data_3BY5 # _entry.id 3BY5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.338 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3BY5 RCSB RCSB046102 WWPDB D_1000046102 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id NYSGXRC-10037i _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3BY5 _pdbx_database_status.recvd_initial_deposition_date 2008-01-15 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Patskovsky, Y.' 1 ? 'Bonanno, J.B.' 2 ? 'Sojitra, S.' 3 ? 'Rutter, M.' 4 ? 'Iizuka, M.' 5 ? 'Maletic, M.' 6 ? 'Wasserman, S.R.' 7 ? 'Sauder, J.M.' 8 0000-0002-0254-4955 'Burley, S.K.' 9 0000-0002-2487-9713 'Almo, S.C.' 10 ? 'New York SGX Research Center for Structural Genomics (NYSGXRC)' 11 ? # _citation.id primary _citation.title 'Crystal structure of cobalamin biosynthesis protein from Agrobacterium tumefaciens str. C58.' _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 _citation_author.identifier_ORCID primary 'Patskovsky, Y.' 1 ? primary 'Bonanno, J.B.' 2 ? primary 'Sojitra, S.' 3 ? primary 'Rutter, M.' 4 ? primary 'Iizuka, M.' 5 ? primary 'Maletic, M.' 6 ? primary 'Wasserman, S.R.' 7 ? primary 'Sauder, J.M.' 8 ? primary 'Burley, S.K.' 9 0000-0002-2487-9713 primary 'Almo, S.C.' 10 ? # _cell.entry_id 3BY5 _cell.length_a 72.023 _cell.length_b 72.023 _cell.length_c 141.069 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? _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 3BY5 _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _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 'Cobalamin biosynthesis protein' 15882.149 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 water nat water 18.015 13 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Protein AGR_C_5076p' # _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)SLELGQA(MSE)VTVAGIGCRKGAASDAIIAAVRAAERAFGVTVDYLATAPLKADEAGLAEAAKGLSLSLEIVAQ ERLEAVAAET(MSE)TFSQASLDHSGSPSVSEAAALAAAGAGARLVAPRLVVGDVTVAIA(MSE)TSDAPHGSRSAIEYG EQEEGHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;MSLELGQAMVTVAGIGCRKGAASDAIIAAVRAAERAFGVTVDYLATAPLKADEAGLAEAAKGLSLSLEIVAQERLEAVAA ETMTFSQASLDHSGSPSVSEAAALAAAGAGARLVAPRLVVGDVTVAIAMTSDAPHGSRSAIEYGEQEEGHHHHHH ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier NYSGXRC-10037i # 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 SER n 1 3 LEU n 1 4 GLU n 1 5 LEU n 1 6 GLY n 1 7 GLN n 1 8 ALA n 1 9 MSE n 1 10 VAL n 1 11 THR n 1 12 VAL n 1 13 ALA n 1 14 GLY n 1 15 ILE n 1 16 GLY n 1 17 CYS n 1 18 ARG n 1 19 LYS n 1 20 GLY n 1 21 ALA n 1 22 ALA n 1 23 SER n 1 24 ASP n 1 25 ALA n 1 26 ILE n 1 27 ILE n 1 28 ALA n 1 29 ALA n 1 30 VAL n 1 31 ARG n 1 32 ALA n 1 33 ALA n 1 34 GLU n 1 35 ARG n 1 36 ALA n 1 37 PHE n 1 38 GLY n 1 39 VAL n 1 40 THR n 1 41 VAL n 1 42 ASP n 1 43 TYR n 1 44 LEU n 1 45 ALA n 1 46 THR n 1 47 ALA n 1 48 PRO n 1 49 LEU n 1 50 LYS n 1 51 ALA n 1 52 ASP n 1 53 GLU n 1 54 ALA n 1 55 GLY n 1 56 LEU n 1 57 ALA n 1 58 GLU n 1 59 ALA n 1 60 ALA n 1 61 LYS n 1 62 GLY n 1 63 LEU n 1 64 SER n 1 65 LEU n 1 66 SER n 1 67 LEU n 1 68 GLU n 1 69 ILE n 1 70 VAL n 1 71 ALA n 1 72 GLN n 1 73 GLU n 1 74 ARG n 1 75 LEU n 1 76 GLU n 1 77 ALA n 1 78 VAL n 1 79 ALA n 1 80 ALA n 1 81 GLU n 1 82 THR n 1 83 MSE n 1 84 THR n 1 85 PHE n 1 86 SER n 1 87 GLN n 1 88 ALA n 1 89 SER n 1 90 LEU n 1 91 ASP n 1 92 HIS n 1 93 SER n 