data_3B09 # _entry.id 3B09 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3B09 RCSB RCSB029915 WWPDB D_1000029915 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3B09 _pdbx_database_status.recvd_initial_deposition_date 2011-06-07 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Budiman, C.' 1 'Angkawidjaja, C.' 2 'Motoike, H.' 3 'Koga, Y.' 4 'Takano, K.' 5 'Kanaya, S.' 6 # _citation.id primary _citation.title 'Crystal structure of N-domain of FKBP22 from Shewanella sp. SIB1: dimer dissociation by disruption of Val-Leu knot' _citation.journal_abbrev 'Protein Sci.' _citation.journal_volume 20 _citation.page_first 1755 _citation.page_last 1764 _citation.year 2011 _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 21837652 _citation.pdbx_database_id_DOI 10.1002/pro.714 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Budiman, C.' 1 primary 'Angkawidjaja, C.' 2 primary 'Motoike, H.' 3 primary 'Koga, Y.' 4 primary 'Takano, K.' 5 primary 'Kanaya, S.' 6 # _cell.entry_id 3B09 _cell.length_a 39.703 _cell.length_b 39.703 _cell.length_c 101.600 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 3B09 _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _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 'Peptidyl-prolyl cis-trans isomerase' 9706.961 1 5.2.1.8 ? 'N-terminal domain, residues 1-68' ? 2 water nat water 18.015 28 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'FKBP22, FK506-binding protein' # _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)GSSHHHHHHSSGLVPRGSH(MSE)SDLFST(MSE)EQHASYGVGRQ(MSE)GEQLAANSFEGIDIPAVQAGLADA FAGKESAVS(MSE)EELQVAFTEISRRL ; _entity_poly.pdbx_seq_one_letter_code_can ;MGSSHHHHHHSSGLVPRGSHMSDLFSTMEQHASYGVGRQMGEQLAANSFEGIDIPAVQAGLADAFAGKESAVSMEELQVA FTEISRRL ; _entity_poly.pdbx_strand_id A _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 MSE n 1 2 GLY n 1 3 SER n 1 4 SER n 1 5 HIS n 1 6 HIS n 1 7 HIS n 1 8 HIS n 1 9 HIS n 1 10 HIS n 1 11 SER n 1 12 SER n 1 13 GLY n 1 14 LEU n 1 15 VAL n 1 16 PRO n 1 17 ARG n 1 18 GLY n 1 19 SER n 1 20 HIS n 1 21 MSE n 1 22 SER n 1 23 ASP n 1 24 LEU n 1 25 PHE n 1 26 SER n 1 27 THR n 1 28 MSE n 1 29 GLU n 1 30 GLN n 1 31 HIS n 1 32 ALA n 1 33 SER n 1 34 TYR n 1 35 GLY n 1 36 VAL n 1 37 GLY n 1 38 ARG n 1 39 GLN n 1 40 MSE n 1 41 GLY n 1 42 GLU n 1 43 GLN n 1 44 LEU n 1 45 ALA n 1 46 ALA n 1 47 ASN n 1 48 SER n 1 49 PHE n 1 50 GLU n 1 51 GLY n 1 52 ILE n 1 53 ASP n 1 54 ILE n 1 55 PRO n 1 56 ALA n 1 57 VAL n 1 58 GLN n 1 59 ALA n 1 60 GLY n 1 61 LEU n 1 62 ALA n 1 63 ASP n 1 64 ALA n 1 65 PHE n 1 66 ALA n 1 67 GLY n 1 68 LYS n 1 69 GLU n 1 70 SER n 1 71 ALA n 1 72 VAL n 1 73 SER n 1 74 MSE n 1 75 GLU n 1 76 GLU n 1 77 LEU n 1 78 GLN n 1 79 VAL n 1 80 ALA n 1 81 PHE n 1 82 THR n 1 83 GLU n 1 84 ILE n 1 85 SER n 1 86 ARG n 1 87 ARG n 1 88 LEU n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene fklB _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain SIB1 _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 Shewanella _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 117911 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _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 pET28a _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q765B0_9GAMM _struct_ref.pdbx_db_accession Q765B0 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code MSDLFSTMEQHASYGVGRQMGEQLAANSFEGIDIPAVQAGLADAFAGKESAVSMEELQVAFTEISRRL _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3B09 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 21 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 88 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q765B0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 68 _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 68 # 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 3B09 MSE A 1 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -19 1 1 3B09 GLY A 2 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -18 2 1 3B09 SER A 3 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -17 3 1 3B09 SER A 4 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -16 4 1 3B09 HIS A 5 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -15 5 1 3B09 HIS A 6 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -14 6 1 3B09 HIS A 7 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -13 7 1 3B09 HIS A 8 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -12 8 1 3B09 HIS A 9 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -11 9 1 3B09 HIS A 10 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -10 10 1 3B09 SER A 11 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -9 11 1 3B09 SER A 12 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -8 12 1 3B09 GLY A 13 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -7 13 1 3B09 LEU A 14 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -6 14 1 3B09 VAL A 15 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -5 15 1 3B09 PRO A 16 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -4 16 1 3B09 ARG A 17 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -3 17 1 3B09 GLY A 18 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -2 18 1 3B09 SER A 19 ? UNP Q765B0 ? ? 'EXPRESSION TAG' -1 19 1 3B09 HIS A 20 ? UNP Q765B0 ? ? 'EXPRESSION TAG' 0 20 # 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 3B09 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.38 _exptl_crystal.density_percent_sol 48.35 _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 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.2 _exptl_crystal_grow.pdbx_details '0.1M Na/K Phosphate, 20% PEG 1000, 0.2 M NaCl, pH 6.2, VAPOR DIFFUSION, SITTING 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 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2010-07-15 _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 mirrors _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 0.97888 1.0 2 0.97919 1.0 3 0.96500 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL44B2' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL44B2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.97888, 0.97919, 0.96500' # _reflns.entry_id 3B09 _reflns.observed_criterion_sigma_I 5.0 _reflns.observed_criterion_sigma_F 5.0 _reflns.d_resolution_low 50.0 _reflns.d_resolution_high 1.9 _reflns.number_obs 7712 _reflns.number_all ? _reflns.percent_possible_obs 98.3 _reflns.pdbx_Rmerge_I_obs 0.114 _reflns.pdbx_Rsym_value 0.119 _reflns.pdbx_netI_over_sigmaI 18.2 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.4 _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 1.90 _reflns_shell.d_res_low 1.93 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.423 _reflns_shell.pdbx_Rsym_value 0.398 _reflns_shell.meanI_over_sigI_obs 2.6 _reflns_shell.pdbx_redundancy 5.3 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 364 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3B09 _refine.ls_number_reflns_obs 7299 _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 34.38 _refine.ls_d_res_high 1.90 _refine.ls_percent_reflns_obs 97.95 _refine.ls_R_factor_obs 0.23386 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23179 _refine.ls_R_factor_R_free 0.27597 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 353 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.927 _refine.correlation_coeff_Fo_to_Fc_free 0.890 _refine.B_iso_mean 30.920 _refine.aniso_B[1][1] 1.03 _refine.aniso_B[2][2] 1.03 _refine.aniso_B[3][3] -1.54 _refine.aniso_B[1][2] 0.51 _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 1.40 _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_Free 0.143 _refine.overall_SU_ML 0.091 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 2.996 _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _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 487 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 28 _refine_hist.number_atoms_total 515 _refine_hist.d_res_high 1.90 _refine_hist.d_res_low 34.38 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.008 0.022 ? 497 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.015 1.939 ? 669 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 7.448 5.000 ? 66 ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 42.833 25.200 ? 25 ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 20.107 15.000 ? 83 ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 14.891 15.000 ? 3 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.082 0.200 ? 73 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.019 0.020 ? 385 ? 'X-RAY DIFFRACTION' r_mcbond_it 2.182 1.500 ? 322 ? 'X-RAY DIFFRACTION' r_mcangle_it 3.868 2.000 ? 507 ? 'X-RAY DIFFRACTION' r_scbond_it 6.682 3.000 ? 175 ? 'X-RAY DIFFRACTION' r_scangle_it 10.069 4.500 ? 161 ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.899 _refine_ls_shell.d_res_low 1.948 _refine_ls_shell.number_reflns_R_work 521 _refine_ls_shell.R_factor_R_work 0.278 _refine_ls_shell.percent_reflns_obs 99.27 _refine_ls_shell.R_factor_R_free 0.288 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 26 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? # _struct.entry_id 3B09 _struct.title 'Crystal structure of the N-domain of FKBP22 from Shewanella sp. SIB1' _struct.pdbx_descriptor 'Peptidyl-prolyl cis-trans isomerase (E.C.5.2.1.8)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3B09 _struct_keywords.pdbx_keywords CHAPERONE _struct_keywords.text 'Val-Leu zipper, helices, Chaperone' # 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 ? # _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 SER A 26 ? ASN A 47 ? SER A 6 ASN A 27 1 ? 22 HELX_P HELX_P2 2 ASP A 53 ? ALA A 66 ? ASP A 33 ALA A 46 1 ? 14 HELX_P HELX_P3 3 SER A 73 ? ARG A 86 ? SER A 53 ARG A 66 1 ? 