data_3BJ9 # _entry.id 3BJ9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.314 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3BJ9 RCSB RCSB045588 WWPDB D_1000045588 # _pdbx_database_status.entry_id 3BJ9 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-12-03 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Morstadt, L.M.' 1 'Bohm, A.A.' 2 'Stollar, B.D.' 3 'Baleja, J.D.' 4 # _citation.id primary _citation.title 'Engineering and characterization of a single chain surrogate light chain variable domain.' _citation.journal_abbrev 'Protein Sci.' _citation.journal_volume 17 _citation.page_first 458 _citation.page_last 465 _citation.year 2008 _citation.journal_id_ASTM PRCIEI _citation.country US _citation.journal_id_ISSN 0961-8368 _citation.journal_id_CSD 0795 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18287279 _citation.pdbx_database_id_DOI 10.1110/ps.073269808 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Morstadt, L.' 1 ? primary 'Bohm, A.' 2 ? primary 'Yuksel, D.' 3 ? primary 'Kumar, K.' 4 ? primary 'Stollar, B.D.' 5 ? primary 'Baleja, J.D.' 6 ? # _cell.entry_id 3BJ9 _cell.length_a 43.811 _cell.length_b 67.176 _cell.length_c 99.830 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 3BJ9 _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 'Immunoglobulin iota chain, Immunoglobulin lambda-like polypeptide 1' 12937.543 1 ? 'Ig domain of VpreB fused to J-segment of 14.1' 'Fusion protein consists of Ig domain of VPREB protein and J-fragment of Ig lambda-5' ? 2 non-polymer syn 1,2-ETHANEDIOL 62.068 3 ? ? ? ? 3 water nat water 18.015 111 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name ;Vpre, B protein, VpreB protein, CD179a antigen, Immunoglobulin-related protein 14.1, Immunoglobulin omega polypeptide, Ig lambda-5, CD179b antigen ; # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;VLHQPPAMSSALGTTIRLTCTLRNDHDIGVYSVYWYQQRPGHPPRFLLRYFSQSDKSQGPQVPPRFSGSKDVARNRGYLS ISELQPEDEAMYYCAMGARSTHVFGSGTQLTVLSAA ; _entity_poly.pdbx_seq_one_letter_code_can ;VLHQPPAMSSALGTTIRLTCTLRNDHDIGVYSVYWYQQRPGHPPRFLLRYFSQSDKSQGPQVPPRFSGSKDVARNRGYLS ISELQPEDEAMYYCAMGARSTHVFGSGTQLTVLSAA ; _entity_poly.pdbx_strand_id 1 _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 VAL n 1 2 LEU n 1 3 HIS n 1 4 GLN n 1 5 PRO n 1 6 PRO n 1 7 ALA n 1 8 MET n 1 9 SER n 1 10 SER n 1 11 ALA n 1 12 LEU n 1 13 GLY n 1 14 THR n 1 15 THR n 1 16 ILE n 1 17 ARG n 1 18 LEU n 1 19 THR n 1 20 CYS n 1 21 THR n 1 22 LEU n 1 23 ARG n 1 24 ASN n 1 25 ASP n 1 26 HIS n 1 27 ASP n 1 28 ILE n 1 29 GLY n 1 30 VAL n 1 31 TYR n 1 32 SER n 1 33 VAL n 1 34 TYR n 1 35 TRP n 1 36 TYR n 1 37 GLN n 1 38 GLN n 1 39 ARG n 1 40 PRO n 1 41 GLY n 1 42 HIS n 1 43 PRO n 1 44 PRO n 1 45 ARG n 1 46 PHE n 1 47 LEU n 1 48 LEU n 1 49 ARG n 1 50 TYR n 1 51 PHE n 1 52 SER n 1 53 GLN n 1 54 SER n 1 55 ASP n 1 56 LYS n 1 57 SER n 1 58 GLN n 1 59 GLY n 1 60 PRO n 1 61 GLN n 1 62 VAL n 1 63 PRO n 1 64 PRO n 1 65 ARG n 1 66 PHE n 1 67 SER n 1 68 GLY n 1 69 SER n 1 70 LYS n 1 71 ASP n 1 72 VAL n 1 73 ALA n 1 