data_1WKC # _entry.id 1WKC # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1WKC RCSB RCSB023672 WWPDB D_1000023672 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id ttk003001367.1 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1WKC _pdbx_database_status.recvd_initial_deposition_date 2004-05-31 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yanai, H.' 1 'Tsuge, H.' 2 'Utsunomiya, H.' 3 'Yokoyama, S.' 4 'Kuramitsu, S.' 5 'RIKEN Structural Genomics/Proteomics Initiative (RSGI)' 6 # _citation.id primary _citation.title 'Crystal structure of a 5-formyltetrahydrofolate cycloligase-related protein from Thermus thermophilus HB8' _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 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Yanai, H.' 1 primary 'Tsuge, H.' 2 primary 'Utsunomiya, H.' 3 primary 'Yokoyama, S.' 4 primary 'Kuramitsu, S.' 5 # _cell.entry_id 1WKC _cell.length_a 54.010 _cell.length_b 73.370 _cell.length_c 107.220 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WKC _symmetry.space_group_name_H-M 'I 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _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 'HB8 TT1367 protein' 20457.561 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 4 ? ? ? ? 3 water nat water 18.015 146 ? ? ? ? # _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 ;(MSE)TKAELRRRARAAWRRLDLKALSRAVGAALLPWLRERGFRHILLYHPLPHELNLLPL(MSE)EAYPARYYLPKVAG KGLTVHPFGPLAPGPFGLLEPTTPPEDPRVLDLVVVPGLAFDREGYRLGHGQGFYDRFLKEVRAATVGVVPQALLFPALP RDPWDVPVDHLATEAGVEAVKRPAPGPGGLLD ; _entity_poly.pdbx_seq_one_letter_code_can ;MTKAELRRRARAAWRRLDLKALSRAVGAALLPWLRERGFRHILLYHPLPHELNLLPLMEAYPARYYLPKVAGKGLTVHPF GPLAPGPFGLLEPTTPPEDPRVLDLVVVPGLAFDREGYRLGHGQGFYDRFLKEVRAATVGVVPQALLFPALPRDPWDVPV DHLATEAGVEAVKRPAPGPGGLLD ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ttk003001367.1 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MSE n 1 2 THR n 1 3 LYS n 1 4 ALA n 1 5 GLU n 1 6 LEU n 1 7 ARG n 1 8 ARG n 1 9 ARG n 1 10 ALA n 1 11 ARG n 1 12 ALA n 1 13 ALA n 1 14 TRP n 1 15 ARG n 1 16 ARG n 1 17 LEU n 1 18 ASP n 1 19 LEU n 1 20 LYS n 1 21 ALA n 1 22 LEU n 1 23 SER n 1 24 ARG n 1 25 ALA n 1 26 VAL n 1 27 GLY n 1 28 ALA n 1 29 ALA n 1 30 LEU n 1 31 LEU n 1 32 PRO n 1 33 TRP n 1 34 LEU n 1 35 ARG n 1 36 GLU n 1 37 ARG n 1 38 GLY n 1 39 PHE n 1 40 ARG n 1 41 HIS n 1 42 ILE n 1 43 LEU n 1 44 LEU n 1 45 TYR n 1 46 HIS n 1 47 PRO n 1 48 LEU n 1 49 PRO n 1 50 HIS n 1 51 GLU n 1 52 LEU n 1 53 ASN n 1 54 LEU n 1 55 LEU n 1 56 PRO n 1 57 LEU n 1 58 MSE n 1 59 GLU n 1 60 ALA n 1 61 TYR n 1 62 PRO n 1 63 ALA n 1 64 ARG n 1 65 TYR n 1 66 TYR n 1 67 LEU n 1 68 PRO n 1 69 LYS n 1 70 VAL n 1 71 ALA n 1 72 GLY n 1 73 LYS n 1 74 GLY n 1 75 LEU n 1 76 THR n 1 77 VAL n 1 78 HIS n 1 79 PRO n 1 80 PHE n 1 81 GLY n 1 82 PRO n 1 83 LEU n 1 84 ALA n 1 85 PRO n 1 86 GLY n 1 87 PRO n 1 88 PHE n 1 89 GLY n 1 90 LEU n 1 91 LEU n 1 92 GLU n 1 93 PRO n 1 94 THR n 1 95 THR n 1 96 PRO n 1 97 PRO n 1 98 GLU n 1 99 ASP n 1 100 PRO n 1 101 ARG n 1 102 VAL n 1 103 LEU n 1 104 ASP n 1 105 LEU n 1 106 VAL n 1 107 VAL n 1 108 VAL n 1 109 PRO n 1 110 GLY n 1 111 LEU n 1 112 ALA n 1 113 PHE n 1 114 ASP n 1 115 ARG n 1 116 GLU n 1 117 GLY n 1 118 TYR n 1 119 ARG n 1 120 LEU n 1 121 GLY n 1 122 HIS n 1 123 GLY n 1 124 GLN n 1 125 GLY n 1 126 PHE n 1 127 TYR n 1 128 ASP n 1 129 ARG n 1 130 PHE n 1 131 LEU n 1 132 LYS n 1 133 GLU n 1 134 VAL n 1 135 ARG n 1 136 ALA n 1 137 ALA n 1 138 THR n 1 139 VAL n 1 140 GLY n 