data_2GKQ # _entry.id 2GKQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2GKQ RCSB RCSB037239 WWPDB D_1000037239 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2008-12-02 _pdbx_database_PDB_obs_spr.pdb_id 3ETY _pdbx_database_PDB_obs_spr.replace_pdb_id 2GKQ _pdbx_database_PDB_obs_spr.details ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2AVR '2AVR is a native FadA structure and the current model is FadA L14A mutant' unspecified PDB 2gl2 . unspecified PDB 2gld . unspecified # _pdbx_database_status.entry_id 2GKQ _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2006-04-03 _pdbx_database_status.status_code OBS _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry N _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nithianantham, S.' 1 'Xu, M.' 2 'Wu, N.' 3 'Shoham, M.' 4 'Han, Y.W.' 5 # _citation.id primary _citation.title 'Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.F' _citation.journal_volume 62 _citation.page_first 1215 _citation.page_last 1217 _citation.year 2006 _citation.journal_id_ASTM ? _citation.country DK _citation.journal_id_ISSN 1744-3091 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17142900 _citation.pdbx_database_id_DOI 10.1107/S1744309106045593 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Nithianantham, S.' 1 primary 'Xu, M.' 2 primary 'Wu, N.' 3 primary 'Han, Y.W.' 4 primary 'Shoham, M.' 5 # _cell.length_a 60.970 _cell.length_b 60.970 _cell.length_c 84.163 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.entry_id 2GKQ _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _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.space_group_name_H-M 'P 61' _symmetry.entry_id 2GKQ _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 169 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'adhesion A' 13627.759 1 ? L14A 'residues 19-129' ? 2 water nat water 18.015 104 ? ? ? ? # _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 ;ATDAASLVGELQAADAEYQNLANQEEARFNEERAQADAARQALAQNEQVYNELSQRAQRLQAEANTRFYKSQYQELASKY EDALKKLEAEMEQQKAVISDFEKIQALRAGNLEHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;ATDAASLVGELQAADAEYQNLANQEEARFNEERAQADAARQALAQNEQVYNELSQRAQRLQAEANTRFYKSQYQELASKY EDALKKLEAEMEQQKAVISDFEKIQALRAGNLEHHHHHH ; _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 ALA n 1 2 THR n 1 3 ASP n 1 4 ALA n 1 5 ALA n 1 6 SER n 1 7 LEU n 1 8 VAL n 1 9 GLY n 1 10 GLU n 1 11 LEU n 1 12 GLN n 1 13 ALA n 1 14 ALA n 1 15 ASP n 1 16 ALA n 1 17 GLU n 1 18 TYR n 1 19 GLN n 1 20 ASN n 1 21 LEU n 1 22 ALA n 1 23 ASN n 1 24 GLN n 1 25 GLU n 1 26 GLU n 1 27 ALA n 1 28 ARG n 1 29 PHE n 1 30 ASN n 1 31 GLU n 1 32 GLU n 1 33 ARG n 1 34 ALA n 1 35 GLN n 1 36 ALA n 1 37 ASP n 1 38 ALA n 1 39 ALA n 1 40 ARG n 1 41 GLN n 1 42 ALA n 1 43 LEU n 1 44 ALA n 1 45 GLN n 1 46 ASN n 1 47 GLU n 1 48 GLN n 1 49 VAL n 1 50 TYR n 1 51 ASN n 1 52 GLU n 1 53 LEU n 1 54 SER n 1 55 GLN n 1 56 ARG n 1 57 ALA n 1 58 GLN n 1 59 ARG n 1 60 LEU n 1 61 GLN n 1 62 ALA n 1 63 GLU n 1 64 ALA n 1 65 ASN n 1 66 THR n 1 67 ARG n 1 68 PHE n 1 69 TYR n 1 70 LYS n 1 71 SER n 1 72 GLN n 1 73 TYR n 1 74 GLN n 1 75 GLU n 1 76 LEU n 1 77 ALA n 1 78 SER n 1 79 LYS n 1 80 TYR n 1 81 GLU n 1 82 ASP n 1 83 ALA n 1 84 LEU n 1 85 LYS n 1 86 LYS n 1 87 LEU n 1 88 GLU n 1 89 ALA n 1 90 GLU n 1 91 MET n 1 92 GLU n 1 93 GLN n 1 94 GLN n 1 95 LYS n 1 96 ALA