74 ARG n 1 75 ASN n 1 76 ARG n 1 77 GLY n 1 78 TYR n 1 79 LEU n 1 80 SER n 1 81 ILE n 1 82 SER n 1 83 GLU n 1 84 LEU n 1 85 GLN n 1 86 PRO n 1 87 GLU n 1 88 ASP n 1 89 GLU n 1 90 ALA n 1 91 MET n 1 92 TYR n 1 93 TYR n 1 94 CYS n 1 95 ALA n 1 96 MET n 1 97 GLY n 1 98 ALA n 1 99 ARG n 1 100 SER n 1 101 THR n 1 102 HIS n 1 103 VAL n 1 104 PHE n 1 105 GLY n 1 106 SER n 1 107 GLY n 1 108 THR n 1 109 GLN n 1 110 LEU n 1 111 THR n 1 112 VAL n 1 113 LEU n 1 114 SER n 1 115 ALA n 1 116 ALA 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 human _entity_src_gen.gene_src_genus Homo _entity_src_gen.pdbx_gene_src_gene 'VPREB1, VPREB' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 'BL21(DE)pLysE' _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 pIg203 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code VPREB_HUMAN _struct_ref.pdbx_db_accession P12018 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;VLHQPPAMSSALGTTIRLTCTLRNDHDIGVYSVYWYQQRPGHPPRFLLRYFSQSDKSQGPQVPPRFSGSKDVARNRGYLS ISELQPEDEAMYYCAMGARSS ; _struct_ref.pdbx_align_begin 22 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3BJ9 _struct_ref_seq.pdbx_strand_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 100 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P12018 _struct_ref_seq.db_align_beg 22 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 121 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 3 _struct_ref_seq.pdbx_auth_seq_align_end 102 # 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 3BJ9 THR 1 101 ? UNP P12018 ? ? 'SEE REMARK 999' 103 1 1 3BJ9 HIS 1 102 ? UNP P12018 ? ? 'SEE REMARK 999' 104 2 1 3BJ9 VAL 1 103 ? UNP P12018 ? ? 'SEE REMARK 999' 105 3 1 3BJ9 PHE 1 104 ? UNP P12018 ? ? 'SEE REMARK 999' 106 4 1 3BJ9 GLY 1 105 ? UNP P12018 ? ? 'SEE REMARK 999' 107 5 1 3BJ9 GLY 1 107 ? UNP P12018 ? ? 'SEE REMARK 999' 109 6 1 3BJ9 THR 1 108 ? UNP P12018 ? ? 'SEE REMARK 999' 110 7 1 3BJ9 GLN 1 109 ? UNP P12018 ? ? 'SEE REMARK 999' 111 8 1 3BJ9 LEU 1 110 ? UNP P12018 ? ? 'SEE REMARK 999' 112 9 1 3BJ9 THR 1 111 ? UNP P12018 ? ? 'SEE REMARK 999' 113 10 1 3BJ9 VAL 1 112 ? UNP P12018 ? ? 'SEE REMARK 999' 114 11 1 3BJ9 LEU 1 113 ? UNP P12018 ? ? 'SEE REMARK 999' 115 12 1 3BJ9 SER 1 114 ? UNP P12018 ? ? 'SEE REMARK 999' 116 13 1 3BJ9 ALA 1 115 ? UNP P12018 ? ? 'EXPRESSION TAG' 117 14 1 3BJ9 ALA 1 116 ? UNP P12018 ? ? 'EXPRESSION TAG' 118 15 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 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 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3BJ9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.84 _exptl_crystal.density_percent_sol 56.62 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details ;0.1M Imidazole, 1M Sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _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 OXFORD _diffrn_detector.pdbx_collection_date 2006-11-30 _diffrn_detector.details mirrors # _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 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'SEALED