ASP ASP A . n A 1 27 THR 27 54 54 THR THR A . n A 1 28 LYS 28 55 55 LYS LYS A . n A 1 29 ALA 29 56 56 ALA ALA A . n A 1 30 PRO 30 57 57 PRO PRO A . n A 1 31 GLY 31 58 58 GLY GLY A . n A 1 32 LYS 32 59 59 LYS LYS A . n A 1 33 GLU 33 60 60 GLU GLU A . n A 1 34 ASP 34 61 61 ASP ASP A . n A 1 35 TYR 35 62 62 TYR TYR A . n A 1 36 ASN 36 63 63 ASN ASN A . n A 1 37 LEU 37 64 64 LEU LEU A . n A 1 38 SER 38 65 65 SER SER A . n A 1 39 GLU 39 66 66 GLU GLU A . n A 1 40 GLY 40 67 67 GLY GLY A . n A 1 41 GLN 41 68 68 GLN GLN A . n A 1 42 LEU 42 69 69 LEU LEU A . n A 1 43 MSE 43 70 70 MSE MSE A . n A 1 44 ASN 44 71 71 ASN ASN A . n A 1 45 LYS 45 72 72 LYS LYS A . n A 1 46 PHE 46 73 73 PHE PHE A . n A 1 47 LYS 47 74 74 LYS LYS A . n A 1 48 ASN 48 75 75 ASN ASN A . n A 1 49 ASN 49 76 76 ASN ASN A . n A 1 50 ILE 50 77 77 ILE ILE A . n A 1 51 VAL 51 78 78 VAL VAL A . n A 1 52 ILE 52 79 79 ILE ILE A . n A 1 53 VAL 53 80 80 VAL VAL A . n A 1 54 GLY 54 81 81 GLY GLY A . n A 1 55 LEU 55 82 82 LEU LEU A . n A 1 56 SER 56 83 83 SER SER A . n A 1 57 GLU 57 84 84 GLU GLU A . n A 1 58 ILE 58 85 85 ILE ILE A . n A 1 59 ASP 59 86 86 ASP ASP A . n A 1 60 ASN 60 87 87 ASN ASN A . n A 1 61 THR 61 88 88 THR THR A . n A 1 62 ASP 62 89 89 ASP ASP A . n A 1 63 ASP 63 90 90 ASP ASP A . n A 1 64 LEU 64 91 91 LEU LEU A . n A 1 65 LYS 65 92 92 LYS LYS A . n A 1 66 ARG 66 93 93 ARG ARG A . n A 1 67 GLY 67 94 94 GLY GLY A . n A 1 68 GLU 68 95 95 GLU GLU A . n A 1 69 LYS 69 96 96 LYS LYS A . n A 1 70 ILE 70 97 97 ILE ILE A . n A 1 71 LYS 71 98 98 LYS LYS A . n A 1 72 VAL 72 99 99 VAL VAL A . n A 1 73 TRP 73 100 100 TRP TRP A . n A 1 74 PHE 74 101 101 PHE PHE A . n A 1 75 HIS 75 102 102 HIS HIS A . n A 1 76 THR 76 103 103 THR THR A . n A 1 77 ARG 77 104 104 ARG ARG A . n A 1 78 LYS 78 105 105 LYS LYS A . n A 1 79 GLU 79 106 106 GLU GLU A . n A 1 80 SER 80 107 107 SER SER A . n A 1 81 ASN 81 108 108 ASN ASN A . n A 1 82 PRO 82 109 109 PRO PRO A . n A 1 83 PRO 83 110 110 PRO PRO A . n A 1 84 SER 84 111 111 SER SER A . n A 1 85 ALA 85 112 112 ALA ALA A . n A 1 86 THR 86 113 113 THR THR A . n A 1 87 ILE 87 114 114 ILE ILE A . n A 1 88 GLN 88 115 115 GLN GLN A . n A 1 89 LYS 89 116 116 LYS LYS A . n A 1 90 TYR 90 117 117 TYR TYR A . n A 1 91 GLU 91 118 118 GLU GLU A . n A 1 92 LEU 92 119 119 LEU LEU A . n A 1 93 LEU 93 120 120 LEU LEU A . n # _pdbx_SG_project.project_name PSI:Biology _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 2PE 1 200 200 2PE 2PE A . C 3 HOH 1 301 201 HOH HOH A . C 3 HOH 2 302 202 HOH HOH A . C 3 HOH 3 303 203 HOH HOH A . C 3 HOH 4 304 204 HOH HOH A . C 3 HOH 5 305 205 HOH HOH A . C 3 HOH 6 306 206 HOH HOH A . C 3 HOH 7 307 207 HOH HOH A . C 3 HOH 8 308 208 HOH HOH A . C 3 HOH 9 309 209 HOH HOH A . C 3 HOH 10 310 210 HOH HOH A . C 3 HOH 11 311 211 HOH HOH A . C 3 HOH 12 312 212 HOH HOH A . C 3 HOH 13 313 213 HOH HOH A . C 3 HOH 14 314 214 HOH HOH A . C 3 HOH 15 315 215 HOH HOH A . C 3 HOH 16 316 216 HOH HOH A . C 3 HOH 17 317 217 HOH HOH A . C 3 HOH 18 318 218 HOH HOH A . C 3 HOH 19 319 219 HOH HOH