1 94 GLY n 1 95 SER n 1 96 PRO n 1 97 SER n 1 98 VAL n 1 99 SER n 1 100 GLU n 1 101 ALA n 1 102 ALA n 1 103 ALA n 1 104 LEU n 1 105 ALA n 1 106 ALA n 1 107 ALA n 1 108 GLY n 1 109 ALA n 1 110 GLY n 1 111 ALA n 1 112 ARG n 1 113 LEU n 1 114 VAL n 1 115 ALA n 1 116 PRO n 1 117 ARG n 1 118 LEU n 1 119 VAL n 1 120 VAL n 1 121 GLY n 1 122 ASP n 1 123 VAL n 1 124 THR n 1 125 VAL n 1 126 ALA n 1 127 ILE n 1 128 ALA n 1 129 MSE n 1 130 THR n 1 131 SER n 1 132 ASP n 1 133 ALA n 1 134 PRO n 1 135 HIS n 1 136 GLY n 1 137 SER n 1 138 ARG n 1 139 SER n 1 140 ALA n 1 141 ILE n 1 142 GLU n 1 143 TYR n 1 144 GLY n 1 145 GLU n 1 146 GLN n 1 147 GLU n 1 148 GLU n 1 149 GLY n 1 150 HIS n 1 151 HIS n 1 152 HIS n 1 153 HIS n 1 154 HIS n 1 155 HIS 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 Agrobacterium _entity_src_gen.pdbx_gene_src_gene chiG _entity_src_gen.gene_src_species 'Agrobacterium tumefaciens' _entity_src_gen.gene_src_strain C58 _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 'Agrobacterium tumefaciens str.' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 176299 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc 33970 _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 pET _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name 'BC-pSGX3(BC)' _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q8UBQ4_AGRT5 _struct_ref.pdbx_db_accession Q8UBQ4 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ELGQAMVTVAGIGCRKGAASDAIIAAVRAAERAFGVTVDYLATAPLKADEAGLAEAAKGLSLSLEIVAQERLEAVAAETM TFSQASLDHSGSPSVSEAAALAAAGAGARLVAPRLVVGDVTVAIAMTSDAPHGSRSAIEYGEQE ; _struct_ref.pdbx_align_begin 2 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3BY5 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 147 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q8UBQ4 _struct_ref_seq.db_align_beg 2 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 145 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 145 # 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 3BY5 MSE A 1 ? UNP Q8UBQ4 ? ? 'expression tag' -1 1 1 3BY5 SER A 2 ? UNP Q8UBQ4 ? ? 'expression tag' 0 2 1 3BY5 LEU A 3 ? UNP Q8UBQ4 ? ? 'expression tag' 1 3 1 3BY5 GLU A 148 ? UNP Q8UBQ4 ? ? 'expression tag' 146 4 1 3BY5 GLY A 149 ? UNP Q8UBQ4 ? ? 'expression tag' 147 5 1 3BY5 HIS A 150 ? UNP Q8UBQ4 ? ? 'expression tag' 148 6 1 3BY5 HIS A 151 ? UNP Q8UBQ4 ? ? 'expression tag' 149 7 1 3BY5 HIS A 152 ? UNP Q8UBQ4 ? ? 'expression tag' 150 8 1 3BY5 HIS A 153 ? UNP Q8UBQ4 ? ? 'expression tag' 151 9 1 3BY5 HIS A 154 ? UNP Q8UBQ4 ? ? 'expression tag' 152 10 1 3BY5 HIS A 155 ? UNP Q8UBQ4 ? ? 'expression tag' 153 11 # 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 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3BY5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.22 _exptl_crystal.density_percent_sol 44.51 _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.temp 294 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.2 _exptl_crystal_grow.pdbx_details '100mM Bis-Tris pH 5.2, 29% PEG 3350, 200mM Ammonium sulfate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 77.