TUBE' _diffrn_source.type 'OXFORD DIFFRACTION ENHANCE ULTRA' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 3BJ9 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 55.73 _reflns.d_resolution_high 2 _reflns.number_obs 9712 _reflns.number_all 9774 _reflns.percent_possible_obs 99.36 _reflns.pdbx_Rmerge_I_obs 0.09 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 17.5 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 7.7 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.d_res_high 2.000 _reflns_shell.d_res_low 2.050 _reflns_shell.percent_possible_all 92.38 _reflns_shell.Rmerge_I_obs 0.235 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 7.3 _reflns_shell.pdbx_redundancy 5.6 _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_diffrn_id ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_Rrim_I_all ? # _refine.entry_id 3BJ9 _refine.ls_number_reflns_obs 9712 _refine.ls_number_reflns_all 9774 _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 15.97 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 99.36 _refine.ls_R_factor_obs 0.18338 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.18096 _refine.ls_R_factor_R_free 0.23015 _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 519 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.939 _refine.correlation_coeff_Fo_to_Fc_free 0.895 _refine.B_iso_mean 14.819 _refine.aniso_B[1][1] -0.05 _refine.aniso_B[2][2] 0.08 _refine.aniso_B[3][3] -0.03 _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 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 'MOLECULAR REPLACEMENT' _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 0.165 _refine.pdbx_overall_ESU_R_Free 0.157 _refine.overall_SU_ML 0.094 _refine.overall_SU_B 3.250 _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 960 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 111 _refine_hist.number_atoms_total 1083 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 15.97 # 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 0.011 0.021 ? 1000 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.622 1.941 ? 1361 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 15.567 5.000 ? 129 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 31.453 22.500 ? 48 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 14.724 15.000 ? 158 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 12.762 15.000 ? 11 'X-RAY DIFFRACTION' ? r_chiral_restr 0.134 0.200 ? 141 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 792 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.221 0.200 ? 438 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.307 0.200 ? 655 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.197 0.200 ? 110 '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 0.281 0.200 ? 50 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.179 0.200 ? 18 '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 0.831 1.500 ? 632 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.344 2.000 ? 