n 1 97 VAL n 1 98 ILE n 1 99 SER n 1 100 ASP n 1 101 PHE n 1 102 GLU n 1 103 LYS n 1 104 ILE n 1 105 GLN n 1 106 ALA n 1 107 LEU n 1 108 ARG n 1 109 ALA n 1 110 GLY n 1 111 ASN n 1 112 LEU n 1 113 GLU n 1 114 HIS n 1 115 HIS n 1 116 HIS n 1 117 HIS n 1 118 HIS n 1 119 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 Fusobacterium _entity_src_gen.pdbx_gene_src_gene ? _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 'Fusobacterium nucleatum' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 851 _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 BL21' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 511693 _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 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain BL21 _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 pYH1378 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name GB _struct_ref.db_code AAW33965 _struct_ref.pdbx_db_accession 57117488 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;ATDAASLVGELQALDAEYQNLANQEEARFNEERAQADAARQALAQNEQVYNELSQRAQRLQAEANTRFYKSQYQELASKY EDALKKLEAEMEQQKAVISDFEKIQALRAGN ; _struct_ref.pdbx_align_begin 19 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2GKQ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 111 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 57117488 _struct_ref_seq.db_align_beg 19 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 129 _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 111 # 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 2GKQ ALA A 14 ? GB 57117488 LEU 32 ENGINEERED 14 1 1 2GKQ LEU A 112 ? GB 57117488 ? ? 'EXPRESSION TAG' 112 2 1 2GKQ GLU A 113 ? GB 57117488 ? ? 'EXPRESSION TAG' 113 3 1 2GKQ HIS A 114 ? GB 57117488 ? ? 'EXPRESSION TAG' 114 4 1 2GKQ HIS A 115 ? GB 57117488 ? ? 'EXPRESSION TAG' 115 5 1 2GKQ HIS A 116 ? GB 57117488 ? ? 'EXPRESSION TAG' 116 6 1 2GKQ HIS A 117 ? GB 57117488 ? ? 'EXPRESSION TAG' 117 7 1 2GKQ HIS A 118 ? GB 57117488 ? ? 'EXPRESSION TAG' 118 8 1 2GKQ HIS A 119 ? GB 57117488 ? ? 'EXPRESSION TAG' 119 9 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 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.crystals_number 1 _exptl.entry_id 2GKQ _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 3.31 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 62.88 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.temp 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details 'Sodium citrate, Sodium chloride, pH 5.6, VAPOR DIFFUSION, temperature 295K' _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 CUSTOM-MADE _diffrn_detector.pdbx_collection_date 2006-03-01 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator GRAPHITE _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97899 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-BM' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97899 _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-BM # _reflns.entry_id 2GKQ _reflns.d_resolution_high 2.500 _reflns.d_resolution_low 50.000 _reflns.number_obs 5078 _reflns.pdbx_Rmerge_I_obs 0.117 _reflns.pdbx_netI_over_sigmaI ? _reflns.pdbx_chi_squared 1.131 _reflns.pdbx_redundancy 4.000 _reflns.percent_possible_obs 85.500 _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.number_all 5081 _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _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_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.50 _reflns_shell.d_res_low 2.59 _reflns_shell.number_measured_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs 234 _reflns_shell.Rmerge_I_obs 0.524 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 0.538 _reflns_shell.pdbx_redundancy 2.00 _reflns_shell.percent_possible_obs 41.10 _reflns_shell.number_unique_all ? _reflns_shell.percent_possible_all 41.1 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2GKQ _refine.ls_d_res_high 2.53 _refine.ls_d_res_low 32.9 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 81.500 _refine.ls_number_reflns_obs 5044 _refine.ls_R_factor_R_work 0.244 _refine.ls_R_factor_R_free 0.299 _refine.ls_percent_reflns_R_free 8.400 _refine.ls_number_reflns_R_free 523 _refine.B_iso_mean 74.606 _refine.solvent_model_param_bsol 71.438 _refine.aniso_B[1][1] 18.385 _refine.aniso_B[2][2] 18.385 _refine.aniso_B[3][3] -36.770 _refine.aniso_B[1][2] -1.913 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 5078 _refine.ls_R_factor_all 0.287 _refine.ls_R_factor_obs 0.261 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'pdb entry 2AVR' _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 2GKQ _refine_analyze.Luzzati_coordinate_error_obs 0.418 _refine_analyze.Luzzati_sigma_a_obs 0.395 _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 862 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 104 _refine_hist.number_atoms_total 966 _refine_hist.d_res_high 2.53 _refine_hist.d_res_low 32.9 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d ? 0.008 ? ? 'X-RAY DIFFRACTION' ? c_angle_deg ? 1.014 ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? 1.197 1.500 ? 'X-RAY DIFFRACTION' ? c_scbond_it ? 2.107 2.000 ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? 2.036 2.000 ? 'X-RAY DIFFRACTION' ? c_scangle_it ? 3.408 2.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.50 _refine_ls_shell.d_res_low 2.59 _refine_ls_shell.number_reflns_obs 135 _refine_ls_shell.number_reflns_R_free 15 _refine_ls_shell.R_factor_R_work 0.34 _refine_ls_shell.R_factor_R_free 0.38 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_obs 41.1 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 protein_rep.param protein.top 'X-RAY DIFFRACTION' 2 water_rep.param water.top 'X-RAY DIFFRACTION' 3 ? ? 'X-RAY DIFFRACTION' 4 ? ? 'X-RAY DIFFRACTION' # _struct.entry_id 2GKQ _struct.title 'Crystal structure of bacterial adhesin FadA L14A mutant' _struct.pdbx_descriptor 'adhesion A' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2GKQ _struct_keywords.pdbx_keywords 'CELL ADHESION' _struct_keywords.text 'antiparallel helix-loop-helix, FadA L14A mutant, CELL ADHESION' # 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 monomer _struct_biol.pdbx_parent_biol_id ? # 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 6 ? ALA A 64 ? SER A 6 ALA A 64 1 ? 59 HELX_P HELX_P2 2 ASN A 65 ? ARG A 67 ? ASN A 65 ARG A 67 5 ? 3 HELX_P HELX_P3 3 TYR A 69 ? LYS A 103 ? TYR A 69 LYS A 103 1 ? 