1 141 VAL n 1 142 VAL n 1 143 PRO n 1 144 GLN n 1 145 ALA n 1 146 LEU n 1 147 LEU n 1 148 PHE n 1 149 PRO n 1 150 ALA n 1 151 LEU n 1 152 PRO n 1 153 ARG n 1 154 ASP n 1 155 PRO n 1 156 TRP n 1 157 ASP n 1 158 VAL n 1 159 PRO n 1 160 VAL n 1 161 ASP n 1 162 HIS n 1 163 LEU n 1 164 ALA n 1 165 THR n 1 166 GLU n 1 167 ALA n 1 168 GLY n 1 169 VAL n 1 170 GLU n 1 171 ALA n 1 172 VAL n 1 173 LYS n 1 174 ARG n 1 175 PRO n 1 176 ALA n 1 177 PRO n 1 178 GLY n 1 179 PRO n 1 180 GLY n 1 181 GLY n 1 182 LEU n 1 183 LEU n 1 184 ASP 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 Thermus _entity_src_gen.pdbx_gene_src_gene ? _entity_src_gen.gene_src_species 'Thermus thermophilus' _entity_src_gen.gene_src_strain HB8 _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 'Thermus thermophilus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 300852 _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 Escherichia _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 ? _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 'B834(DE3)' _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name GB _struct_ref.db_code YP_144877 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MTKAELRRRARAAWRRLDLKALSRAVGAALLPWLRERGFRHILLYHPLPHELNLLPLMEAYPARYYLPKVAGKGLTVHPF GPLAPGPFGLLEPTTPPEDPRVLDLVVVPGLAFDREGYRLGHGQGFYDRFLKEVRAATVGVVPQALLFPALPRDPWDVPV DHLATEAGVEAVKRPAPGPGGLLD ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession 55981580 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1WKC _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 184 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 55981580 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 184 _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 184 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 1WKC MSE A 1 ? GB 55981580 MET 1 'MODIFIED RESIDUE' 1 1 1 1WKC MSE A 58 ? GB 55981580 MET 58 'MODIFIED RESIDUE' 58 2 # 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 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 1WKC _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.7 _exptl_crystal.density_percent_sol 53.3 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _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 'RIGAKU JUPITER 210' _diffrn_detector.pdbx_collection_date 2004-04-20 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.97923 1.0 2 0.97954 1.0 3 0.90000 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL26B2' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL26B2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.97923, 0.97954, 0.90000' # _reflns.entry_id 1WKC _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 1.7 _reflns.d_resolution_low 60.86 _reflns.number_all ? _reflns.number_obs 23751 _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.043 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 21.7 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.04 _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 # _reflns_shell.d_res_high 1.7 _reflns_shell.d_res_low 1.76 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.264 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 7.13 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1WKC _refine.ls_number_reflns_obs 22527 _refine.ls_number_reflns_all 22548 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.93 _refine.ls_d_res_high 1.70 _refine.ls_percent_reflns_obs 99.52 _refine.ls_R_factor_obs 0.21995 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21834 _refine.ls_R_factor_R_free 0.25082 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.1 _refine.ls_number_reflns_R_free 1212 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.942 _refine.correlation_coeff_Fo_to_Fc_free 0.918 _refine.B_iso_mean 24.702 _refine.aniso_B[1][1] 0.02 _refine.aniso_B[2][2] 0.02 _refine.aniso_B[3][3] -0.04 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.114 _refine.pdbx_overall_ESU_R_Free 0.112 _refine.overall_SU_ML 0.067 _refine.overall_SU_B 1.972 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 1338 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 20 _refine_hist.number_atoms_solvent 146 _refine_hist.number_atoms_total 1504 _refine_hist.d_res_high 1.70 _refine_hist.d_res_low 19.93 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.022 0.021 ? 1395 'X-RAY DIFFRACTION' ? r_bond_other_d 0.002 0.020 ? 1327 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.028 1.995 ? 1905 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.975 3.000 ? 3055 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.891 5.000 ? 166 'X-RAY DIFFRACTION' ? r_chiral_restr 0.121 0.200 ? 204 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.010 0.020 ? 1511 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.008 0.020 ? 300 'X-RAY DIFFRACTION' ? r_nbd_refined 0.235 0.200 ? 308 'X-RAY DIFFRACTION' ? r_nbd_other 0.252 0.200 ? 1543 'X-RAY DIFFRACTION' ? r_nbtor_other 0.090 0.200 ? 862 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.182 0.200 ? 102 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.277 0.200 ? 22 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.278 0.200 ? 74 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.534 0.200 ? 12 'X-RAY DIFFRACTION' ? r_mcbond_it 1.348 1.500 ? 845 'X-RAY DIFFRACTION' ? r_mcangle_it 2.333 2.000 ? 1361 'X-RAY DIFFRACTION' ? r_scbond_it 3.243 3.000 ? 550 'X-RAY DIFFRACTION' ? r_scangle_it 5.292 4.500 ? 544 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.700 _refine_ls_shell.d_res_low 1.744 _refine_ls_shell.number_reflns_R_work 1651 _refine_ls_shell.R_factor_R_work 0.212 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.237 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 90 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # _struct.entry_id 1WKC _struct.title 'Crystal structure of a 5-formyltetrahydrofolate cycloligase-related protein from Thermus thermophilus HB8' _struct.pdbx_descriptor 'HB8 TT1367 protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1WKC _struct_keywords.pdbx_keywords 'STRUCTURAL GENOMICS, UNKNOWN FUNCTION' _struct_keywords.text 'HB8, STRUCTURAL GENOMICS, RIKEN Structural Genomics/Proteomics Initiative, RSGI, UNKNOWN FUNCTION' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 3 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 THR A 2 ? ARG A 16 ? THR A 2 ARG A 16 1 ? 15 HELX_P HELX_P2 2 ASP A 18 ? GLY A 38 ? ASP A 18 GLY A 38 1 ? 21 HELX_P HELX_P3 3 PRO A 56 ? TYR A 61 ? PRO A 56 TYR A 61 1 ? 6 HELX_P HELX_P4 4 ASP A 99 ? LEU A 103 ? ASP A 99 LEU A 103 5 ? 5 HELX_P HELX_P5 5 GLY A 125 ? VAL A 134 ? GLY A 125 VAL A 134 1 ? 10 HELX_P HELX_P6 6 PRO A 143 ? ALA A 145 ? PRO A 143 ALA A 145 5 ? 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A MSE 1 C ? ? ? 1_555 A THR 2 N ? ? A MSE 1 A THR 2 1_555 ? ? ? ? ? ? ? 1.322 ? covale2 covale ? ? A LEU 57 C ? ? ? 1_555 A MSE 58 N ? ? A LEU 57 A MSE 58 1_555 ? ? ? ? ? ? ? 1.340 ? covale3 covale ? ? A MSE 58 C ? ? ? 