data_4R03 # _entry.id 4R03 # _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 4R03 pdb_00004r03 10.2210/pdb4r03/pdb RCSB RCSB086730 ? ? WWPDB D_1000086730 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-418938 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4R03 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2014-07-29 _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 'Structures of single-layer beta-sheet proteins evolved from beta-hairpin repeats.' _citation.journal_abbrev 'Protein Sci.' _citation.journal_volume 28 _citation.page_first 1676 _citation.page_last 1689 _citation.year 2019 _citation.journal_id_ASTM PRCIEI _citation.country US _citation.journal_id_ISSN 1469-896X _citation.journal_id_CSD 0795 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 31306512 _citation.pdbx_database_id_DOI 10.1002/pro.3683 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Xu, Q.' 1 ? primary 'Biancalana, M.' 2 ? primary 'Grant, J.C.' 3 ? primary 'Chiu, H.J.' 4 ? primary 'Jaroszewski, L.' 5 ? primary 'Knuth, M.W.' 6 ? primary 'Lesley, S.A.' 7 ? primary 'Godzik, A.' 8 ? primary 'Elsliger, M.A.' 9 ? primary 'Deacon, A.M.' 10 ? primary 'Wilson, I.A.' 11 0000-0002-6469-2419 # _cell.entry_id 4R03 _cell.length_a 59.001 _cell.length_b 71.697 _cell.length_c 82.683 _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 4R03 _symmetry.Int_Tables_number 24 _symmetry.space_group_name_H-M 'I 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' 13272.422 1 ? ? 'UNP residues 29-136' ? 2 non-polymer syn '(4S)-2-METHYL-2,4-PENTANEDIOL' 118.174 1 ? ? ? ? 3 non-polymer syn 'CITRIC ACID' 192.124 1 ? ? ? ? 4 non-polymer syn 'PHOSPHATE ION' 94.971 2 ? ? ? ? 5 water nat water 18.015 188 ? ? ? ? # _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 ;GKDYLYDTKEENGKIISKVVFLQENGLLNKQVRYEFQYNENGKVSEKKAFRWDRTNDEWVPFYQITYQYDDQSGEIKTNY G(MSE)WDKKKKNFSLNVQN(MSE)IIPSTNYEEIFS ; _entity_poly.pdbx_seq_one_letter_code_can ;GKDYLYDTKEENGKIISKVVFLQENGLLNKQVRYEFQYNENGKVSEKKAFRWDRTNDEWVPFYQITYQYDDQSGEIKTNY GMWDKKKKNFSLNVQNMIIPSTNYEEIFS ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier JCSG-418938 # 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 LYS n 1 3 ASP n 1 4 TYR n 1 5 LEU n 1 6 TYR n 1 7 ASP n 1 8 THR n 1 9 LYS n 1 10 GLU n 1 11 GLU n 1 12 ASN n 1 13 GLY n 1 14 LYS n 1 15 ILE n 1 16 ILE n 1 17 SER n 1 18 LYS n 1 19 VAL n 1 20 VAL n 1 21 PHE n 1 22 LEU n 1 23 GLN n 1 24 GLU n 1 25 ASN n 1 26 GLY n 1 27 LEU n 1 28 LEU n 1 29 ASN n 1 30 LYS n 1 31 GLN n 1 32 VAL n 1 33 ARG n 1 34 TYR n 1 35 GLU n 1 36 PHE n 1 37 GLN n 1 38 TYR n 1 39 ASN n 1 40 GLU n 1 41 ASN n 1 42 GLY n 1 43 LYS n 1 44 VAL n 1 45 SER n 1 46 GLU n 1 47 LYS n 1 48 LYS n 1 49 ALA n 1 50 PHE n 1 51 ARG n 1 52 TRP n 1 53 ASP n 1 54 ARG n 1 55 THR n 1 56 ASN n 1 57 ASP n 1 58 GLU n 1 59 TRP n 1 60 VAL n 1 61 PRO n 1 62 PHE n 1 63 TYR n 1 64 GLN n 1 65 ILE n 1 66 THR n 1 67 TYR n 1 68 GLN n 1 69 TYR n 1 70 ASP n 1 71 ASP n 1 72 GLN n 1 73 SER n 1 74 GLY n 1 75 GLU n 1 76 ILE n 1 77 LYS n 1 78 THR n 1 79 ASN n 1 80 TYR n 1 81 GLY n 1 82 MSE n 1 83 TRP n 1 84 ASP n 1 85 LYS n 1 86 LYS n 1 87 LYS n 1 88 LYS n 1 89 ASN n 1 90 PHE n 1 91 SER n 1 92 LEU n 1 93 ASN n 1 94 VAL n 1 95 GLN n 1 96 ASN n 1 97 MSE n 1 98 ILE n 1 99 ILE n 1 100 PRO n 1 101 SER n 1 102 THR n 1 103 ASN n 1 104 TYR n 1 105 GLU n 1 106 GLU n 1 107 ILE n 1 108 PHE n 