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2007-07-19 _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 Diamond _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9796 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 31-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 31-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9796 # _reflns.entry_id 3BY5 _reflns.observed_criterion_sigma_I -5.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.000 _reflns.d_resolution_high 2.52 _reflns.number_obs 4985 _reflns.number_all ? _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.138 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 3.7000 _reflns.B_iso_Wilson_estimate 52.388 _reflns.pdbx_redundancy 6.400 _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 2.52 _reflns_shell.d_res_low 2.61 _reflns_shell.percent_possible_all 97.2 _reflns_shell.Rmerge_I_obs 0.890 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.200 _reflns_shell.pdbx_redundancy 5.30 _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 3BY5 _refine.ls_number_reflns_obs 4822 _refine.ls_number_reflns_all ? _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 20.00 _refine.ls_d_res_high 2.52 _refine.ls_percent_reflns_obs 99.78 _refine.ls_R_factor_obs 0.21289 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21144 _refine.ls_R_factor_R_free 0.27187 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 2.7 _refine.ls_number_reflns_R_free 133 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.951 _refine.correlation_coeff_Fo_to_Fc_free 0.923 _refine.B_iso_mean 48.940 _refine.aniso_B[1][1] 2.97 _refine.aniso_B[2][2] 2.97 _refine.aniso_B[3][3] -4.46 _refine.aniso_B[1][2] 1.49 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _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 SAD _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 0.428 _refine.pdbx_overall_ESU_R_Free 0.293 _refine.overall_SU_ML 0.196 _refine.overall_SU_B 9.750 _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 846 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 13 _refine_hist.number_atoms_total 864 _refine_hist.d_res_high 2.52 _refine_hist.d_res_low 20.00 # 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 0.007 0.022 ? 856 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.132 1.979 ? 1165 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.232 5.000 ? 122 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 40.196 23.846 ? 26 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 17.874 15.000 ? 129 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 9.727 15.000 ? 6 'X-RAY DIFFRACTION' ? r_chiral_restr 0.067 0.200 ? 149 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.003 0.020 ? 622 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.132 0.300 ? 375 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.281 0.500 ? 613 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.145 0.500 ? 44 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.100 0.300 ? 20 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.129 0.500 ? 4 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 2.953 2.000 ? 617 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 4.853 3.000 ? 953 'X-RAY DIFFRACTION' ? r_scbond_it 5.286 3.000 ? 255 'X-RAY DIFFRACTION' ? r_scangle_it 8.759 5.000 ? 