1_555 A GLU 59 N ? ? A MSE 58 A GLU 59 1_555 ? ? ? ? ? ? ? 1.321 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 7 ? B ? 3 ? # 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 ? parallel A 4 5 ? parallel A 5 6 ? parallel A 6 7 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? 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 GLY A 74 ? PRO A 79 ? GLY A 74 PRO A 79 A 2 ARG A 64 ? ALA A 71 ? ARG A 64 ALA A 71 A 3 HIS A 41 ? LEU A 43 ? HIS A 41 LEU A 43 A 4 LEU A 105 ? VAL A 108 ? LEU A 105 VAL A 108 A 5 ALA A 137 ? VAL A 141 ? ALA A 137 VAL A 141 A 6 HIS A 162 ? THR A 165 ? HIS A 162 THR A 165 A 7 GLY A 168 ? ALA A 171 ? GLY A 168 ALA A 171 B 1 ARG A 119 ? LEU A 120 ? ARG A 119 LEU A 120 B 2 ALA A 112 ? ASP A 114 ? ALA A 112 ASP A 114 B 3 LEU A 147 ? PHE A 148 ? LEU A 147 PHE A 148 # 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 HIS A 78 ? O HIS A 78 N LEU A 67 ? N LEU A 67 A 2 3 O ARG A 64 ? O ARG A 64 N ILE A 42 ? N ILE A 42 A 3 4 N LEU A 43 ? N LEU A 43 O LEU A 105 ? O LEU A 105 A 4 5 N VAL A 108 ? N VAL A 108 O VAL A 139 ? O VAL A 139 A 5 6 N GLY A 140 ? N GLY A 140 O ALA A 164 ? O ALA A 164 A 6 7 N LEU A 163 ? N LEU A 163 O GLU A 170 ? O GLU A 170 B 1 2 O LEU A 120 ? O LEU A 120 N ALA A 112 ? N ALA A 112 B 2 3 N PHE A 113 ? N PHE A 113 O PHE A 148 ? O PHE A 148 # 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 ? ? ? ? 10 'BINDING SITE FOR RESIDUE SO4 A 200' AC2 Software ? ? ? ? 11 'BINDING SITE FOR RESIDUE SO4 A 201' AC3 Software ? ? ? ? 9 'BINDING SITE FOR RESIDUE SO4 A 202' AC4 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE SO4 A 203' # 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 10 ARG A 119 ? ARG A 119 . ? 1_555 ? 2 AC1 10 GLY A 121 ? GLY A 121 . ? 1_555 ? 3 AC1 10 HIS A 122 ? HIS A 122 . ? 1_555 ? 4 AC1 10 GLY A 123 ? GLY A 123 . ? 1_555 ? 5 AC1 10 GLN A 124 ? GLN A 124 . ? 1_555 ? 6 AC1 10 GLY A 125 ? GLY A 125 . ? 1_555 ? 7 AC1 10 PHE A 126 ? PHE A 126 . ? 1_555 ? 8 AC1 10 TYR A 127 ? TYR A 127 . ? 1_555 ? 9 AC1 10 HOH F . ? HOH A 204 . ? 1_555 ? 10 AC1 10 HOH F . ? HOH A 313 . ? 1_555 ? 11 AC2 11 LYS A 3 ? LYS A 3 . ? 1_555 ? 12 AC2 11 ARG A 119 ? ARG A 119 . ? 1_555 ? 13 AC2 11 LEU A 120 ? LEU A 120 . ? 1_555 ? 14 AC2 11 GLY A 121 ? GLY A 121 . ? 1_555 ? 15 AC2 11 HIS A 122 ? HIS A 122 . ? 1_555 ? 16 AC2 11 GLY A 123 ? GLY A 123 . ? 1_555 ? 17 AC2 11 HOH F . ? HOH A 228 . ? 1_555 ? 18 AC2 11 HOH F . ? HOH A 233 . ? 1_555 ? 19 AC2 11 HOH F . ? HOH A 254 . ? 1_555 ? 20 AC2 11 HOH F . ? HOH A 278 . ? 1_555 ? 21 AC2 11 HOH F . ? HOH A 299 . ? 1_555 ? 22 AC3 9 THR A 2 ? THR A 2 . ? 1_555 ? 23 AC3 9 LYS A 3 ? LYS A 3 . ? 1_555 ? 24 AC3 9 ARG A 37 ? ARG A 37 . ? 8_455 ? 25 AC3 9 ALA A 137 ? ALA A 137 . ? 8_455 ? 26 AC3 9 ASP A 161 ? ASP A 161 . ? 8_455 ? 27 AC3 9 HIS A 162 ? HIS A 162 . ? 8_455 ? 28 AC3 9 HOH F . ? HOH A 232 . ? 8_455 ? 29 AC3 9 HOH F . ? HOH A 267 . ? 1_555 ? 30 AC3 9 HOH F . ? HOH A 300 . ? 1_555 ? 31 AC4 4 GLU A 116 ? GLU A 116 . ? 1_555 ? 32 AC4 4 PRO A 149 ? PRO A 149 . ? 1_555 ? 33 AC4 4 ALA A 150 ? ALA A 150 . ? 1_555 ? 34 AC4 4 HOH F . ? HOH A 209 . ? 