1 109 SER n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene BDI_3222 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 8503 / DSM 20701 / NCTC 11152' _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Parabacteroides distasonis ATCC 8503' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 435591 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia Coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain PB1 _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A6LGW3_PARD8 _struct_ref.pdbx_db_accession A6LGW3 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;KDYLYDTKEENGKIISKVVFLQENGLLNKQVRYEFQYNENGKVSEKKAFRWDRTNDEWVPFYQITYQYDDQSGEIKTNYG MWDKKKKNFSLNVQNMIIPSTNYEEIFS ; _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 4R03 _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 109 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A6LGW3 _struct_ref_seq.db_align_beg 29 _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 29 _struct_ref_seq.pdbx_auth_seq_align_end 136 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4R03 _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 A6LGW3 _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 CIT non-polymer . 'CITRIC ACID' ? 'C6 H8 O7' 192.124 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MPD non-polymer . '(4S)-2-METHYL-2,4-PENTANEDIOL' ? 'C6 H14 O2' 118.174 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 PO4 non-polymer . 'PHOSPHATE ION' ? 'O4 P -3' 94.971 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 4R03 # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 3.29 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 62.66 _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 4.2 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '40.00% 2-methyl-2,4-pentanediol, 0.1M phosphate-citrate pH 4.2, 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 2014-06-10 # _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 0.97934 1.0 3 0.97907 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 0.95369,0.97934,0.97907 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 4R03 _reflns.d_resolution_high 1.50 _reflns.d_resolution_low 27.084 _reflns.number_obs 27948 _reflns.pdbx_Rmerge_I_obs 0.045 _reflns.pdbx_netI_over_sigmaI 14.960 _reflns.percent_possible_obs 98.200 _reflns.B_iso_Wilson_estimate 18.114 _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 1.500 1.600 10277 ? 4505 0.483 1.9 ? ? ? ? ? 91.200 1 1 1.600 1.660 7844 ? 2397 0.347 3.3 ? ? ? ? ? 99.700 2 1 1.660 1.730 8912 ? 2431 0.263 4.7 ? ? ? ? ? 99.900 3 1 1.730 1.830 10443 ? 2857 0.181 6.7 ? ? ? ? ? 99.900 4 1 1.830 1.940 9033 ? 2480 0.108 10.9 ? ? ? ? ? 99.800 5 1 1.940 2.090 9457 ? 2596 0.071 15.9 ? ? ? ? ? 99.800 6 1 2.090 2.300 9552 ? 2624 0.054 20.5 ? ? ? ? ? 99.700 7 1 2.300 2.630 9395 ? 2596 0.045 23.6 ? ? ? ? ? 99.700 8 1 2.630 3.310 9500 ? 2667 0.033 30.7 ? ? ? ? ? 99.400 9 1 3.310 27.084 9596 ? 2759 0.027 38.0 ? ? ? ? ? 98.800 10 1 # _refine.entry_id 4R03 _refine.ls_d_res_high 1.5000 _refine.ls_d_res_low 27.084 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 98.1500 _refine.ls_number_reflns_obs 26540 _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. CITRATE (CIT), PHOSPHATE (PO4), AND 2-METHYL-2,4-PENTANEDIOL (MPD) WERE PRESENT IN PURIFICATION/CRYSTALLIZATION CONDITIONS. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1675 _refine.ls_R_factor_R_work 0.1664 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.1876 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.0000 _refine.ls_number_reflns_R_free 1407 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 22.8870 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.1400 _refine.aniso_B[2][2] 0.2500 _refine.aniso_B[3][3] -0.3900 _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 0.9690 _refine.correlation_coeff_Fo_to_Fc_free 0.9580 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.0610 _refine.pdbx_overall_ESU_R_Free 0.0620 _refine.overall_SU_ML 0.0420 _refine.overall_SU_B 1.1750 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 74.870 _refine.B_iso_min 9.410 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.250 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 925 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 31 _refine_hist.number_atoms_solvent 188 _refine_hist.number_atoms_total 1144 _refine_hist.d_res_high 1.5000 _refine_hist.d_res_low 27.084 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 1057 0.020 0.022 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 979 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1441 1.736 1.972 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 2276 0.784 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 132 6.173 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 60 41.862 26.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 206 11.530 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 3 9.996 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 140 0.115 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 1218 0.009 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 250 0.002 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 462 1.924 1.814 ? ? 'X-RAY DIFFRACTION' r_mcbond_other 461 1.912 1.812 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 583 3.077 2.722 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 1.5000 _refine_ls_shell.d_res_low 1.5390 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 85.0900 _refine_ls_shell.number_reflns_R_work 1680 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.3070 _refine_ls_shell.R_factor_R_free 0.3280 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 89 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1769 _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 DUF3836 family protein (BDI_3222) from Parabacteroides distasonis ATCC 8503 at 1.50 A resolution' _struct.entry_id 4R03 _struct.pdbx_model_type_details ? _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.text ;PF12930 family protein, DUF3836, 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 4R03 # 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 4 ? F N N 5 ? # _struct_biol.id 1 _struct_biol.details 'CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.' # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id THR _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 102 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id SER _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 109 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id THR _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 129 _struct_conf.end_auth_comp_id SER _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 136 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 8 # _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 81 C ? ? ? 