989 'X-RAY DIFFRACTION' ? r_scbond_it 1.754 3.000 ? 425 'X-RAY DIFFRACTION' ? r_scangle_it 2.544 4.500 ? 368 '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 2.000 _refine_ls_shell.d_res_low 2.050 _refine_ls_shell.number_reflns_R_work 635 _refine_ls_shell.R_factor_R_work 0.183 _refine_ls_shell.percent_reflns_obs 92.38 _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 44 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_obs ? # _struct.entry_id 3BJ9 _struct.title 'Crystal structure of the Surrogate Light Chain Variable Domain VpreBJ' _struct.pdbx_descriptor 'Immunoglobulin iota chain' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3BJ9 _struct_keywords.pdbx_keywords 'IMMUNE SYSTEM' _struct_keywords.text 'immunoglobulin domain, beta sheet, Polymorphism, IMMUNE SYSTEM' # 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 3 ? # 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 ASP A 27 ? TYR A 31 ? ASP 1 29 TYR 1 33 5 ? 5 HELX_P HELX_P2 2 VAL A 72 ? ARG A 74 ? VAL 1 74 ARG 1 76 5 ? 3 HELX_P HELX_P3 3 GLN A 85 ? GLU A 89 ? GLN 1 87 GLU 1 91 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_conn.id disulf1 _struct_conn.conn_type_id disulf _struct_conn.pdbx_leaving_atom_flag ? _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 20 _struct_conn.ptnr1_label_atom_id SG _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 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 94 _struct_conn.ptnr2_label_atom_id SG _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id 1 _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 22 _struct_conn.ptnr2_auth_asym_id 1 _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 96 _struct_conn.ptnr2_symmetry 1_555 _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 2.017 _struct_conn.pdbx_value_order ? # _struct_conn_type.id disulf _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 ARG 23 A . ? ARG 25 1 ASN 24 A ? ASN 26 1 1 -17.32 2 ARG 99 A . ? ARG 101 1 SER 100 A ? SER 102 1 1 -23.23 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 6 ? C ? 4 ? # 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 B 1 2 ? parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel B 5 6 ? anti-parallel C 1 2 ? parallel C 2 3 ? anti-parallel C 3 4 ? 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 2 ? HIS A 3 ? LEU 1 4 HIS 1 5 A 2 ILE A 16 ? LEU A 22 ? ILE 1 18 LEU 1 24 A 3 ARG A 76 ? ILE A 81 ? ARG 1 78 ILE 1 83 A 4 PHE A 66 ? ASP A 71 ? PHE 1 68 ASP 1 73 B 1 ALA A 7 ? ALA A 11 ? ALA 1 9 ALA 1 13 B 2 THR A 108 ? LEU A 113 ? THR 1 110 LEU 1 115 B 3 ALA A 90 ? MET A 96 ? ALA 1 92 MET 1 98 B 4 VAL A 33 ? GLN A 38 ? VAL 1 35 GLN 1 40 B 5 ARG A 45 ? SER A 52 ? ARG 1 47 SER 1 54 B 6 ASP A 55 ? GLN A 58 ? ASP 1 57 GLN 1 60 C 1 ALA A 7 ? ALA A 11 ? ALA 1 9 ALA 1 13 C 2 THR A 108 ? LEU A 113 ? THR 1 110 LEU 1 115 C 3 ALA A 90 ? MET A 96 ? ALA 1 92 MET 1 98 C 4 VAL A 103 ? PHE A 104 ? VAL 1 105 PHE 1 106 # 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 HIS A 3 ? N HIS 1 5 O THR A 21 ? O THR 1 23 A 2 3 N LEU A 18 ? N LEU 1 