1_555 ? # _database_PDB_matrix.entry_id 1WKC _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1WKC _atom_sites.fract_transf_matrix[1][1] 0.018515 _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] 0.013630 _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] 0.009327 _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 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 MSE 1 1 1 MSE MSE A . n A 1 2 THR 2 2 2 THR THR A . n A 1 3 LYS 3 3 3 LYS LYS A . n A 1 4 ALA 4 4 4 ALA ALA A . n A 1 5 GLU 5 5 5 GLU GLU A . n A 1 6 LEU 6 6 6 LEU LEU A . n A 1 7 ARG 7 7 7 ARG ARG A . n A 1 8 ARG 8 8 8 ARG ARG A . n A 1 9 ARG 9 9 9 ARG ARG A . n A 1 10 ALA 10 10 10 ALA ALA A . n A 1 11 ARG 11 11 11 ARG ARG A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 ALA 13 13 13 ALA ALA A . n A 1 14 TRP 14 14 14 TRP TRP A . n A 1 15 ARG 15 15 15 ARG ARG A . n A 1 16 ARG 16 16 16 ARG ARG A . n A 1 17 LEU 17 17 17 LEU LEU A . n A 1 18 ASP 18 18 18 ASP ASP A . n A 1 19 LEU 19 19 19 LEU LEU A . n A 1 20 LYS 20 20 20 LYS LYS A . n A 1 21 ALA 21 21 21 ALA ALA A . n A 1 22 LEU 22 22 22 LEU LEU A . n A 1 23 SER 23 23 23 SER SER A . n A 1 24 ARG 24 24 24 ARG ARG A . n A 1 25 ALA 25 25 25 ALA ALA A . n A 1 26 VAL 26 26 26 VAL VAL A . n A 1 27 GLY 27 27 27 GLY GLY A . n A 1 28 ALA 28 28 28 ALA ALA A . n A 1 29 ALA 29 29 29 ALA ALA A . n A 1 30 LEU 30 30 30 LEU LEU A . n A 1 31 LEU 31 31 31 LEU LEU A . n A 1 32 PRO 32 32 32 PRO PRO A . n A 1 33 TRP 33 33 33 TRP TRP A . n A 1 34 LEU 34 34 34 LEU LEU A . n A 1 35 ARG 35 35 35 ARG ARG A . n A 1 36 GLU 36 36 36 GLU GLU A . n A 1 37 ARG 37 37 37 ARG ARG A . n A 1 38 GLY 38 38 38 GLY GLY A . n A 1 39 PHE 39 39 39 PHE PHE A . n A 1 40 ARG 40 40 40 ARG ARG A . n A 1 41 HIS 41 41 41 HIS HIS A . n A 1 42 ILE 42 42 42 ILE ILE A . n A 1 43 LEU 43 43 43 LEU LEU A . n A 1 44 LEU 44 44 44 LEU LEU A . n A 1 45 TYR 45 45 45 TYR TYR A . n A 1 46 HIS 46 46 46 HIS HIS A . n A 1 47 PRO 47 47 47 PRO PRO A . n A 1 48 LEU 48 48 48 LEU LEU A . n A 1 49 PRO 49 49 49 PRO PRO A . n A 1 50 HIS 50 50 50 HIS HIS A . n A 1 51 GLU 51 51 51 GLU GLU A . n A 1 52 LEU 52 52 52 LEU LEU A . n A 1 53 ASN 53 53 53 ASN ASN A . n A 1 54 LEU 54 54 54 LEU LEU A . n A 1 55 LEU 55 55 55 LEU LEU A . n A 1 56 PRO 56 56 56 PRO PRO A . n A 1 57 LEU 57 57 57 LEU LEU A . n A 1 58 MSE 58 58 58 MSE MSE A . n A 1 59 GLU 59 59 59 GLU GLU A . n A 1 60 ALA 60 60 60 ALA ALA A . n A 1 61 TYR 61 61 61 TYR TYR A . n A 1 62 PRO 62 62 62 PRO PRO A . n A 1 63 ALA 63 63 63 ALA ALA A . n A 1 64 ARG 64 64 64 ARG ARG A . n A 1 65 TYR 65 65 65 TYR TYR A . n A 1 66 TYR 66 66 66 TYR TYR A . n A 1 67 LEU 67 67 67 LEU LEU A . n A 1 68 PRO 68 68 68 PRO PRO A . n A 1 69 LYS 69 69 69 LYS LYS A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 ALA 71 71 71 ALA ALA A . n A 1 72 GLY 72 72 72 GLY GLY A . n A 1 73 LYS 73 73 73 LYS LYS A . n A 1 74 GLY 74 74 74 GLY GLY A . n A 1 75 LEU 75 75 75 LEU LEU A . n A 1 76 THR 76 76 76 THR THR A . n A 1 77 VAL 77 77 77 VAL VAL A . n A 1 78 HIS 78 78 78 HIS HIS A . n A 1 79 PRO 79 79 79 PRO PRO A . n A 1 80 PHE 80 80 80 PHE PHE A . n A 1 81 GLY 81 81 81 GLY GLY A . n A 1 82 PRO 82 82 82 PRO PRO A . n A 1 83 LEU 83 83 83 LEU LEU A . n A 1 84 ALA 84 84 84 ALA ALA A . n A 1 85 PRO 85 85 ? ? ? A . n A 1 86 GLY 86 86 ? ? ? A . n A 1 87 PRO 87 87 ? ? ? A . n A 1 88 PHE 88 88 ? ? ? A . n A 1 89 GLY 89 89 ? ? ? A . n A 1 90 LEU 90 90 ? ? ? A . n A 1 91 LEU 91 91 ? ? ? A . n A 1 92 GLU 92 92 92 GLU GLU A . n A 1 93 PRO 93 93 93 PRO PRO A . n A 1 94 THR 94 94 94 THR THR A . n A 1 95 THR 95 95 95 THR THR A . n A 1 96 PRO 96 96 96 PRO PRO A . n A 1 97 PRO 97 97 97 PRO PRO A . n A 1 98 GLU 98 98 98 GLU GLU A . n A 1 99 ASP 99 99 99 ASP ASP A . n A 1 100 PRO 100 100 100 PRO PRO A . n A 1 101 ARG 101 101 101 ARG ARG A . n A 1 102 VAL 102 102 102 VAL VAL A . n A 1 103 LEU 103 103 103 LEU LEU