1_555 A MSE 82 N ? ? A GLY 108 A MSE 109 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale2 covale both ? A MSE 82 C ? ? ? 1_555 A TRP 83 N ? ? A MSE 109 A TRP 110 1_555 ? ? ? ? ? ? ? 1.340 ? ? covale3 covale both ? A ASN 96 C ? ? ? 1_555 A MSE 97 N A ? A ASN 123 A MSE 124 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale4 covale both ? A ASN 96 C ? ? ? 1_555 A MSE 97 N B ? A ASN 123 A MSE 124 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale5 covale both ? A MSE 97 C A ? ? 1_555 A ILE 98 N ? ? A MSE 124 A ILE 125 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale6 covale both ? A MSE 97 C B ? ? 1_555 A ILE 98 N ? ? A MSE 124 A ILE 125 1_555 ? ? ? ? ? ? ? 1.330 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 7 _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 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel A 6 7 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LYS A 2 ? GLU A 11 ? LYS A 29 GLU A 38 A 2 LYS A 14 ? GLU A 24 ? LYS A 41 GLU A 51 A 3 LEU A 27 ? TYR A 38 ? LEU A 54 TYR A 65 A 4 VAL A 44 ? ASP A 53 ? VAL A 71 ASP A 80 A 5 GLU A 58 ? TYR A 69 ? GLU A 85 TYR A 96 A 6 GLU A 75 ? ASP A 84 ? GLU A 102 ASP A 111 A 7 ASN A 89 ? PRO A 100 ? ASN A 116 PRO A 127 # 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 LEU A 5 ? N LEU A 32 O PHE A 21 ? O PHE A 48 A 2 3 N VAL A 20 ? N VAL A 47 O VAL A 32 ? O VAL A 59 A 3 4 N ARG A 33 ? N ARG A 60 O PHE A 50 ? O PHE A 77 A 4 5 N ASP A 53 ? N ASP A 80 O GLU A 58 ? O GLU A 85 A 5 6 N GLN A 68 ? N GLN A 95 O LYS A 77 ? O LYS A 104 A 6 7 N MSE A 82 ? N MSE A 109 O LEU A 92 ? O LEU A 119 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A MPD 201 ? 6 'BINDING SITE FOR RESIDUE MPD A 201' AC2 Software A CIT 202 ? 11 'BINDING SITE FOR RESIDUE CIT A 202' AC3 Software A PO4 203 ? 7 'BINDING SITE FOR RESIDUE PO4 A 203' AC4 Software A PO4 204 ? 3 'BINDING SITE FOR RESIDUE PO4 A 204' # 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 ASN A 29 ? ASN A 56 . ? 1_555 ? 2 AC1 6 ARG A 54 ? ARG A 81 . ? 1_555 ? 3 AC1 6 GLU A 106 ? GLU A 133 . ? 7_555 ? 4 AC1 6 HOH F . ? HOH A 315 . ? 1_555 ? 5 AC1 6 HOH F . ? HOH A 341 . ? 1_555 ? 6 AC1 6 HOH F . ? HOH A 411 . ? 7_555 ? 7 AC2 11 ASN A 29 ? ASN A 56 . ? 1_555 ? 8 AC2 11 LYS A 30 ? LYS A 57 . ? 1_555 ? 9 AC2 11 TRP A 52 ? TRP A 79 . ? 1_555 ? 10 AC2 11 ARG A 54 ? ARG A 81 . ? 1_555 ? 11 AC2 11 ASP A 57 ? ASP A 84 . ? 1_555 ? 12 AC2 11 LYS A 85 ? LYS A 112 . ? 8_565 ? 13 AC2 11 LYS A 86 ? LYS A 113 . ? 8_565 ? 14 AC2 11 HOH F . ? HOH A 308 . ? 1_555 ? 15 AC2 11 HOH F . ? HOH A 409 . ? 8_565 ? 16 AC2 11 HOH F . ? HOH A 486 . ? 1_555 ? 17 AC2 11 HOH F . ? HOH A 487 . ? 1_555 ? 18 AC3 7 VAL A 19 ? VAL A 46 . ? 1_555 ? 19 AC3 7 LYS A 30 ? LYS A 57 . ? 1_555 ? 20 AC3 7 ARG A 33 ? ARG A 60 . ? 1_555 ? 21 AC3 7 TRP A 59 ? TRP A 86 . ? 1_555 ? 22 AC3 7 HOH F . ? HOH A 380 . ? 1_555 ? 23 AC3 7 HOH F . ? HOH A 464 . ? 1_555 ? 24 AC3 7 HOH F . ? HOH A 469 . ? 1_555 ? 25 AC4 3 GLU A 11 ? GLU A 38 . ? 7_455 ? 26 AC4 3 HOH F . ? HOH A 470 . ? 1_555 ? 27 AC4 3 HOH F . ? HOH A 471 . ? 