35 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _atom_sites.entry_id 2GKQ _atom_sites.fract_transf_matrix[1][1] 0.016402 _atom_sites.fract_transf_matrix[1][2] 0.009469 _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] 0.018939 _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] 0.011882 _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 ALA 1 1 ? ? ? A . n A 1 2 THR 2 2 ? ? ? A . n A 1 3 ASP 3 3 ? ? ? A . n A 1 4 ALA 4 4 4 ALA ALA A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 SER 6 6 6 SER SER A . n A 1 7 LEU 7 7 7 LEU LEU A . n A 1 8 VAL 8 8 8 VAL VAL A . n A 1 9 GLY 9 9 9 GLY GLY A . n A 1 10 GLU 10 10 10 GLU GLU A . n A 1 11 LEU 11 11 11 LEU LEU A . n A 1 12 GLN 12 12 12 GLN GLN A . n A 1 13 ALA 13 13 13 ALA ALA A . n A 1 14 ALA 14 14 14 ALA ALA A . n A 1 15 ASP 15 15 15 ASP ASP A . n A 1 16 ALA 16 16 16 ALA ALA A . n A 1 17 GLU 17 17 17 GLU GLU A . n A 1 18 TYR 18 18 18 TYR TYR A . n A 1 19 GLN 19 19 19 GLN GLN A . n A 1 20 ASN 20 20 20 ASN ASN A . n A 1 21 LEU 21 21 21 LEU LEU A . n A 1 22 ALA 22 22 22 ALA ALA A . n A 1 23 ASN 23 23 23 ASN ASN A . n A 1 24 GLN 24 24 24 GLN GLN A . n A 1 25 GLU 25 25 25 GLU GLU A . n A 1 26 GLU 26 26 26 GLU GLU A . n A 1 27 ALA 27 27 27 ALA ALA A . n A 1 28 ARG 28 28 28 ARG ARG A . n A 1 29 PHE 29 29 29 PHE PHE A . n A 1 30 ASN 30 30 30 ASN ASN A . n A 1 31 GLU 31 31 31 GLU GLU A . n A 1 32 GLU 32 32 32 GLU GLU A . n A 1 33 ARG 33 33 33 ARG ARG A . n A 1 34 ALA 34 34 34 ALA ALA A . n A 1 35 GLN 35 35 35 GLN GLN A . n A 1 36 ALA 36 36 36 ALA ALA A . n A 1 37 ASP 37 37 37 ASP ASP A . n A 1 38 ALA 38 38 38 ALA ALA A . n A 1 39 ALA 39 39 39 ALA ALA A . n A 1 40 ARG 40 40 40 ARG ARG A . n A 1 41 GLN 41 41 41 GLN GLN A . n A 1 42 ALA 42 42 42 ALA ALA A . n A 1 43 LEU 43 43 43 LEU LEU A . n A 1 44 ALA 44 44 44 ALA ALA A . n A 1 45 GLN 45 45 45 GLN GLN A . n A 1 46 ASN 46 46 46 ASN ASN A . n A 1 47 GLU 47 47 47 GLU GLU A . n A 1 48 GLN 48 48 48 GLN GLN A . n A 1 49 VAL 49 49 49 VAL VAL A . n A 1 50 TYR 50 50 50 TYR TYR A . n A 1 51 ASN 51 51 51 ASN ASN A . n A 1 52 GLU 52 52 52 GLU GLU A . n A 1 53 LEU 53 53 53 LEU LEU A . n A 1 54 SER 54 54 54 SER SER A . n A 1 55 GLN 55 55 55 GLN GLN A . n A 1 56 ARG 56 56 56 ARG ARG A . n A 1 57 ALA 57 57 57 ALA ALA A . n A 1 58 GLN 58 58 58 GLN GLN A . n A 1 59 ARG 59 59 59 ARG ARG A . n A 1 60 LEU 60 60 60 LEU LEU A . n A 1 61 GLN 61 61 61 GLN GLN A . n A 1 62 ALA 62 62 62 ALA ALA A . n A 1 63 GLU 63 63 63 GLU GLU A . n A 1 64 ALA 64 64 64 ALA ALA A . n A 1 65 ASN 65 65 65 ASN ASN A . n A 1 66 THR 66 66 66 THR THR A . n A 1 67 ARG 67 67 67 ARG ARG A . n A 1 68 PHE 68 68 68 PHE PHE A . n A 1 69 TYR 69 69 69 TYR TYR A . n A 1 70 LYS 70 70 70 LYS LYS A . n A 1 71 SER 71 71 71 SER SER A . n A 1 72 GLN 72 72 72 GLN GLN A . n A 1 73 TYR 73 73 73 TYR TYR A . n A 1 74 GLN 74 74 74 GLN GLN A . n A 1 75 GLU 75 75 75 GLU GLU A . n A 1 76 LEU 76 76 76 LEU LEU A . n A 1 77 ALA 77 77 77 ALA ALA A . n A 1 78 SER 78 78 78 SER SER A . n A 1 79 LYS 79 79 79 LYS LYS A . n A 1 80 TYR 80 80 80 TYR TYR A . n A 1 81 GLU 81 81 81 GLU GLU A . n A 1 82 ASP 82 82 82 ASP ASP A . n A 1 83 ALA 83 83 83 ALA ALA A . n A 1 84 LEU 84 84 84 LEU LEU A . n A 1 85 LYS 85 85 85 LYS LYS A . n A 1 86 LYS 86 86 86 LYS LYS A . n A 1 87 LEU 87 87 87 LEU LEU A . n A 1 88 GLU 88 88 88 GLU GLU A . n A 1 89 ALA 89 89 89 ALA ALA A . n A 1 90 GLU 90 90 90 GLU GLU A . n A 1 91 MET 91 91 91 MET MET A . n A 1 92 GLU 92 92 92 GLU GLU A . n A 1 93 GLN 93 93 93 GLN GLN A . n A 1 94 GLN 94 94 94 GLN GLN A . n A 1 95 LYS 95 95 95 LYS LYS A . n A 1 96 ALA 96 96 96 ALA ALA A . n A 1 97 VAL 97 97 