A . n A 1 104 ASP 104 104 104 ASP ASP A . n A 1 105 LEU 105 105 105 LEU LEU A . n A 1 106 VAL 106 106 106 VAL VAL A . n A 1 107 VAL 107 107 107 VAL VAL A . n A 1 108 VAL 108 108 108 VAL VAL A . n A 1 109 PRO 109 109 109 PRO PRO A . n A 1 110 GLY 110 110 110 GLY GLY A . n A 1 111 LEU 111 111 111 LEU LEU A . n A 1 112 ALA 112 112 112 ALA ALA A . n A 1 113 PHE 113 113 113 PHE PHE A . n A 1 114 ASP 114 114 114 ASP ASP A . n A 1 115 ARG 115 115 115 ARG ARG A . n A 1 116 GLU 116 116 116 GLU GLU A . n A 1 117 GLY 117 117 117 GLY GLY A . n A 1 118 TYR 118 118 118 TYR TYR A . n A 1 119 ARG 119 119 119 ARG ARG A . n A 1 120 LEU 120 120 120 LEU LEU A . n A 1 121 GLY 121 121 121 GLY GLY A . n A 1 122 HIS 122 122 122 HIS HIS A . n A 1 123 GLY 123 123 123 GLY GLY A . n A 1 124 GLN 124 124 124 GLN GLN A . n A 1 125 GLY 125 125 125 GLY GLY A . n A 1 126 PHE 126 126 126 PHE PHE A . n A 1 127 TYR 127 127 127 TYR TYR A . n A 1 128 ASP 128 128 128 ASP ASP A . n A 1 129 ARG 129 129 129 ARG ARG A . n A 1 130 PHE 130 130 130 PHE PHE A . n A 1 131 LEU 131 131 131 LEU LEU A . n A 1 132 LYS 132 132 132 LYS LYS A . n A 1 133 GLU 133 133 133 GLU GLU A . n A 1 134 VAL 134 134 134 VAL VAL A . n A 1 135 ARG 135 135 135 ARG ARG A . n A 1 136 ALA 136 136 136 ALA ALA A . n A 1 137 ALA 137 137 137 ALA ALA A . n A 1 138 THR 138 138 138 THR THR A . n A 1 139 VAL 139 139 139 VAL VAL A . n A 1 140 GLY 140 140 140 GLY GLY A . n A 1 141 VAL 141 141 141 VAL VAL A . n A 1 142 VAL 142 142 142 VAL VAL A . n A 1 143 PRO 143 143 143 PRO PRO A . n A 1 144 GLN 144 144 144 GLN GLN A . n A 1 145 ALA 145 145 145 ALA ALA A . n A 1 146 LEU 146 146 146 LEU LEU A . n A 1 147 LEU 147 147 147 LEU LEU A . n A 1 148 PHE 148 148 148 PHE PHE A . n A 1 149 PRO 149 149 149 PRO PRO A . n A 1 150 ALA 150 150 150 ALA ALA A . n A 1 151 LEU 151 151 151 LEU LEU A . n A 1 152 PRO 152 152 152 PRO PRO A . n A 1 153 ARG 153 153 153 ARG ARG A . n A 1 154 ASP 154 154 154 ASP ASP A . n A 1 155 PRO 155 155 155 PRO PRO A . n A 1 156 TRP 156 156 156 TRP TRP A . n A 1 157 ASP 157 157 157 ASP ASP A . n A 1 158 VAL 158 158 158 VAL VAL A . n A 1 159 PRO 159 159 159 PRO PRO A . n A 1 160 VAL 160 160 160 VAL VAL A . n A 1 161 ASP 161 161 161 ASP ASP A . n A 1 162 HIS 162 162 162 HIS HIS A . n A 1 163 LEU 163 163 163 LEU LEU A . n A 1 164 ALA 164 164 164 ALA ALA A . n A 1 165 THR 165 165 165 THR THR A . n A 1 166 GLU 166 166 166 GLU GLU A . n A 1 167 ALA 167 167 167 ALA ALA A . n A 1 168 GLY 168 168 168 GLY GLY A . n A 1 169 VAL 169 169 169 VAL VAL A . n A 1 170 GLU 170 170 170 GLU GLU A . n A 1 171 ALA 171 171 171 ALA ALA A . n A 1 172 VAL 172 172 172 VAL VAL A . n A 1 173 LYS 173 173 173 LYS LYS A . n A 1 174 ARG 174 174 174 ARG ARG A . n A 1 175 PRO 175 175 175 PRO PRO A . n A 1 176 ALA 176 176 ? ? ? A . n A 1 177 PRO 177 177 ? ? ? A . n A 1 178 GLY 178 178 ? ? ? A . n A 1 179 PRO 179 179 ? ? ? A . n A 1 180 GLY 180 180 ? ? ? A . n A 1 181 GLY 181 181 ? ? ? A . n A 1 182 LEU 182 182 ? ? ? A . n A 1 183 LEU 183 183 ? ? ? A . n A 1 184 ASP 184 184 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _pdbx_SG_project.full_name_of_center 'RIKEN Structural Genomics/Proteomics Initiative' _pdbx_SG_project.initial_of_center RSGI # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SO4 1 200 200 SO4 SO4 A . C 2 SO4 1 201 201 SO4 SO4 A . D 2 SO4 1 202 202 SO4 SO4 A . E 2 SO4 1 203 203 SO4 SO4 A . F 3 HOH 1 204 1 HOH HOH A . F 3 HOH 2 205 2 HOH HOH A . F 3 HOH 3 206 3 HOH HOH A . F 3 HOH 4 207 4 