1_555 ? # _atom_sites.entry_id 4R03 _atom_sites.fract_transf_matrix[1][1] 0.016949 _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] 0.013948 _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] 0.012094 _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 P 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 LYS 2 29 29 LYS LYS A . n A 1 3 ASP 3 30 30 ASP ASP A . n A 1 4 TYR 4 31 31 TYR TYR A . n A 1 5 LEU 5 32 32 LEU LEU A . n A 1 6 TYR 6 33 33 TYR TYR A . n A 1 7 ASP 7 34 34 ASP ASP A . n A 1 8 THR 8 35 35 THR THR A . n A 1 9 LYS 9 36 36 LYS LYS A . n A 1 10 GLU 10 37 37 GLU GLU A . n A 1 11 GLU 11 38 38 GLU GLU A . n A 1 12 ASN 12 39 39 ASN ASN A . n A 1 13 GLY 13 40 40 GLY GLY A . n A 1 14 LYS 14 41 41 LYS LYS A . n A 1 15 ILE 15 42 42 ILE ILE A . n A 1 16 ILE 16 43 43 ILE ILE A . n A 1 17 SER 17 44 44 SER SER A . n A 1 18 LYS 18 45 45 LYS LYS A . n A 1 19 VAL 19 46 46 VAL VAL A . n A 1 20 VAL 20 47 47 VAL VAL A . n A 1 21 PHE 21 48 48 PHE PHE A . n A 1 22 LEU 22 49 49 LEU LEU A . n A 1 23 GLN 23 50 50 GLN GLN A . n A 1 24 GLU 24 51 51 GLU GLU A . n A 1 25 ASN 25 52 52 ASN ASN A . n A 1 26 GLY 26 53 53 GLY GLY A . n A 1 27 LEU 27 54 54 LEU LEU A . n A 1 28 LEU 28 55 55 LEU LEU A . n A 1 29 ASN 29 56 56 ASN ASN A . n A 1 30 LYS 30 57 57 LYS LYS A . n A 1 31 GLN 31 58 58 GLN GLN A . n A 1 32 VAL 32 59 59 VAL VAL A . n A 1 33 ARG 33 60 60 ARG ARG A . n A 1 34 TYR 34 61 61 TYR TYR A . n A 1 35 GLU 35 62 62 GLU GLU A . n A 1 36 PHE 36 63 63 PHE PHE A . n A 1 37 GLN 37 64 64 GLN GLN A . n A 1 38 TYR 38 65 65 TYR TYR A . n A 1 39 ASN 39 66 66 ASN ASN A . n A 1 40 GLU 40 67 67 GLU GLU A . n A 1 41 ASN 41 68 68 ASN ASN A . n A 1 42 GLY 42 69 69 GLY GLY A . n A 1 43 LYS 43 70 70 LYS LYS A . n A 1 44 VAL 44 71 71 VAL VAL A . n A 1 45 SER 45 72 72 SER SER A . n A 1 46 GLU 46 73 73 GLU GLU A . n A 1 47 LYS 47 74 74 LYS LYS A . n A 1 48 LYS 48 75 75 LYS LYS A . n A 1 49 ALA 49 76 76 ALA ALA A . n A 1 50 PHE 50 77 77 PHE PHE A . n A 1 51 ARG 51 78 78 ARG ARG A . n A 1 52 TRP 52 79 79 TRP TRP A . n A 1 53 ASP 53 80 80 ASP ASP A . n A 1 54 ARG 54 81 81 ARG ARG A . n A 1 55 THR 55 82 82 THR THR A . n A 1 56 ASN 56 83 83 ASN ASN A . n A 1 57 ASP 57 84 84 ASP ASP A . n A 1 58 GLU 58 85 85 GLU GLU A . n A 1 59 TRP 59 86 86 TRP TRP A . n A 1 60 VAL 60 87 87 VAL VAL A . n A 1 61 PRO 61 88 88 PRO PRO A . n A 1 62 PHE 62 89 89 PHE PHE A . n A 1 63 TYR 63 90 90 TYR TYR A . n A 1 64 GLN 64 91 91 GLN GLN A . n A 1 65 ILE 65 92 92 ILE ILE A . n A 1 66 THR 66 93 93 THR THR A . n A 1 67 TYR 67 94 94 TYR TYR A . n A 1 68 GLN 68 95 95 GLN GLN A . n A 1 69 TYR 69 96 96 TYR TYR A . n A 1 70 ASP 70 97 97 ASP ASP A . n A 1 71 ASP 71 98 98 ASP ASP A . n A 1 72 GLN 72 99 99 GLN GLN A . n A 1 73 SER 73 100 100 SER SER A . n A 1 74 GLY 74 101 101 GLY GLY A . n A 1 75 GLU 75 102 102 GLU GLU A . n A 1 76 ILE 76 103 103 ILE ILE A . n A 1 77 LYS 77 104 104 LYS LYS A . n A 1 78 THR 78 105 105 THR THR A . n A 1 79 ASN 79 106 106 ASN ASN A . n A 1 80 TYR 80 107 107 TYR TYR A . n A 1 81 GLY 81 108 108 GLY GLY A . n A 1 82 MSE 82 109 109 MSE MSE A . n A 1 83 TRP 83 110 110 TRP TRP A . n A 1 84 ASP 84 111 111 ASP ASP A . n A 1 85 LYS 85 112 112 LYS LYS A . n A 1 86 LYS 86 113 113 LYS LYS A . n A 1 87 LYS 87 114 114 LYS LYS A . n A 1 88 LYS 88 115 115 LYS LYS A . n A 1 89 ASN 89 116 116 ASN ASN A . n A 1 90 PHE 90 117 117 PHE PHE A . n A 1 91 SER 91 118 118 SER SER A . n A 1 92 LEU 92 119 119 LEU LEU A . n A 1 93 ASN 93 120 120 ASN ASN A . n A 1 94 VAL 94 121 121 VAL VAL A . n A 1 95 GLN 95 122 122 