212 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.520 _refine_ls_shell.d_res_low 2.585 _refine_ls_shell.number_reflns_R_work 334 _refine_ls_shell.R_factor_R_work 0.372 _refine_ls_shell.percent_reflns_obs 96.91 _refine_ls_shell.R_factor_R_free 0.349 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 11 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3BY5 _struct.title 'Crystal structure of cobalamin biosynthesis protein chiG from Agrobacterium tumefaciens str. C58' _struct.pdbx_descriptor 'Cobalamin biosynthesis protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3BY5 _struct_keywords.pdbx_keywords 'BIOSYNTHETIC PROTEIN' _struct_keywords.text ;STRUCTURAL GENOMICS, UNKNOWN FUNCTION, UNCHARACTERIZED PROTEIN, COBALAMIN BIOSYNTHESIS PROTEIN, PROTEIN STRUCTURE INITIATIVE, PSI-2, New York SGX Research Center for Structural Genomics, NYSGXRC, BIOSYNTHETIC PROTEIN ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # 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 ALA A 22 ? GLY A 38 ? ALA A 20 GLY A 36 1 ? 17 HELX_P HELX_P2 2 GLU A 53 ? LEU A 63 ? GLU A 51 LEU A 61 1 ? 11 HELX_P HELX_P3 3 ALA A 71 ? PHE A 85 ? ALA A 69 PHE A 83 1 ? 15 HELX_P HELX_P4 4 SER A 86 ? LEU A 90 ? SER A 84 LEU A 88 5 ? 5 HELX_P HELX_P5 5 SER A 97 ? GLY A 108 ? SER A 95 GLY A 106 1 ? 12 # _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 THR 82 C ? ? ? 1_555 A MSE 83 N ? ? A THR 80 A MSE 81 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale2 covale both ? A MSE 83 C ? ? ? 1_555 A THR 84 N ? ? A MSE 81 A THR 82 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale3 covale both ? A ALA 128 C ? ? ? 1_555 A MSE 129 N ? ? A ALA 126 A MSE 127 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale4 covale both ? A MSE 129 C ? ? ? 1_555 A THR 130 N ? ? A MSE 127 A THR 128 1_555 ? ? ? ? ? ? ? 1.328 ? ? # _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 ? 5 ? B ? 5 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? parallel A 2 3 ? parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? parallel B 2 3 ? parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 LEU A 67 ? ILE A 69 ? LEU A 65 ILE A 67 A 2 TYR A 43 ? THR A 46 ? TYR A 41 THR A 44 A 3 THR A 11 ? CYS A 17 ? THR A 9 CYS A 15 A 4 VAL A 123 ? MSE A 129 ? VAL A 121 MSE A 127 A 5 ARG A 112 ? LEU A 113 ? ARG A 110 LEU A 111 B 1 LEU A 67 ? ILE A 69 ? LEU A 65 ILE A 67 B 2 TYR A 43 ? THR A 46 ? TYR A 41 THR A 44 B 3 THR A 11 ? CYS A 17 ? THR A 9 CYS A 15 B 4 VAL A 123 ? MSE A 129 ? VAL A 121 MSE A 127 B 5 LEU A 118 ? VAL A 120 ? LEU A 116 VAL A 118 # 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 GLU A 68 ? O GLU A 66 N THR A 46 ? N THR A 44 A 2 3 O ALA A 45 ? O ALA A 43 N ILE A 15 ? N ILE A 13 A 3 4 N GLY A 14 ? N GLY A 12 O ALA A 126 ? O ALA A 124 A 4 5 O MSE A 129 ? O MSE A 127 N ARG A 112 ? N ARG A 110 B 1 2 O GLU A 68 ? O GLU A 66 N THR A 46 ? N THR A 44 B 2 3 O ALA A 45 ? O ALA A 43 N ILE A 15 ? N ILE A 13 B 3 4 N GLY A 14 ? N GLY A 12 O ALA A 126 ? O ALA A 124 B 4 5 O VAL A 125 ? O VAL A 123 N LEU A 118 ? N LEU A 116 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id SO4 _struct_site.pdbx_auth_seq_id 201 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 3 _struct_site.details 'BINDING SITE FOR RESIDUE SO4 A 201' # 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 3 SER A 97 ? SER A 95 . ? 1_555 ? 2 AC1 3 SER A 99 ? SER A 97 . ? 1_555 ? 3 AC1 3 THR A 124 ? THR A 122 . ? 