14 # _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 THR 27 C ? ? ? 1_555 A MSE 28 N ? ? A THR 7 A MSE 8 1_555 ? ? ? ? ? ? ? 1.332 ? covale2 covale ? ? A MSE 28 C ? ? ? 1_555 A GLU 29 N ? ? A MSE 8 A GLU 9 1_555 ? ? ? ? ? ? ? 1.328 ? covale3 covale ? ? A GLN 39 C ? ? ? 1_555 A MSE 40 N ? ? A GLN 19 A MSE 20 1_555 ? ? ? ? ? ? ? 1.326 ? covale4 covale ? ? A MSE 40 C ? ? ? 1_555 A GLY 41 N ? ? A MSE 20 A GLY 21 1_555 ? ? ? ? ? ? ? 1.331 ? covale5 covale ? ? A SER 73 C ? ? ? 1_555 A MSE 74 N ? ? A SER 53 A MSE 54 1_555 ? ? ? ? ? ? ? 1.327 ? covale6 covale ? ? A MSE 74 C ? ? ? 1_555 A GLU 75 N ? ? A MSE 54 A GLU 55 1_555 ? ? ? ? ? ? ? 1.330 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 3B09 _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 3B09 _atom_sites.fract_transf_matrix[1][1] 0.025187 _atom_sites.fract_transf_matrix[1][2] 0.014542 _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] 0.029083 _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] 0.009843 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MSE 1 -19 ? ? ? A . n A 1 2 GLY 2 -18 ? ? ? A . n A 1 3 SER 3 -17 ? ? ? A . n A 1 4 SER 4 -16 ? ? ? A . n A 1 5 HIS 5 -15 ? ? ? A . n A 1 6 HIS 6 -14 ? ? ? A . n A 1 7 HIS 7 -13 ? ? ? A . n A 1 8 HIS 8 -12 ? ? ? A . n A 1 9 HIS 9 -11 ? ? ? A . n A 1 10 HIS 10 -10 ? ? ? A . n A 1 11 SER 11 -9 ? ? ? A . n A 1 12 SER 12 -8 ? ? ? A . n A 1 13 GLY 13 -7 ? ? ? A . n A 1 14 LEU 14 -6 ? ? ? A . n A 1 15 VAL 15 -5 ? ? ? A . n A 1 16 PRO 16 -4 ? ? ? A . n A 1 17 ARG 17 -3 ? ? ? A . n A 1 18 GLY 18 -2 ? ? ? A . n A 1 19 SER 19 -1 ? ? ? A . n A 1 20 HIS 20 0 ? ? ? A . n A 1 21 MSE 21 1 ? ? ? A . n A 1 22 SER 22 2 ? ? ? A . n A 1 23 ASP 23 3 3 ASP ASP A . n A 1 24 LEU 24 4 4 LEU LEU A . n A 1 25 PHE 25 5 5 PHE PHE A . n A 1 26 SER 26 6 6 SER SER A . n A 1 27 THR 27 7 7 THR THR A . n A 1 28 MSE 28 8 8 MSE MSE A . n A 1 29 GLU 29 9 9 GLU GLU A . n A 1 30 GLN 30 10 10 GLN GLN A . n A 1 31 HIS 31 11 11 HIS HIS A . n A 1 32 ALA 32 12 12 ALA ALA A . n A 1 33 SER 33 13 13 SER SER A . n A 1 34 TYR 34 14 14 TYR TYR A . n A 1 35 GLY 35 15 15 GLY GLY A . n A 1 36 VAL 36 16 16 VAL VAL A . n A 1 37 GLY 37 17 17 GLY GLY A . n A 1 38 ARG 38 18 18 ARG ARG A . n A 1 39 GLN 39 19 19 GLN GLN A . n A 1 40 MSE 40 20 20 MSE MSE A . n A 1 41 GLY 41 21 21 GLY GLY A . n A 1 42 GLU 42 22 22 GLU GLU A . n A 1 43 GLN 43 23 23 GLN GLN A . n A 1 44 LEU 44 24 24 LEU LEU A . n A 1 45 ALA 45 25 25 ALA ALA A . n A 1 46 ALA 46 26 26 ALA ALA A . n A 1 47 ASN 47 27 27 ASN ASN A . n A 1 48 SER 48 28 28 SER SER A . n A 1 49 PHE 49 29 29 PHE PHE A . n A 1 50 GLU 50 30 30 GLU GLU A . n A 1 51 GLY 51 31 31 GLY GLY A . n A 1 52 ILE 52 32 32 ILE ILE A . n A 1 53 ASP 53 33 33 ASP ASP A . n A 1 54 ILE 54 34 34 ILE ILE A . n A 1 55 PRO 55 35 35 PRO PRO A . n A 1 56 ALA 56 36 36 ALA ALA A . n A 1 57 VAL 57 37 37 VAL VAL A . n A 1 58 GLN 58 38 38 GLN GLN A . n A 1 59 ALA 59 39 39 ALA ALA A . n A 1 60 GLY 60 40 40 GLY GLY A . n A 1 61 LEU 61 41 41 LEU LEU A . n A 1 62 ALA 62 42 42 ALA ALA A . n A 1 63 ASP 63 43 43 ASP ASP A . n A 1 64 ALA 64 44 44 ALA ALA A . n A 1 65 PHE 65 45 45 PHE PHE A . n A 1 66 ALA 66 46 46 ALA ALA A . n A 1 67 GLY 67 47 47 GLY GLY A . n A 1 68 LYS 68 48 48 LYS LYS A . n A 1 69 GLU 69 