GLN GLN A . n A 1 96 ASN 96 123 123 ASN ASN A . n A 1 97 MSE 97 124 124 MSE MSE A . n A 1 98 ILE 98 125 125 ILE ILE A . n A 1 99 ILE 99 126 126 ILE ILE A . n A 1 100 PRO 100 127 127 PRO PRO A . n A 1 101 SER 101 128 128 SER SER A . n A 1 102 THR 102 129 129 THR THR A . n A 1 103 ASN 103 130 130 ASN ASN A . n A 1 104 TYR 104 131 131 TYR TYR A . n A 1 105 GLU 105 132 132 GLU GLU A . n A 1 106 GLU 106 133 133 GLU GLU A . n A 1 107 ILE 107 134 134 ILE ILE A . n A 1 108 PHE 108 135 135 PHE PHE A . n A 1 109 SER 109 136 136 SER SER 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 MPD 1 201 141 MPD MPD A . C 3 CIT 1 202 142 CIT CIT A . D 4 PO4 1 203 143 PO4 PO4 A . E 4 PO4 1 204 144 PO4 PO4 A . F 5 HOH 1 301 145 HOH HOH A . F 5 HOH 2 302 146 HOH HOH A . F 5 HOH 3 303 147 HOH HOH A . F 5 HOH 4 304 148 HOH HOH A . F 5 HOH 5 305 149 HOH HOH A . F 5 HOH 6 306 150 HOH HOH A . F 5 HOH 7 307 151 HOH HOH A . F 5 HOH 8 308 152 HOH HOH A . F 5 HOH 9 309 153 HOH HOH A . F 5 HOH 10 310 154 HOH HOH A . F 5 HOH 11 311 155 HOH HOH A . F 5 HOH 12 312 156 HOH HOH A . F 5 HOH 13 313 157 HOH HOH A . F 5 HOH 14 314 158 HOH HOH A . F 5 HOH 15 315 159 HOH HOH A . F 5 HOH 16 316 160 HOH HOH A . F 5 HOH 17 317 161 HOH HOH A . F 5 HOH 18 318 162 HOH HOH A . F 5 HOH 19 319 163 HOH HOH A . F 5 HOH 20 320 164 HOH HOH A . F 5 HOH 21 321 165 HOH HOH A . F 5 HOH 22 322 166 HOH HOH A . F 5 HOH 23 323 167 HOH HOH A . F 5 HOH 24 324 168 HOH HOH A . F 5 HOH 25 325 169 HOH HOH A . F 5 HOH 26 326 170 HOH HOH A . F 5 HOH 27 327 171 HOH HOH A . F 5 HOH 28 328 172 HOH HOH A . F 5 HOH 29 329 173 HOH HOH A . F 5 HOH 30 330 174 HOH HOH A . F 5 HOH 31 331 175 HOH HOH A . F 5 HOH 32 332 176 HOH HOH A . F 5 HOH 33 333 177 HOH HOH A . F 5 HOH 34 334 178 HOH HOH A . F 5 HOH 35 335 179 HOH HOH A . F 5 HOH 36 336 180 HOH HOH A . F 5 HOH 37 337 181 HOH HOH A . F 5 HOH 38 338 182 HOH HOH A . F 5 HOH 39 339 183 HOH HOH A . F 5 HOH 40 340 184 HOH HOH A . F 5 HOH 41 341 185 HOH HOH A . F 5 HOH 42 342 186 HOH HOH A . F 5 HOH 43 343 187 HOH HOH A . F 5 HOH 44 344 188 HOH HOH A . F 5 HOH 45 345 189 HOH HOH A . F 5 HOH 46 346 190 HOH HOH A . F 5 HOH 47 347 191 HOH HOH A . F 5 HOH 48 348 192 HOH HOH A . F 5 HOH 49 349 193 HOH HOH A . F 5 HOH 50 350 194 HOH HOH A . F 5 HOH 51 351 195 HOH HOH A . F 5 HOH 52 352 196 HOH HOH A . F 5 HOH 53 353 197 HOH HOH A . F 5 HOH 54 354 198 HOH HOH A . F 5 HOH 55 355 199 HOH HOH A . F 5 HOH 56 356 200 HOH HOH A . F 5 HOH 57 357 201 HOH HOH A . F 5 HOH 58 358 202 HOH HOH A . F 5 HOH 59 359 203 HOH HOH A . F 5 HOH 60 360 204 HOH HOH A . F 5 HOH 61 361 205 HOH HOH A . F 5 HOH 62 362 206 HOH HOH A . F 5 HOH 63 363 207 HOH HOH A . F 5 HOH 64 364 208 HOH HOH A . F 5 HOH 65 365 209 HOH HOH A . F 5 HOH 66 366 210 HOH HOH A . F 5 HOH 67 367 211 HOH HOH A . F 5 HOH 68 368 212 HOH HOH A . F 5 HOH 69 369 213 HOH HOH A . F 5 HOH 70 370 214 HOH HOH A . F 5 HOH 71 371 215 HOH HOH A . F 5 HOH 72 372 216 HOH HOH A . F 5 HOH 73 373 217 HOH HOH A . F 5 HOH 74 374 218 HOH HOH A . F 5 HOH 75 375 219 HOH HOH A . F 5 HOH 76 376 220 HOH HOH A . F 5 HOH 77 377 221 HOH HOH A . F 5 HOH 78 378 222 HOH HOH A . F 5 HOH 79 379 223 HOH HOH A . F 5 HOH 80 380 224 HOH HOH A . F 5 HOH 81 381 225 HOH HOH A . F 5 HOH 82 382 226 HOH HOH A . F 5 HOH 83 383 227 HOH HOH A . F 5 HOH 84 384 228 HOH HOH A . F 5 HOH 85 385 229 HOH HOH A . F 5 HOH 86 386 230 HOH HOH A . F 5 HOH 87 387 231 HOH HOH A . F 5 HOH 88 388 232 HOH HOH A . F 5 HOH 89 389 233 HOH HOH A . F 5 HOH 90 390 234 HOH HOH A . F 5 HOH 91 391 235 HOH HOH A . F 5 HOH 92 392 236 HOH HOH A . F 5 HOH 93 393 237 HOH HOH A . F 5 HOH 94 394 238 HOH HOH A . F 5 HOH 95 395 239 HOH HOH A . F 5 HOH 96 396 240 HOH HOH A . F 5 HOH 97 397 241 HOH HOH A . F 5 HOH 98 398 242 HOH HOH A . F 5 HOH 99 399 243 HOH HOH A . F 5 HOH 100 400 244 HOH HOH A . F 5 HOH 101 401 245 HOH HOH A . F 5 HOH 102 402 246 HOH HOH A . F 5 HOH 103 403 247 HOH HOH A . F 5 HOH 104 404 248 HOH HOH A . F 5 HOH 105 405 249 HOH HOH A . F 5 HOH 106 406 250 HOH HOH A . F 5 HOH 107 407 251 HOH HOH A . F 5 HOH 108 408 252 HOH HOH A . F 5 HOH 109 409 253 HOH HOH A . F 5 HOH 110 410 254 HOH HOH A . F 5 HOH 111 411 255 HOH HOH A . F 5 HOH 112 412 256 HOH HOH A . F 5 HOH 113 413 257 HOH HOH A . F 5 HOH 114 414 258 HOH HOH A . F 5 HOH 115 415 259 HOH HOH A . F 5 HOH 116 416 260 HOH HOH A . F 5 HOH 117 417 261 HOH HOH A . F 5 HOH 118 418 262 HOH HOH A . F 5 HOH 119 419 263 HOH HOH A . F 5 HOH 120 420 264 HOH HOH A . F 5 HOH 121 421 265 HOH HOH A . F 5 HOH 122 422 266 HOH HOH A . F 5 HOH 123 423 267 HOH HOH A . F 5 HOH 124 424 268 HOH HOH A . F 5 HOH 125 425 269 HOH HOH A . F 5 HOH 126 426 270 HOH HOH A . F 5 HOH 127 427 271 HOH HOH A . F 5 HOH 128 428 272 HOH HOH A . F 5 HOH 129 429 273 HOH HOH A . F 5 HOH 130 430 274 HOH HOH A . F 5 HOH 131 431 275 HOH HOH A . F 5 HOH 132 432 276 HOH HOH A . F 5 HOH 133 433 277 HOH HOH A . F 5 HOH 134 434 278 HOH HOH A . F 5 HOH 135 435 279 HOH HOH A . F 5 HOH 136 436 280 HOH HOH A . F 5 HOH 137 437 281 HOH HOH A . F 5 HOH 138 438 282 HOH HOH A . F 5 HOH 139 439 283 HOH HOH A . F 5 HOH 140 440 284 HOH HOH A . F 5 HOH 141 441 285 HOH HOH A . F 5 HOH 142 442 286 HOH HOH A . F 5 HOH 143 443 287 HOH HOH A . F 5 HOH 144 444 288 HOH HOH A . F 5 HOH 145 445 289 HOH HOH A . F 5 HOH 146 446 290 HOH HOH A . F 5 HOH 147 447 291 HOH HOH A . F 5 HOH 148 448 292 HOH HOH A . F 5 HOH 149 449 293 HOH HOH A . F 5 HOH 150 450 294 HOH HOH A . F 5 HOH 151 451 295 HOH HOH A . F 5 HOH 152 452 296 HOH HOH A . F 5 HOH 153 453 297 HOH HOH A . F 5 HOH 154 454 298 HOH HOH A . F 5 HOH 155 455 299 HOH HOH A . F 5 HOH 156 456 300 HOH HOH A . F 5 HOH 157 457 301 HOH HOH A . F 5 HOH 158 458 302 HOH HOH A . F 5 HOH 159 459 303 HOH HOH A . F 5 HOH 160 460 304 HOH HOH A . F 5 HOH 161 461 305 HOH HOH A . F 5 HOH 162 462 306 HOH HOH A . F 5 HOH 163 463 307 HOH HOH A . F 5 HOH 164 464 308 HOH HOH A . F 5 HOH 165 465 309 HOH HOH A . F 5 HOH 166 466 310 HOH HOH A . F 5 HOH 167 467 311 HOH HOH A . F 5 HOH 168 468 312 HOH HOH A . F 5 HOH 169 469 313 HOH HOH A . F 5 HOH 170 470 314 HOH HOH A . F 5 HOH 171 471 315 HOH HOH A . F 5 HOH 172 472 316 HOH HOH A . F 5 HOH 173 473 317 HOH HOH A . F 5 HOH 174 474 318 HOH HOH A . F 5 HOH 175 475 319 HOH HOH A . F 5 HOH 176 476 320 HOH HOH A . F 5 HOH 177 477 321 HOH HOH A . F 5 HOH 178 478 322 HOH HOH A . F 5 HOH 179 479 323 HOH HOH A . F 5 HOH 180 480 324 HOH HOH A . F 5 HOH 181 481 325 HOH HOH A . F 5 HOH 182 482 326 HOH HOH A . F 5 HOH 183 483 327 HOH HOH A . F 5 HOH 184 484 328 HOH HOH A . F 5 HOH 185 485 329 HOH HOH A . F 5 HOH 186 486 330 HOH HOH A . F 5 HOH 187 487 331 HOH HOH A . F 5 HOH 188 488 332 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 82 A MSE 109 ? MET SELENOMETHIONINE 2 A MSE 97 A MSE 124 ? 