1_555 ? # _database_PDB_matrix.entry_id 3BY5 _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 3BY5 _atom_sites.fract_transf_matrix[1][1] 0.013884 _atom_sites.fract_transf_matrix[1][2] 0.008016 _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] 0.016032 _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] 0.007089 _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 ? ? ? A . n A 1 2 SER 2 0 ? ? ? A . n A 1 3 LEU 3 1 ? ? ? A . n A 1 4 GLU 4 2 ? ? ? A . n A 1 5 LEU 5 3 ? ? ? A . n A 1 6 GLY 6 4 ? ? ? A . n A 1 7 GLN 7 5 ? ? ? A . n A 1 8 ALA 8 6 ? ? ? A . n A 1 9 MSE 9 7 ? ? ? A . n A 1 10 VAL 10 8 8 VAL VAL A . n A 1 11 THR 11 9 9 THR THR A . n A 1 12 VAL 12 10 10 VAL VAL A . n A 1 13 ALA 13 11 11 ALA ALA A . n A 1 14 GLY 14 12 12 GLY GLY A . n A 1 15 ILE 15 13 13 ILE ILE A . n A 1 16 GLY 16 14 14 GLY GLY A . n A 1 17 CYS 17 15 15 CYS CYS A . n A 1 18 ARG 18 16 16 ARG ARG A . n A 1 19 LYS 19 17 17 LYS LYS A . n A 1 20 GLY 20 18 18 GLY GLY A . n A 1 21 ALA 21 19 19 ALA ALA A . n A 1 22 ALA 22 20 20 ALA ALA A . n A 1 23 SER 23 21 21 SER SER A . n A 1 24 ASP 24 22 22 ASP ASP A . n A 1 25 ALA 25 23 23 ALA ALA A . n A 1 26 ILE 26 24 24 ILE ILE A . n A 1 27 ILE 27 25 25 ILE ILE A . n A 1 28 ALA 28 26 26 ALA ALA A . n A 1 29 ALA 29 27 27 ALA ALA A . n A 1 30 VAL 30 28 28 VAL VAL A . n A 1 31 ARG 31 29 29 ARG ARG A . n A 1 32 ALA 32 30 30 ALA ALA A . n A 1 33 ALA 33 31 31 ALA ALA A . n A 1 34 GLU 34 32 32 GLU GLU A . n A 1 35 ARG 35 33 33 ARG ARG A . n A 1 36 ALA 36 34 34 ALA ALA A . n A 1 37 PHE 37 35 35 PHE PHE A . n A 1 38 GLY 38 36 36 GLY GLY A . n A 1 39 VAL 39 37 37 VAL VAL A . n A 1 40 THR 40 38 38 THR THR A . n A 1 41 VAL 41 39 39 VAL VAL A . n A 1 42 ASP 42 40 40 ASP ASP A . n A 1 43 TYR 43 41 41 TYR TYR A . n A 1 44 LEU 44 42 42 LEU LEU A . n A 1 45 ALA 45 43 43 ALA ALA A . n A 1 46 THR 46 44 44 THR THR A . n A 1 47 ALA 47 45 45 ALA ALA A . n A 1 48 PRO 48 46 46 PRO PRO A . n A 1 49 LEU 49 47 47 LEU LEU A . n A 1 50 LYS 50 48 48 LYS LYS A . n A 1 51 ALA 51 49 49 ALA ALA A . n A 1 52 ASP 52 50 50 ASP ASP A . n A 1 53 GLU 53 51 51 GLU GLU A . n A 1 54 ALA 54 52 52 ALA ALA A . n A 1 55 GLY 55 53 53 GLY GLY A . n A 1 56 LEU 56 54 54 LEU LEU A . n A 1 57 ALA 57 55 55 ALA ALA A . n A 1 58 GLU 58 56 56 GLU GLU A . n A 1 59 ALA 59 57 57 ALA ALA A . n A 1 60 ALA 60 58 58 ALA ALA A . n A 1 61 LYS 61 59 59 LYS LYS A . n A 1 62 GLY 62 60 60 GLY GLY A . n A 1 63 LEU 63 61 61 LEU LEU A . n A 1 64 SER 64 62 62 SER SER A . n A 1 65 LEU 65 63 63 LEU LEU A . n A 1 66 SER 66 64 64 SER SER A . n A 1 67 LEU 67 65 65 LEU LEU A . n A 1 68 GLU 68 66 66 GLU GLU A . n A 1 69 ILE 69 67 67 ILE ILE A . n A 1 70 VAL 70 68 68 VAL VAL A . n A 1 71 ALA 71 69 69 ALA ALA A . n A 1 72 GLN 72 70 70 GLN GLN A . n A 1 73 GLU 73 71 71 GLU GLU A . n A 1 74 ARG 74 72 72 ARG ARG A . n A 1 75 LEU 75 73 73 LEU LEU A . n A 1 76 GLU 76 74 74 GLU GLU A . n A 1 77 ALA 77 75 75 ALA ALA A . n A 1 78 VAL 78 76 76 VAL VAL A . n A 1 79 ALA 79 77 77 ALA ALA A . n A 1 80 ALA 80 78 78 ALA ALA A . n A 1 81 GLU 81 79 79 GLU GLU A . n A 1 82 THR 82 80 80 THR THR A . n A 1 83 MSE 83 81 81 MSE MSE A . n A 1 84 THR 84 82 82 THR THR A . n A 1 85 PHE 85 83 83 PHE PHE A . n A 1 86 SER 86 84 84 SER SER A . n A 1 87 GLN 87 85 85 GLN GLN A . n A 1 88 ALA 88 86 86 ALA ALA A . n A 1 89 SER 89 87 87 SER SER A . n A 1 90 LEU 90 