49 49 GLU GLU A . n A 1 70 SER 70 50 50 SER SER A . n A 1 71 ALA 71 51 51 ALA ALA A . n A 1 72 VAL 72 52 52 VAL VAL A . n A 1 73 SER 73 53 53 SER SER A . n A 1 74 MSE 74 54 54 MSE MSE A . n A 1 75 GLU 75 55 55 GLU GLU A . n A 1 76 GLU 76 56 56 GLU GLU A . n A 1 77 LEU 77 57 57 LEU LEU A . n A 1 78 GLN 78 58 58 GLN GLN A . n A 1 79 VAL 79 59 59 VAL VAL A . n A 1 80 ALA 80 60 60 ALA ALA A . n A 1 81 PHE 81 61 61 PHE PHE A . n A 1 82 THR 82 62 62 THR THR A . n A 1 83 GLU 83 63 63 GLU GLU A . n A 1 84 ILE 84 64 64 ILE ILE A . n A 1 85 SER 85 65 65 SER SER A . n A 1 86 ARG 86 66 66 ARG ARG A . n A 1 87 ARG 87 67 67 ARG ARG A . n A 1 88 LEU 88 68 ? ? ? A . n # 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 28 A MSE 8 ? MET SELENOMETHIONINE 2 A MSE 40 A MSE 20 ? MET SELENOMETHIONINE 3 A MSE 74 A MSE 54 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4120 ? 1 MORE -45 ? 1 'SSA (A^2)' 8070 ? # 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' 5_555 x-y,-y,-z+1/3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 33.8666666667 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2012-04-18 # _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_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal BL44 'data collection' BSS ? 1 SHELXS phasing . ? 2 REFMAC refinement 5.5.0109 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # 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 4 ? ? -38.15 -34.33 2 1 SER A 6 ? ? -104.72 42.57 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 0 A GLU 49 ? CD ? A GLU 69 CD 2 1 Y 0 A GLU 49 ? OE1 ? A GLU 69 OE1 3 1 Y 0 A GLU 49 ? OE2 ? A GLU 69 OE2 # 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 -19 ? A MSE 1 2 1 Y 1 A GLY -18 ? A GLY 2 3 1 Y 1 A SER -17 ? A SER 3 4 1 Y 1 A SER -16 ? A SER 4 5 1 Y 1 A HIS -15 ? A HIS 5 6 1 Y 1 A HIS -14 ? A HIS 6 7 1 Y 1 A HIS -13 ? A HIS 7 8 1 Y 1 A HIS -12 ? A HIS 8 9 1 Y 1 A HIS -11 ? A HIS 9 10 1 Y 1 A HIS -10 ? A HIS 10 11 1 Y 1 A SER -9 ? A SER 11 12 1 Y 1 A SER -8 ? A SER 12 13 1 Y 1 A GLY -7 ? A GLY 13 14 1 Y 1 A LEU -6 ? A LEU 14 15 1 Y 1 A VAL -5 ? A VAL 15 16 1 Y 1 A PRO -4 ? A PRO 16 17 1 Y 1 A ARG -3 ? A ARG 17 18 1 Y 1 A GLY -2 ? A GLY 18 19 1 Y 1 A SER -1 ? A SER 19 20 1 Y 1 A HIS 0 ? A HIS 20 21 1 Y 1 A MSE 1 ? A MSE 21 22 1 Y 1 A SER 2 ? A SER 22 23 1 Y 1 A LEU 68 ? A LEU 88 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # 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 HOH 1 69 1 HOH HOH A . B 2 HOH 2 70 2 HOH HOH A . B 2 HOH 3 71 3 HOH HOH A . B 2 HOH 4 72 6 HOH HOH A . B 2 HOH 5 73 8 HOH HOH A . B 2 HOH 6 74 9 HOH HOH A . B 2 HOH 7 75 10 HOH HOH A . B 2 HOH 8 76 13 HOH HOH A . B 2 HOH 9 77 14 HOH HOH A . B 2 HOH 10 78 15 HOH HOH A . B 2 HOH 11 79 16 HOH HOH A . B 2 HOH 12 80 17 HOH HOH A . B 2 HOH 13 81 21 HOH HOH A . B 2 HOH 14 82 22 HOH HOH A . B 2 HOH 15 83 23 HOH HOH A . B 2 HOH 16 84 24 HOH HOH A . B 2 HOH 17 85 25 HOH HOH A . B 2 HOH 18 86 26 HOH HOH A . B 2 HOH 19 87 27 HOH HOH A . B 2 HOH 20 88 28 HOH HOH A . B 2 HOH 21 89 29 HOH HOH A . B 2 HOH 22 90 30 HOH HOH A . B 2 HOH 23 91 31 HOH HOH A . B 2 HOH 24 92 34 HOH HOH A . B 2 HOH 25 93 35 HOH HOH A . B 2 HOH 26 94 36 HOH HOH A . B 2 HOH 27 95 37 HOH HOH A . B 2 HOH 28 96 39 HOH HOH A . #