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 # _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_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 301 ? F HOH . 2 1 A HOH 397 ? F HOH . 3 1 A HOH 482 ? F HOH . # 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 2014-08-27 2 'Structure model' 1 1 2014-12-24 3 'Structure model' 1 2 2017-11-22 4 'Structure model' 1 3 2020-04-22 5 'Structure model' 1 4 2023-02-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Structure summary' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' software 2 4 'Structure model' citation 3 4 'Structure model' citation_author 4 4 'Structure model' struct_conn 5 5 'Structure model' database_2 6 5 'Structure model' struct_ref_seq_dif 7 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_citation.country' 4 4 'Structure model' '_citation.journal_abbrev' 5 4 'Structure model' '_citation.journal_id_ASTM' 6 4 'Structure model' '_citation.journal_id_CSD' 7 4 'Structure model' '_citation.journal_id_ISSN' 8 4 'Structure model' '_citation.journal_volume' 9 4 'Structure model' '_citation.page_first' 10 4 'Structure model' '_citation.page_last' 11 4 'Structure model' '_citation.pdbx_database_id_DOI' 12 4 'Structure model' '_citation.pdbx_database_id_PubMed' 13 4 'Structure model' '_citation.title' 14 4 'Structure model' '_citation.year' 15 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 16 5 'Structure model' '_database_2.pdbx_DOI' 17 5 'Structure model' '_database_2.pdbx_database_accession' 18 5 'Structure model' '_struct_ref_seq_dif.details' 19 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 20 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 21 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _phasing.method MAD # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 4 SHARP . ? package 'Eric de La Fortelle' sharp-develop@globalphasing.com phasing http://www.globalphasing.com/sharp/ ? ? 5 XSCALE 'January 10, 2014 BUILT=20140307' ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 6 REFMAC 5.8.0069 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 7 XDS . ? ? ? ? 'data reduction' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.entry_id 4R03 _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 29-136 OF 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 60 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _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 60 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _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 60 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 117.27 _pdbx_validate_rmsd_angle.angle_target_value 120.30 _pdbx_validate_rmsd_angle.angle_deviation -3.03 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # 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 ASN A 39 ? ? 49.62 -126.10 2 1 PHE A 89 ? ? -122.00 -53.26 3 1 PHE A 117 ? ? -101.97 50.32 # 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 98 ? CG ? A ASP 71 CG 2 1 Y 1 A ASP 98 ? OD1 ? A ASP 71 OD1 3 1 Y 1 A ASP 98 ? OD2 ? A ASP 71 OD2 4 1 Y 1 A GLN 99 ? CG ? A GLN 72 CG 5 1 Y 1 A GLN 99 ? CD ? A GLN 72 CD 6 1 Y 1 A GLN 99 ? OE1 ? A GLN 72 OE1 7 1 Y 1 A GLN 99 ? NE2 ? A GLN 72 NE2 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '(4S)-2-METHYL-2,4-PENTANEDIOL' MPD 3 'CITRIC ACID' CIT 4 'PHOSPHATE ION' PO4 5 water HOH #