88 88 LEU LEU A . n A 1 91 ASP 91 89 89 ASP ASP A . n A 1 92 HIS 92 90 90 HIS HIS A . n A 1 93 SER 93 91 91 SER SER A . n A 1 94 GLY 94 92 92 GLY GLY A . n A 1 95 SER 95 93 93 SER SER A . n A 1 96 PRO 96 94 94 PRO PRO A . n A 1 97 SER 97 95 95 SER SER A . n A 1 98 VAL 98 96 96 VAL VAL A . n A 1 99 SER 99 97 97 SER SER A . n A 1 100 GLU 100 98 98 GLU GLU A . n A 1 101 ALA 101 99 99 ALA ALA A . n A 1 102 ALA 102 100 100 ALA ALA A . n A 1 103 ALA 103 101 101 ALA ALA A . n A 1 104 LEU 104 102 102 LEU LEU A . n A 1 105 ALA 105 103 103 ALA ALA A . n A 1 106 ALA 106 104 104 ALA ALA A . n A 1 107 ALA 107 105 105 ALA ALA A . n A 1 108 GLY 108 106 106 GLY GLY A . n A 1 109 ALA 109 107 107 ALA ALA A . n A 1 110 GLY 110 108 108 GLY GLY A . n A 1 111 ALA 111 109 109 ALA ALA A . n A 1 112 ARG 112 110 110 ARG ARG A . n A 1 113 LEU 113 111 111 LEU LEU A . n A 1 114 VAL 114 112 112 VAL VAL A . n A 1 115 ALA 115 113 113 ALA ALA A . n A 1 116 PRO 116 114 114 PRO PRO A . n A 1 117 ARG 117 115 115 ARG ARG A . n A 1 118 LEU 118 116 116 LEU LEU A . n A 1 119 VAL 119 117 117 VAL VAL A . n A 1 120 VAL 120 118 118 VAL VAL A . n A 1 121 GLY 121 119 119 GLY GLY A . n A 1 122 ASP 122 120 120 ASP ASP A . n A 1 123 VAL 123 121 121 VAL VAL A . n A 1 124 THR 124 122 122 THR THR A . n A 1 125 VAL 125 123 123 VAL VAL A . n A 1 126 ALA 126 124 124 ALA ALA A . n A 1 127 ILE 127 125 125 ILE ILE A . n A 1 128 ALA 128 126 126 ALA ALA A . n A 1 129 MSE 129 127 127 MSE MSE A . n A 1 130 THR 130 128 128 THR THR A . n A 1 131 SER 131 129 129 SER SER A . n A 1 132 ASP 132 130 130 ASP ASP A . n A 1 133 ALA 133 131 ? ? ? A . n A 1 134 PRO 134 132 ? ? ? A . n A 1 135 HIS 135 133 ? ? ? A . n A 1 136 GLY 136 134 ? ? ? A . n A 1 137 SER 137 135 ? ? ? A . n A 1 138 ARG 138 136 ? ? ? A . n A 1 139 SER 139 137 ? ? ? A . n A 1 140 ALA 140 138 ? ? ? A . n A 1 141 ILE 141 139 ? ? ? A . n A 1 142 GLU 142 140 ? ? ? A . n A 1 143 TYR 143 141 ? ? ? A . n A 1 144 GLY 144 142 ? ? ? A . n A 1 145 GLU 145 143 ? ? ? A . n A 1 146 GLN 146 144 ? ? ? A . n A 1 147 GLU 147 145 ? ? ? A . n A 1 148 GLU 148 146 ? ? ? A . n A 1 149 GLY 149 147 ? ? ? A . n A 1 150 HIS 150 148 ? ? ? A . n A 1 151 HIS 151 149 ? ? ? A . n A 1 152 HIS 152 150 ? ? ? A . n A 1 153 HIS 153 151 ? ? ? A . n A 1 154 HIS 154 152 ? ? ? A . n A 1 155 HIS 155 153 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'New York SGX Research Center for Structural Genomics' _pdbx_SG_project.initial_of_center NYSGXRC # 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 1 201 1 SO4 SO4 A . C 3 HOH 1 301 1 HOH HOH A . C 3 HOH 2 302 2 HOH HOH A . C 3 HOH 3 304 4 HOH HOH A . C 3 HOH 4 305 5 HOH HOH A . C 3 HOH 5 306 6 HOH HOH A . C 3 HOH 6 307 7 HOH HOH A . C 3 HOH 7 308 8 HOH HOH A . C 3 HOH 8 309 9 HOH HOH A . C 3 HOH 9 310 10 HOH HOH A . C 3 HOH 10 311 11 HOH HOH A . C 3 HOH 11 312 12 HOH HOH A . C 3 HOH 12 313 13 HOH HOH A . C 3 HOH 13 314 14 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 83 A MSE 81 ? MET SELENOMETHIONINE 2 A MSE 129 A MSE 127 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_assembly_prop.biol_id 1 _pdbx_struct_assembly_prop.type 'ABSA (A^2)' _pdbx_struct_assembly_prop.value 1170 _pdbx_struct_assembly_prop.details ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 17_555 x-y+1/3,-y+2/3,-z+2/3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 