HOH HOH A . F 3 HOH 5 208 5 HOH HOH A . F 3 HOH 6 209 6 HOH HOH A . F 3 HOH 7 210 7 HOH HOH A . F 3 HOH 8 211 8 HOH HOH A . F 3 HOH 9 212 9 HOH HOH A . F 3 HOH 10 213 10 HOH HOH A . F 3 HOH 11 214 11 HOH HOH A . F 3 HOH 12 215 12 HOH HOH A . F 3 HOH 13 216 13 HOH HOH A . F 3 HOH 14 217 14 HOH HOH A . F 3 HOH 15 218 15 HOH HOH A . F 3 HOH 16 219 16 HOH HOH A . F 3 HOH 17 220 18 HOH HOH A . F 3 HOH 18 221 19 HOH HOH A . F 3 HOH 19 222 20 HOH HOH A . F 3 HOH 20 223 21 HOH HOH A . F 3 HOH 21 224 22 HOH HOH A . F 3 HOH 22 225 23 HOH HOH A . F 3 HOH 23 226 24 HOH HOH A . F 3 HOH 24 227 25 HOH HOH A . F 3 HOH 25 228 26 HOH HOH A . F 3 HOH 26 229 27 HOH HOH A . F 3 HOH 27 230 28 HOH HOH A . F 3 HOH 28 231 29 HOH HOH A . F 3 HOH 29 232 30 HOH HOH A . F 3 HOH 30 233 31 HOH HOH A . F 3 HOH 31 234 32 HOH HOH A . F 3 HOH 32 235 33 HOH HOH A . F 3 HOH 33 236 34 HOH HOH A . F 3 HOH 34 237 35 HOH HOH A . F 3 HOH 35 238 36 HOH HOH A . F 3 HOH 36 239 37 HOH HOH A . F 3 HOH 37 240 38 HOH HOH A . F 3 HOH 38 241 39 HOH HOH A . F 3 HOH 39 242 40 HOH HOH A . F 3 HOH 40 243 41 HOH HOH A . F 3 HOH 41 244 42 HOH HOH A . F 3 HOH 42 245 43 HOH HOH A . F 3 HOH 43 246 44 HOH HOH A . F 3 HOH 44 247 45 HOH HOH A . F 3 HOH 45 248 46 HOH HOH A . F 3 HOH 46 249 47 HOH HOH A . F 3 HOH 47 250 48 HOH HOH A . F 3 HOH 48 251 49 HOH HOH A . F 3 HOH 49 252 50 HOH HOH A . F 3 HOH 50 253 51 HOH HOH A . F 3 HOH 51 254 53 HOH HOH A . F 3 HOH 52 255 54 HOH HOH A . F 3 HOH 53 256 55 HOH HOH A . F 3 HOH 54 257 56 HOH HOH A . F 3 HOH 55 258 57 HOH HOH A . F 3 HOH 56 259 58 HOH HOH A . F 3 HOH 57 260 59 HOH HOH A . F 3 HOH 58 261 60 HOH HOH A . F 3 HOH 59 262 61 HOH HOH A . F 3 HOH 60 263 62 HOH HOH A . F 3 HOH 61 264 63 HOH HOH A . F 3 HOH 62 265 64 HOH HOH A . F 3 HOH 63 266 65 HOH HOH A . F 3 HOH 64 267 66 HOH HOH A . F 3 HOH 65 268 67 HOH HOH A . F 3 HOH 66 269 68 HOH HOH A . F 3 HOH 67 270 69 HOH HOH A . F 3 HOH 68 271 70 HOH HOH A . F 3 HOH 69 272 71 HOH HOH A . F 3 HOH 70 273 72 HOH HOH A . F 3 HOH 71 274 73 HOH HOH A . F 3 HOH 72 275 75 HOH HOH A . F 3 HOH 73 276 76 HOH HOH A . F 3 HOH 74 277 77 HOH HOH A . F 3 HOH 75 278 78 HOH HOH A . F 3 HOH 76 279 79 HOH HOH A . F 3 HOH 77 280 80 HOH HOH A . F 3 HOH 78 281 81 HOH HOH A . F 3 HOH 79 282 82 HOH HOH A . F 3 HOH 80 283 83 HOH HOH A . F 3 HOH 81 284 84 HOH HOH A . F 3 HOH 82 285 85 HOH HOH A . F 3 HOH 83 286 86 HOH HOH A . F 3 HOH 84 287 88 HOH HOH A . F 3 HOH 85 288 89 HOH HOH A . F 3 HOH 86 289 90 HOH HOH A . F 3 HOH 87 290 91 HOH HOH A . F 3 HOH 88 291 94 HOH HOH A . F 3 HOH 89 292 96 HOH HOH A . F 3 HOH 90 293 98 HOH HOH A . F 3 HOH 91 294 99 HOH HOH A . F 3 HOH 92 295 100 HOH HOH A . F 3 HOH 93 296 101 HOH HOH A . F 3 HOH 94 297 102 HOH HOH A . F 3 HOH 95 298 103 HOH HOH A . F 3 HOH 96 299 104 HOH HOH A . F 3 HOH 97 300 105 HOH HOH A . F 3 HOH 98 301 106 HOH HOH A . F 3 HOH 99 302 107 HOH HOH A . F 3 HOH 100 303 108 HOH HOH A . F 3 HOH 101 304 109 HOH HOH A . F 3 HOH 102 305 110 HOH HOH A . F 3 HOH 103 306 111 HOH HOH A . F 3 HOH 104 307 112 HOH HOH A . F 3 HOH 105 308 113 HOH HOH A . F 3 HOH 106 309 114 HOH HOH A . F 3 HOH 107 310 115 HOH HOH A . F 3 HOH 108 311 116 HOH HOH A . F 3 HOH 109 312 117 HOH HOH A . F 3 HOH 110 313 119 HOH HOH A . F 3 HOH 111 314 120 HOH HOH A . F 3 HOH 112 315 121 HOH HOH A . F 3 HOH 113 316 122 HOH HOH A . F 3 HOH 114 317 124 HOH HOH A . F 3 HOH 115 318 125 HOH HOH A . F 3 HOH 116 319 126 HOH HOH A . F 3 HOH 117 320 127 HOH HOH A . F 3 HOH 118 321 128 HOH HOH A . F 