A . C 3 HOH 20 320 220 HOH HOH A . C 3 HOH 21 321 221 HOH HOH A . C 3 HOH 22 322 222 HOH HOH A . C 3 HOH 23 323 223 HOH HOH A . C 3 HOH 24 324 224 HOH HOH A . C 3 HOH 25 325 225 HOH HOH A . C 3 HOH 26 326 226 HOH HOH A . C 3 HOH 27 327 227 HOH HOH A . C 3 HOH 28 328 228 HOH HOH A . C 3 HOH 29 329 229 HOH HOH A . C 3 HOH 30 330 230 HOH HOH A . C 3 HOH 31 331 231 HOH HOH A . C 3 HOH 32 332 232 HOH HOH A . C 3 HOH 33 333 233 HOH HOH A . C 3 HOH 34 334 234 HOH HOH A . C 3 HOH 35 335 235 HOH HOH A . C 3 HOH 36 336 236 HOH HOH A . C 3 HOH 37 337 237 HOH HOH A . C 3 HOH 38 338 238 HOH HOH A . C 3 HOH 39 339 239 HOH HOH A . C 3 HOH 40 340 240 HOH HOH A . C 3 HOH 41 341 241 HOH HOH A . C 3 HOH 42 342 242 HOH HOH A . C 3 HOH 43 343 243 HOH HOH A . C 3 HOH 44 344 244 HOH HOH A . C 3 HOH 45 345 245 HOH HOH A . C 3 HOH 46 346 246 HOH HOH A . C 3 HOH 47 347 247 HOH HOH A . C 3 HOH 48 348 248 HOH HOH A . C 3 HOH 49 349 249 HOH HOH A . C 3 HOH 50 350 250 HOH HOH A . C 3 HOH 51 351 251 HOH HOH A . C 3 HOH 52 352 252 HOH HOH A . C 3 HOH 53 353 253 HOH HOH A . C 3 HOH 54 354 254 HOH HOH A . C 3 HOH 55 355 255 HOH HOH A . C 3 HOH 56 356 256 HOH HOH A . C 3 HOH 57 357 257 HOH HOH A . C 3 HOH 58 358 258 HOH HOH A . C 3 HOH 59 359 259 HOH HOH A . C 3 HOH 60 360 260 HOH HOH A . C 3 HOH 61 361 261 HOH HOH A . C 3 HOH 62 362 262 HOH HOH A . C 3 HOH 63 363 263 HOH HOH A . C 3 HOH 64 364 264 HOH HOH A . C 3 HOH 65 365 265 HOH HOH A . C 3 HOH 66 366 266 HOH HOH A . C 3 HOH 67 367 267 HOH HOH A . C 3 HOH 68 368 268 HOH HOH A . C 3 HOH 69 369 269 HOH HOH A . C 3 HOH 70 370 270 HOH HOH A . C 3 HOH 71 371 271 HOH HOH A . C 3 HOH 72 372 272 HOH HOH A . C 3 HOH 73 373 273 HOH HOH A . C 3 HOH 74 374 274 HOH HOH A . C 3 HOH 75 375 275 HOH HOH A . C 3 HOH 76 376 276 HOH HOH A . C 3 HOH 77 377 277 HOH HOH A . C 3 HOH 78 378 278 HOH HOH A . C 3 HOH 79 379 279 HOH HOH A . C 3 HOH 80 380 280 HOH HOH A . C 3 HOH 81 381 281 HOH HOH A . C 3 HOH 82 382 282 HOH HOH A . C 3 HOH 83 383 283 HOH HOH A . C 3 HOH 84 384 284 HOH HOH A . C 3 HOH 85 385 285 HOH HOH A . C 3 HOH 86 386 286 HOH HOH A . C 3 HOH 87 387 287 HOH HOH A . C 3 HOH 88 388 288 HOH HOH A . C 3 HOH 89 389 289 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 6 A MSE 33 ? MET SELENOMETHIONINE 2 A MSE 43 A MSE 70 ? 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 # _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 2014-08-20 2 'Structure model' 1 1 2014-12-24 3 'Structure model' 1 2 2017-11-22 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' 'Structure summary' 2 3 'Structure model' 'Refinement description' 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 3 'Structure model' software 2 4 'Structure model' database_2 3 4 'Structure model' struct_conn 4 4 'Structure model' struct_ref_seq_dif 5 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 7.7967 _pdbx_refine_tls.origin_y 7.1928 _pdbx_refine_tls.origin_z 8.7526 _pdbx_refine_tls.T[1][1] -0.0511 _pdbx_refine_tls.T[2][2] -0.0311 _pdbx_refine_tls.T[3][3] -0.0591 _pdbx_refine_tls.T[1][2] -0.0216 _pdbx_refine_tls.T[1][3] -0.0052 _pdbx_refine_tls.T[2][3] 0.0031 _pdbx_refine_tls.L[1][1] 1.3475 _pdbx_refine_tls.L[2][2] 1.4624 _pdbx_refine_tls.L[3][3] 2.5841 _pdbx_refine_tls.L[1][2] -0.6103 _pdbx_refine_tls.L[1][3] 0.1497 _pdbx_refine_tls.L[2][3] 0.4900 _pdbx_refine_tls.S[1][1] 0.0620 _pdbx_refine_tls.S[2][2] 0.0031 _pdbx_refine_tls.S[3][3] -0.0651 _pdbx_refine_tls.S[1][2] 0.0001 _pdbx_refine_tls.S[1][3] 0.0116 _pdbx_refine_tls.S[2][3] 0.0131 _pdbx_refine_tls.S[2][1] -0.0663 _pdbx_refine_tls.S[3][1] 0.0350 _pdbx_refine_tls.S[3][2] -0.1071 # _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 120 _pdbx_refine_tls_group.selection_details ? _pdbx_refine_tls_group.beg_label_asym_id . _pdbx_refine_tls_group.beg_label_seq_id . _pdbx_refine_tls_group.end_label_asym_id . _pdbx_refine_tls_group.end_label_seq_id . _pdbx_refine_tls_group.selection ? # _phasing.method MAD # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 4 SHARP . ? package 'Eric de La Fortelle' sharp-develop@globalphasing.com phasing http://www.globalphasing.com/sharp/ ? ? 5 XSCALE 'January 10, 2014 BUILT=20140307' ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 6 BUSTER-TNT 2.10.0 ? program 'Gerard Bricogne' buster-develop@GlobalPhasing.com refinement http://www.globalphasing.com/buster/ ? ? 7 XDS . ? ? ? ? 'data reduction' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? 9 BUSTER 2.10.0 ? ? ? ? refinement ? ? ? # _pdbx_entry_details.entry_id 4QY7 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 29-120 OF THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # 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 ASP 29 ? CG ? A ASP 2 CG 2 1 Y 1 A ASP 29 ? OD1 ? A ASP 2 OD1 3 1 Y 1 A ASP 29 ? OD2 ? A ASP 2 OD2 4 1 Y 1 A GLU 30 ? CG ? A GLU 3 CG 5 1 Y 1 A GLU 30 ? CD ? A GLU 3 CD 6 1 Y 1 A GLU 30 ? OE1 ? A GLU 3 OE1 7 1 Y 1 A GLU 30 ? OE2 ? A GLU 3 OE2 8 1 Y 1 A LYS 32 ? CG ? A LYS 5 CG 9 1 Y 1 A LYS 32 ? CD ? A LYS 5 CD 10 1 Y 1 A LYS 32 ? CE ? A LYS 5 CE 11 1 Y 1 A LYS 32 ? NZ ? A LYS 5 NZ 12 1 Y 1 A ASP 53 ? CG ? A ASP 26 CG 13 1 Y 1 A ASP 53 ? OD1 ? A ASP 26 OD1 14 1 Y 1 A ASP 53 ? OD2 ? A ASP 26 OD2 15 1 N 1 A 2PE 200 ? C8 ? B 2PE 1 C8 16 1 N 1 A 2PE 200 ? C9 ? B 2PE 1 C9 17 1 N 1 A 2PE 200 ? O10 ? B 2PE 1 O10 18 1 N 1 A 2PE 200 ? C11 ? B 2PE 1 C11 19 1 N 1 A 2PE 200 ? C12 ? B 2PE 1 C12 20 1 N 1 A 2PE 200 ? O13 ? B 2PE 1 O13 21 1 N 1 A 2PE 200 ? C14 ? B 2PE 1 C14 22 1 N 1 A 2PE 200 ? C15 ? B 2PE 1 C15 23 1 N 1 A 2PE 200 ? O16 ? B 2PE 1 O16 24 1 N 1 A 2PE 200 ? C17 ? B 2PE 1 C17 25 1 N 1 A 2PE 200 ? C18 ? B 2PE 1 C18 26 1 N 1 A 2PE 200 ? O19 ? B 2PE 1 O19 27 1 N 1 A 2PE 200 ? C20 ? B 2PE 1 C20 28 1 N 1 A 2PE 200 ? C21 ? B 2PE 1 C21 29 1 N 1 A 2PE 200 ? O22 ? B 2PE 1 O22 30 1 N 1 A 2PE 200 ? C23 ? B 2PE 1 C23 31 1 N 1 A 2PE 200 ? C24 ? B 2PE 1 C24 32 1 N 1 A 2PE 200 ? O25 ? B 2PE 1 O25 33 1 N 1 A 2PE 200 ? C26 ? B 2PE 1 C26 34 1 N 1 A 2PE 200 ? C27 ? B 2PE 1 C27 35 1 N 1 A 2PE 200 ? O28 ? B 2PE 1 O28 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'NONAETHYLENE GLYCOL' 2PE 3 water HOH #