41.5824984378 0.0000000000 0.0000000000 -1.0000000000 94.0460000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2008-01-22 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2018-11-14 5 'Structure model' 1 4 2021-02-03 # _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' 'Source and taxonomy' 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Refinement description' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Structure summary' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' 8 5 'Structure model' 'Structure summary' # 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' audit_author 3 5 'Structure model' audit_author 4 5 'Structure model' citation_author 5 5 'Structure model' struct_conn 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.name' 2 4 'Structure model' '_audit_author.identifier_ORCID' 3 5 'Structure model' '_audit_author.identifier_ORCID' 4 5 'Structure model' '_citation_author.identifier_ORCID' 5 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 5 'Structure model' '_struct_ref_seq_dif.details' 7 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 8 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 9 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELX 'model building' . ? 1 REFMAC refinement 5.3.0034 ? 2 MAR345 'data collection' CCD ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 SHELXD phasing . ? 6 # 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 LYS A 48 ? ? -103.77 -95.29 2 1 GLU A 51 ? ? -142.88 -14.05 3 1 THR A 82 ? ? -105.08 -78.58 4 1 SER A 84 ? ? -99.97 42.09 # loop_ _pdbx_validate_peptide_omega.id _pdbx_validate_peptide_omega.PDB_model_num _pdbx_validate_peptide_omega.auth_comp_id_1 _pdbx_validate_peptide_omega.auth_asym_id_1 _pdbx_validate_peptide_omega.auth_seq_id_1 _pdbx_validate_peptide_omega.PDB_ins_code_1 _pdbx_validate_peptide_omega.label_alt_id_1 _pdbx_validate_peptide_omega.auth_comp_id_2 _pdbx_validate_peptide_omega.auth_asym_id_2 _pdbx_validate_peptide_omega.auth_seq_id_2 _pdbx_validate_peptide_omega.PDB_ins_code_2 _pdbx_validate_peptide_omega.label_alt_id_2 _pdbx_validate_peptide_omega.omega 1 1 LEU A 47 ? ? LYS A 48 ? ? -146.02 2 1 ALA A 107 ? ? GLY A 108 ? ? -68.00 # 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 MSE -1 ? A MSE 1 2 1 Y 1 A SER 0 ? A SER 2 3 1 Y 1 A LEU 1 ? A LEU 3 4 1 Y 1 A GLU 2 ? A GLU 4 5 1 Y 1 A LEU 3 ? A LEU 5 6 1 Y 1 A GLY 4 ? A GLY 6 7 1 Y 1 A GLN 5 ? A GLN 7 8 1 Y 1 A ALA 6 ? A ALA 8 9 1 Y 1 A MSE 7 ? A MSE 9 10 1 Y 1 A ALA 131 ? A ALA 133 11 1 Y 1 A PRO 132 ? A PRO 134 12 1 Y 1 A HIS 133 ? A HIS 135 13 1 Y 1 A GLY 134 ? A GLY 136 14 1 Y 1 A SER 135 ? A SER 137 15 1 Y 1 A ARG 136 ? A ARG 138 16 1 Y 1 A SER 137 ? A SER 139 17 1 Y 1 A ALA 138 ? A ALA 140 18 1 Y 1 A ILE 139 ? A ILE 141 19 1 Y 1 A GLU 140 ? A GLU 142 20 1 Y 1 A TYR 141 ? A TYR 143 21 1 Y 1 A GLY 142 ? A GLY 144 22 1 Y 1 A GLU 143 ? A GLU 145 23 1 Y 1 A GLN 144 ? A GLN 146 24 1 Y 1 A GLU 145 ? A GLU 147 25 1 Y 1 A GLU 146 ? A GLU 148 26 1 Y 1 A GLY 147 ? A GLY 149 27 1 Y 1 A HIS 148 ? A HIS 150 28 1 Y 1 A HIS 149 ? A HIS 151 29 1 Y 1 A HIS 150 ? A HIS 152 30 1 Y 1 A HIS 151 ? A HIS 153 31 1 Y 1 A HIS 152 ? A HIS 154 32 1 Y 1 A HIS 153 ? A HIS 155 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 water HOH #