3 HOH 119 322 129 HOH HOH A . F 3 HOH 120 323 130 HOH HOH A . F 3 HOH 121 324 131 HOH HOH A . F 3 HOH 122 325 132 HOH HOH A . F 3 HOH 123 326 133 HOH HOH A . F 3 HOH 124 327 134 HOH HOH A . F 3 HOH 125 328 135 HOH HOH A . F 3 HOH 126 329 136 HOH HOH A . F 3 HOH 127 330 137 HOH HOH A . F 3 HOH 128 331 138 HOH HOH A . F 3 HOH 129 332 139 HOH HOH A . F 3 HOH 130 333 140 HOH HOH A . F 3 HOH 131 334 141 HOH HOH A . F 3 HOH 132 335 142 HOH HOH A . F 3 HOH 133 336 143 HOH HOH A . F 3 HOH 134 337 144 HOH HOH A . F 3 HOH 135 338 145 HOH HOH A . F 3 HOH 136 339 146 HOH HOH A . F 3 HOH 137 340 147 HOH HOH A . F 3 HOH 138 341 148 HOH HOH A . F 3 HOH 139 342 149 HOH HOH A . F 3 HOH 140 343 150 HOH HOH A . F 3 HOH 141 344 151 HOH HOH A . F 3 HOH 142 345 152 HOH HOH A . F 3 HOH 143 346 153 HOH HOH A . F 3 HOH 144 347 154 HOH HOH A . F 3 HOH 145 348 155 HOH HOH A . F 3 HOH 146 349 156 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 1 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 58 A MSE 58 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 321 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id F _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2004-12-01 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Source and taxonomy' 3 3 'Structure model' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.1.24 ? 1 CrystalClear 'data reduction' '(MSC/RIGAKU)' ? 2 CrystalClear 'data scaling' '(MSC/RIGAKU)' ? 3 SOLVE phasing . ? 4 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O3 A SO4 202 ? ? O A HOH 300 ? ? 2.09 2 1 NH2 A ARG 64 ? ? O A HOH 275 ? ? 2.14 3 1 SE A MSE 58 ? ? O A HOH 307 ? ? 2.16 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 318 ? ? 1_555 O A HOH 318 ? ? 2_655 1.56 2 1 O A HOH 304 ? ? 1_555 O A HOH 304 ? ? 3_655 1.58 3 1 O A HOH 286 ? ? 1_555 O A HOH 312 ? ? 3_655 2.13 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CB _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 VAL _pdbx_validate_rmsd_bond.auth_seq_id_1 142 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 CG2 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 VAL _pdbx_validate_rmsd_bond.auth_seq_id_2 142 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.385 _pdbx_validate_rmsd_bond.bond_target_value 1.524 _pdbx_validate_rmsd_bond.bond_deviation -0.139 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.021 _pdbx_validate_rmsd_bond.linker_flag N # _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 64 _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 64 _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 64 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 117.22 _pdbx_validate_rmsd_angle.angle_target_value 120.30 _pdbx_validate_rmsd_angle.angle_deviation -3.08 _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 LEU A 44 ? ? -99.82 -147.99 2 1 ARG A 135 ? ? -119.44 78.69 3 1 ALA A 150 ? ? -34.33 120.34 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A PRO 85 ? A PRO 85 2 1 Y 1 A GLY 86 ? A GLY 86 3 1 Y 1 A PRO 87 ? A PRO 87 4 1 Y 1 A PHE 88 ? A PHE 88 5 1 Y 1 A GLY 89 ? A GLY 89 6 1 Y 1 A LEU 90 ? A LEU 90 7 1 Y 1 A LEU 91 ? A LEU 91 8 1 Y 1 A ALA 176 ? A ALA 176 9 1 Y 1 A PRO 177 ? A PRO 177 10 1 Y 1 A GLY 178 ? A GLY 178 11 1 Y 1 A PRO 179 ? A PRO 179 12 1 Y 1 A GLY 180 ? A GLY 180 13 1 Y 1 A GLY 181 ? A GLY 181 14 1 Y 1 A LEU 182 ? A LEU 182 15 1 Y 1 A LEU 183 ? A LEU 183 16 1 Y 1 A ASP 184 ? A ASP 184 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 water HOH #