20 O LEU A 79 ? O LEU 1 81 A 3 4 O SER A 80 ? O SER 1 82 N SER A 67 ? N SER 1 69 B 1 2 N SER A 10 ? N SER 1 12 O LEU A 113 ? O LEU 1 115 B 2 3 O LEU A 110 ? O LEU 1 112 N ALA A 90 ? N ALA 1 92 B 3 4 O ALA A 95 ? O ALA 1 97 N TYR A 34 ? N TYR 1 36 B 4 5 N VAL A 33 ? N VAL 1 35 O TYR A 50 ? O TYR 1 52 B 5 6 N ARG A 49 ? N ARG 1 51 O SER A 57 ? O SER 1 59 C 1 2 N SER A 10 ? N SER 1 12 O LEU A 113 ? O LEU 1 115 C 2 3 O LEU A 110 ? O LEU 1 112 N ALA A 90 ? N ALA 1 92 C 3 4 N MET A 96 ? N MET 1 98 O VAL A 103 ? O VAL 1 105 # 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 ? ? ? ? 4 'BINDING SITE FOR RESIDUE EDO 1 1' AC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE EDO 1 119' AC3 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE EDO 1 120' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 GLN A 58 ? GLN 1 60 . ? 1_555 ? 2 AC1 4 GLY A 59 ? GLY 1 61 . ? 1_555 ? 3 AC1 4 HOH E . ? HOH 1 180 . ? 1_555 ? 4 AC1 4 HOH E . ? HOH 1 205 . ? 1_555 ? 5 AC2 6 GLN A 37 ? GLN 1 39 . ? 1_555 ? 6 AC2 6 ARG A 45 ? ARG 1 47 . ? 1_555 ? 7 AC2 6 PRO A 63 ? PRO 1 65 . ? 1_555 ? 8 AC2 6 HOH E . ? HOH 1 136 . ? 1_555 ? 9 AC2 6 HOH E . ? HOH 1 201 . ? 1_555 ? 10 AC2 6 HOH E . ? HOH 1 224 . ? 1_555 ? 11 AC3 5 PRO A 6 ? PRO 1 8 . ? 1_555 ? 12 AC3 5 SER A 106 ? SER 1 108 . ? 1_555 ? 13 AC3 5 GLY A 107 ? GLY 1 109 . ? 1_555 ? 14 AC3 5 HOH E . ? HOH 1 199 . ? 1_555 ? 15 AC3 5 HOH E . ? HOH 1 231 . ? 1_555 ? # _atom_sites.entry_id 3BJ9 _atom_sites.fract_transf_matrix[1][1] 0.022825 _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] 0.014886 _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] 0.010017 _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 # 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 VAL 1 3 3 VAL VAL 1 . n A 1 2 LEU 2 4 4 LEU LEU 1 . n A 1 3 HIS 3 5 5 HIS HIS 1 . n A 1 4 GLN 4 6 6 GLN GLN 1 . n A 1 5 PRO 5 7 7 PRO PRO 1 . n A 1 6 PRO 6 8 8 PRO PRO 1 . n A 1 7 ALA 7 9 9 ALA ALA 1 . n A 1 8 MET 8 10 10 MET MET 1 . n A 1 9 SER 9 11 11 SER SER 1 . n A 1 10 SER 10 12 12 SER SER 1 . n A 1 11 ALA 11 13 13 ALA ALA 1 . n A 1 12 LEU 12 14 14 LEU LEU 1 . n A 1 13 GLY 13 15 15 GLY GLY 1 . n A 1 14 THR 14 16 16 THR THR 1 . n A 1 15 THR 15 17 17 THR THR 1 . n A 1 16 ILE 16 18 18 ILE ILE 1 . n A 1 17 ARG 17 19 19 ARG ARG 1 . n A 1 18 LEU 18 20 20 LEU LEU 1 . n A 1 19 THR 19 21 21 THR THR 1 . n A 1 20 CYS 20 22 22 CYS CYS 1 . n A 1 21 THR 21 23 23 THR THR 1 . n A 1 22 LEU 22 24 24 LEU LEU 1 . n A 1 23 ARG 23 25 25 ARG ARG 1 . n A 1 24 ASN 24 26 26 ASN ASN 1 . n A 1 25 ASP 25 27 27 ASP ASP 1 . n A 1 26 HIS 26 28 28 HIS HIS 1 . n A 1 27 ASP 27 29 29 ASP ASP 1 . n A 1 28 ILE 28 30 30 ILE ILE 1 . n A 1 29 GLY 29 31 31 GLY GLY 1 . n A 1 30 VAL 30 32 32 VAL VAL 1 . n A 1 31 TYR 31 33 33 TYR TYR 1 . n A 1 32 SER 32 34 34 SER SER 1 . n A 1 33 VAL 33 35 35 VAL VAL 1 . n A 1 34 TYR 34 36 36 TYR TYR 1 . n A 1 35 TRP 35 37 37 TRP TRP 1 . n A 1 36 TYR 36 38 38 TYR TYR 1 . n A 1 37 GLN 37 39 39 GLN GLN 1 . n A 1 38 GLN 38 40 40 GLN GLN 1 . n A 1 39 ARG 39 41 41 ARG ARG 1 . n A 1 40 PRO 40 42 42 PRO PRO 1 . n A 1 41 GLY 41 43 43 GLY GLY 1 . n A 1 42 HIS 42 44 44 HIS HIS 1 . n A 1 43 PRO 43 45 45 PRO PRO 1 . n A 1 44 PRO 44 46 46 PRO PRO 1 . n A 1 45 ARG 45 47 47 ARG ARG 1 . n A 1 46 PHE 46 48 48 PHE PHE 1 . n A 1 47 LEU 47 49 49 LEU LEU 1 . n A 1 48 LEU 48 50 50 LEU LEU 1 . n A 1 49 ARG 49 51 51 ARG ARG 1 . n A 1 50 TYR 50 52 52 TYR TYR 1 . n A 1 51 PHE 51 53 53 PHE PHE 1 . n A 1 52 SER 52 54 54 SER SER 1 . n A 1 53 GLN 53 55 55 GLN GLN 1 . n A 1 54 SER 54 56 56 SER SER 1 . n A 1 55 ASP 55 57 57 ASP ASP 1 . n A 1 56 LYS 56 58 58 LYS LYS 1 . n A 1 57 SER 57 59 59 SER SER 1 . n A 1 58 GLN 58 60 60 GLN GLN 1 . n A 1 59 GLY 59 61 61 GLY GLY 1 . n A 1 60 PRO 60 62 62 PRO PRO 1 . n A 1 61 GLN 61 63 63 GLN GLN 1 . n A 1 62 VAL 62 64 64 VAL VAL 1 . n A 1 63 PRO 63 65 65 PRO PRO 1 . n A 1 64 PRO 64 66 66 PRO PRO 1 . n A 1 65 ARG 65 67 67 ARG ARG 1 . n A 1 66 PHE 66 68 68 PHE PHE 1 . n A 1 67 SER 67 69 69 SER SER 1 . n A 1 68 GLY 68 70 70 GLY GLY 1 . n A 1 69 SER 69 71 71 SER SER 1 . n A 1 70 LYS 70 72 72 LYS LYS 1 . n A 1 71 ASP 71 73 73 ASP ASP 1 . n A 1 72 VAL 72 74 74 VAL VAL 1 . n A 1 73 ALA 73 75 75 ALA ALA 1 . n A 1 74 ARG 74 76 76 ARG ARG 1 . n A 1 75 ASN 75 77 77 ASN ASN 1 . n A 1 76 ARG 76 78 78 ARG ARG 1 . n A 1 77 GLY 77 79 79 GLY GLY 1 . n A 1 78 TYR 78 80 80 TYR TYR 1 . n A 1 79 LEU 79 81 81 LEU LEU 1 . n A 1 80 SER 80 82 82 SER SER 1 . n A 1 81 ILE 81 83 83 ILE ILE 1 . n A 1 82 SER 82 84 84 SER SER 1 . n A 1 83 GLU 83 85 85 GLU GLU 1 . n A 1 84 LEU 84 86 86 LEU LEU 1 . n A 1 85 GLN 85 87 87 GLN GLN 1 . n A 1 86 PRO 86 88 88 PRO PRO 1 . n A 1 87 GLU 87 89 89 GLU GLU 1 . n A 1 88 ASP 88 90 90 ASP ASP 1 . n A 1 89 GLU 89 91 91 GLU GLU 1 . n A 1 90 ALA 90 92 92 ALA ALA 1 . n A 1 91 MET 91 93 93 MET MET 1 . n A 1 92 TYR 92 94 94 TYR TYR 1 . n A 1 93 TYR 93 95 95 TYR TYR 1 . n A 1 94 CYS 94 96 96 CYS CYS 1 . n A 1 95 ALA 95 97 97 ALA ALA 1 . n A 1 96 MET 96 98 98 MET MET 1 . n A 1 97 GLY 97 99 99 GLY GLY 1 . n A 1 98 ALA 98 100 100 ALA ALA 1 . n A 1 99 ARG 99 101 101 ARG ARG 1 . n A 1 100 SER 100 102 102 SER SER 1 . n A 1 101 THR 101 103 103 THR THR 1 . n A 1 102 HIS 102 104 104 HIS HIS 1 . n A 1 103 VAL 103 105 105 VAL VAL 1 . n A 1 104 PHE 104 106 106 PHE PHE 1 . n A 1 105 GLY 105 107 107 GLY GLY 1 . n A 1 106 SER 106 108 108 SER SER 1 . n A 1 107 GLY 107 109 109 GLY GLY 1 . n A 1 108 THR 108 110 110 THR THR 1 . n A 1 109 GLN 109 111 111 GLN GLN 1 . n A 1 110 LEU 110 112 112 LEU LEU 1 . n A 1 111 THR 111 113 113 THR THR 1 . n A 1 112 VAL 112 114 114 VAL VAL 1 . n A 1 113 LEU 113 115 115 LEU LEU 1 . n A 1 114 SER 114 116 116 SER SER 1 . n A 1 115 ALA 115 117 117 ALA ALA 1 . n A 1 116 ALA 116 118 118 ALA ALA 1 . n # 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 EDO 1 1 1 EDO EDO 1 . C 2 EDO 1 119 1 EDO EDO 1 . D 2 EDO 1 120 1 EDO EDO 1 . E 3 HOH 1 121 4 HOH HOH 1 . E 3 HOH 2 122 6 HOH HOH 1 . E 3 HOH 3 123 7 HOH HOH 1 . E 3 HOH 4 124 9 HOH HOH 1 . E 3 HOH 5 125 11 HOH HOH 1 . E 3 HOH 6 126 16 HOH HOH 1 . E 3 HOH 7 127 17 HOH HOH 1 . E 3 HOH 8 128 18 HOH HOH 1 . E 3 HOH 9 129 19 HOH HOH 1 . E 3 HOH 10 130 20 HOH HOH 1 . E 3 HOH 11 131 21 HOH HOH 1 . E 3 HOH 12 132 22 HOH HOH 1 . E 3 HOH 13 133 23 HOH HOH 1 . E 3 HOH 14 134 24 HOH HOH 1 . E 3 HOH 15 135 25 HOH HOH 1 . E 3 HOH 16 136 26 HOH HOH 1 . E 3 HOH 17 137 27 HOH HOH 1 . E 3 HOH 18 138 28 HOH HOH 1 . E 3 HOH 19 139 29 HOH HOH 1 . E 3 HOH 20 140 30 HOH HOH 1 . E 3 HOH 21 141 31 HOH HOH 1 . E 3 HOH 22 142 32 HOH HOH 1 . E 3 HOH 23 143 35 HOH HOH 1 . E 3 HOH 24 144 37 HOH HOH 1 . E 3 HOH 25 145 38 HOH HOH 1 . E 3 HOH 26 146 42 HOH HOH 1 . E 3 HOH 27 147 43 HOH HOH 1 . E 3 HOH 28 148 44 HOH HOH 1 . E 3 HOH 29 149 46 HOH HOH 1 . E 3 HOH 30 150 47 HOH HOH 1 . E 3 HOH 31 151 50 HOH HOH 1 . E 3 HOH 32 152 51 HOH HOH 1 . E 3 HOH 33 153 52 HOH HOH 1 . E 3 HOH 34 154 53 HOH HOH 1 . E 3 HOH 35 155 54 HOH HOH 1 . E 3 HOH 36 156 55 HOH HOH 1 . E 3 HOH 37 157 56 HOH HOH 1 . E 3 HOH 38 158 58 HOH HOH 1 . E 3 HOH 39 159 60 HOH HOH 1 . E 3 HOH 40 160 61 HOH HOH 1 . E 3 HOH 41 161 63 HOH HOH 1 . E 3 HOH 42 162 64 HOH HOH 1 . E 3 HOH 43 163 65 HOH HOH 1 . E 3 HOH 44 164 68 HOH HOH 1 . E 3 HOH 45 165 69 HOH HOH 1 . E 3 HOH 46 166 70 HOH HOH 1 . E 3 HOH 47 167 71 HOH HOH 1 . E 3 HOH 48 168 72 HOH HOH 1 . E 3 HOH 49 169 74 HOH HOH 1 . E 3 HOH 50 170 75 HOH HOH 1 . E 3 HOH 51 171 77 HOH HOH 1 . E 3 HOH 52 172 78 HOH HOH 1 . E 3 HOH 53 173 79 HOH HOH 1 . E 3 HOH 54 174 80 HOH HOH 1 . E 3 HOH 55 175 82 HOH HOH 1 . E 3 HOH 56 176 83 HOH HOH 1 . E 3 HOH 57 177 84 HOH HOH 1 . E 3 HOH 58 178 85 HOH HOH 1 . E 3 HOH 59 179 86 HOH HOH 1 . E 3 HOH 60 180 87 HOH HOH 1 . E 3 HOH 61 181 88 HOH HOH 1 . E 3 HOH 62 182 90 HOH HOH 1 . E 3 HOH 63 183 92 HOH HOH 1 . E 3 HOH 64 184 93 HOH HOH 1 . E 3 HOH 65 185 94 HOH HOH 1 . E 3 HOH 66 186 95 HOH HOH 1 . E 3 HOH 67 187 96 HOH HOH 1 . E 3 HOH 68 188 2 HOH HOH 1 . E 3 HOH 69 189 3 HOH HOH 1 . E 3 HOH 70 190 4 HOH HOH 1 . E 3 HOH 71 191 7 HOH HOH 1 . E 3 HOH 72 192 8 HOH HOH 1 . E 3 HOH 73 193 10 HOH HOH 1 . E 3 HOH 74 194 3 HOH HOH 1 . E 3 HOH 75 195 4 HOH HOH 1 . E 3 HOH 76 196 6 HOH HOH 1 . E 3 HOH 77 197 7 HOH HOH 1 . E 3 HOH 78 198 8 HOH HOH 1 . E 3 HOH 79 199 9 HOH HOH 1 . E 3 HOH 80 200 11 HOH HOH 1 . E 3 HOH 81 201 13 HOH HOH 1 . E 3 HOH 82 202 14 HOH HOH 1 . E 3 HOH 83 203 15 HOH HOH 1 . E 3 HOH 84 204 16 HOH HOH 1 . E 3 HOH 85 205 19 HOH HOH 1 . E 3 HOH 86 206 20 HOH HOH 1 . E 3 HOH 87 207 22 HOH HOH 1 . E 3 HOH 88 208 23 HOH HOH 1 . E 3 HOH 89 209 26 HOH HOH 1 . E 3 HOH 90 210 27 HOH HOH 1 . E 3 HOH 91 211 36 HOH HOH 1 . E 3 HOH 92 212 39 HOH HOH 1 . E 3 HOH 93 213 45 HOH HOH 1 . E 3 HOH 94 214 53 HOH HOH 1 . E 3 HOH 95 215 59 HOH HOH 1 . E 3 HOH 96 216 60 HOH HOH 1 . E 3 HOH 97 217 62 HOH HOH 1 . E 3 HOH 98 218 64 HOH HOH 1 . E 3 HOH 99 219 65 HOH HOH 1 . E 3 HOH 100 220 67 HOH HOH 1 . E 3 HOH 101 221 3 HOH HOH 1 . E 3 HOH 102 222 4 HOH HOH 1 . E 3 HOH 103 223 5 HOH HOH 1 . E 3 HOH 104 224 6 HOH HOH 1 . E 3 HOH 105 225 11 HOH HOH 1 . E 3 HOH 106 226 18 HOH HOH 1 . E 3 HOH 107 227 1 HOH HOH 1 . E 3 HOH 108 228 1 HOH HOH 1 . E 3 HOH 109 229 2 HOH HOH 1 . E 3 HOH 110 230 3 HOH HOH 1 . E 3 HOH 111 231 6 HOH HOH 1 . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details 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 # _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 1 _pdbx_struct_special_symmetry.auth_comp_id ARG _pdbx_struct_special_symmetry.auth_seq_id 101 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id A _pdbx_struct_special_symmetry.label_comp_id ARG _pdbx_struct_special_symmetry.label_seq_id 99 # 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 2008-03-04 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2018-04-04 4 'Structure model' 1 3 2019-09-04 # _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' Advisory 3 3 'Structure model' 'Data collection' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' diffrn_source 2 3 'Structure model' pdbx_unobs_or_zero_occ_atoms 3 4 'Structure model' pdbx_struct_special_symmetry 4 4 'Structure model' reflns 5 4 'Structure model' reflns_shell # 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' '_diffrn_source.type' 2 4 'Structure model' '_reflns.pdbx_Rsym_value' 3 4 'Structure model' '_reflns_shell.pdbx_Rsym_value' # _phasing.method MR # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal MOSFLM . ? package 'A.G.W. Leslie' andrew@mrc-lmb.cam.ac.uk 'data reduction' http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ ? ? 1 MOLREP . ? other 'A. Vagin' alexei@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/molrep.html Fortran_77 ? 2 REFMAC 5.2.0003 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 3 PDB_EXTRACT 3.004 'September 10, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 4 SCALA . ? ? ? ? 'data scaling' ? ? ? 5 # _pdbx_entry_details.sequence_details ;THE 14 RESIDUES: THVFGSGTQLTVLS BELONG TO THE "J-SEGMENT, FUSED TO THE IG DOMAIN OF VPREB" ; _pdbx_entry_details.entry_id 3BJ9 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? # 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 NE2 1 GLN 87 ? ? OE1 1 GLU 89 ? A 2.08 2 1 O 1 HOH 140 ? ? O 1 HOH 230 ? ? 2.09 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N 1 THR 23 ? ? CA 1 THR 23 ? ? C 1 THR 23 ? ? 94.46 111.00 -16.54 2.70 N 2 1 CB 1 ASP 27 ? A CG 1 ASP 27 ? A OD2 1 ASP 27 ? A 124.40 118.30 6.10 0.90 N 3 1 CB 1 ASP 73 ? ? CG 1 ASP 73 ? ? OD2 1 ASP 73 ? ? 123.84 118.30 5.54 0.90 N 4 1 NH1 1 ARG 101 ? A CZ 1 ARG 101 ? A NH2 1 ARG 101 ? A 138.50 119.40 19.10 1.10 N 5 1 NE 1 ARG 101 ? A CZ 1 ARG 101 ? A NH2 1 ARG 101 ? A 101.71 120.30 -18.59 0.50 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 1 26 ? ? -167.47 7.08 2 1 ASN 1 26 ? ? -167.47 8.40 3 1 ALA 1 92 ? ? 178.60 174.69 4 1 ARG 1 101 ? A 114.62 -97.82 5 1 SER 1 102 ? ? 70.04 -76.93 6 1 SER 1 102 ? ? 78.63 -76.93 # 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 CYS 1 22 ? ? THR 1 23 ? ? -140.23 2 1 ALA 1 100 ? ? ARG 1 101 ? B -132.02 3 1 ARG 1 101 ? A SER 1 102 ? ? 53.01 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-ETHANEDIOL EDO 3 water HOH #