97 VAL VAL A . n A 1 98 ILE 98 98 98 ILE ILE A . n A 1 99 SER 99 99 99 SER SER A . n A 1 100 ASP 100 100 100 ASP ASP A . n A 1 101 PHE 101 101 101 PHE PHE A . n A 1 102 GLU 102 102 102 GLU GLU A . n A 1 103 LYS 103 103 103 LYS LYS A . n A 1 104 ILE 104 104 104 ILE ILE A . n A 1 105 GLN 105 105 105 GLN GLN A . n A 1 106 ALA 106 106 106 ALA ALA A . n A 1 107 LEU 107 107 107 LEU LEU A . n A 1 108 ARG 108 108 108 ARG ARG A . n A 1 109 ALA 109 109 109 ALA ALA A . n A 1 110 GLY 110 110 110 GLY GLY A . n A 1 111 ASN 111 111 111 ASN ASN A . n A 1 112 LEU 112 112 ? ? ? A . n A 1 113 GLU 113 113 ? ? ? A . n A 1 114 HIS 114 114 ? ? ? A . n A 1 115 HIS 115 115 ? ? ? A . n A 1 116 HIS 116 116 ? ? ? A . n A 1 117 HIS 117 117 ? ? ? A . n A 1 118 HIS 118 118 ? ? ? A . n A 1 119 HIS 119 119 ? ? ? A . 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 HOH 1 120 1 HOH WAT A . B 2 HOH 2 121 2 HOH WAT A . B 2 HOH 3 122 3 HOH WAT A . B 2 HOH 4 123 4 HOH WAT A . B 2 HOH 5 124 5 HOH WAT A . B 2 HOH 6 125 6 HOH WAT A . B 2 HOH 7 126 7 HOH WAT A . B 2 HOH 8 127 8 HOH WAT A . B 2 HOH 9 128 9 HOH WAT A . B 2 HOH 10 129 10 HOH WAT A . B 2 HOH 11 130 11 HOH WAT A . B 2 HOH 12 131 12 HOH WAT A . B 2 HOH 13 132 13 HOH WAT A . B 2 HOH 14 133 14 HOH WAT A . B 2 HOH 15 134 15 HOH WAT A . B 2 HOH 16 135 16 HOH WAT A . B 2 HOH 17 136 17 HOH WAT A . B 2 HOH 18 137 18 HOH WAT A . B 2 HOH 19 138 19 HOH WAT A . B 2 HOH 20 139 20 HOH WAT A . B 2 HOH 21 140 21 HOH WAT A . B 2 HOH 22 141 22 HOH WAT A . B 2 HOH 23 142 23 HOH WAT A . B 2 HOH 24 143 24 HOH WAT A . B 2 HOH 25 144 25 HOH WAT A . B 2 HOH 26 145 26 HOH WAT A . B 2 HOH 27 146 27 HOH WAT A . B 2 HOH 28 147 28 HOH WAT A . B 2 HOH 29 148 29 HOH WAT A . B 2 HOH 30 149 30 HOH WAT A . B 2 HOH 31 150 31 HOH WAT A . B 2 HOH 32 151 32 HOH WAT A . B 2 HOH 33 152 33 HOH WAT A . B 2 HOH 34 153 34 HOH WAT A . B 2 HOH 35 154 35 HOH WAT A . B 2 HOH 36 155 36 HOH WAT A . B 2 HOH 37 156 37 HOH WAT A . B 2 HOH 38 157 38 HOH WAT A . B 2 HOH 39 158 39 HOH WAT A . B 2 HOH 40 159 40 HOH WAT A . B 2 HOH 41 160 41 HOH WAT A . B 2 HOH 42 161 42 HOH WAT A . B 2 HOH 43 162 43 HOH WAT A . B 2 HOH 44 163 44 HOH WAT A . B 2 HOH 45 164 45 HOH WAT A . B 2 HOH 46 165 46 HOH WAT A . B 2 HOH 47 166 47 HOH WAT A . B 2 HOH 48 167 48 HOH WAT A . B 2 HOH 49 168 49 HOH WAT A . B 2 HOH 50 169 50 HOH WAT A . B 2 HOH 51 170 51 HOH WAT A . B 2 HOH 52 171 52 HOH WAT A . B 2 HOH 53 172 53 HOH WAT A . B 2 HOH 54 173 54 HOH WAT A . B 2 HOH 55 174 55 HOH WAT A . B 2 HOH 56 175 56 HOH WAT A . B 2 HOH 57 176 57 HOH WAT A . B 2 HOH 58 177 58 HOH WAT A . B 2 HOH 59 178 59 HOH WAT A . B 2 HOH 60 179 60 HOH WAT A . B 2 HOH 61 180 61 HOH WAT A . B 2 HOH 62 181 62 HOH WAT A . B 2 HOH 63 182 63 HOH WAT A . B 2 HOH 64 183 64 HOH WAT A . B 2 HOH 65 184 65 HOH WAT A . B 2 HOH 66 185 66 HOH WAT A . B 2 HOH 67 186 67 HOH WAT A . B 2 HOH 68 187 68 HOH WAT A . B 2 HOH 69 188 69 HOH WAT A . B 2 HOH 70 189 70 HOH WAT A . B 2 HOH 71 190 71 HOH WAT A . B 2 HOH 72 191 72 HOH WAT A . B 2 HOH 73 192 73 HOH WAT A . B 2 HOH 74 193 74 HOH WAT A . B 2 HOH 75 194 75 HOH WAT A . B 2 HOH 76 195 76 HOH WAT A . B 2 HOH 77 196 77 HOH WAT A . B 2 HOH 78 197 78 HOH WAT A . B 2 HOH 79 198 79 HOH WAT A . B 2 HOH 80 199 80 HOH WAT A . B 2 HOH 81 200 81 HOH WAT A . B 2 HOH 82 201 82 HOH WAT A . B 2 HOH 83 202 83 HOH WAT A . B 2 HOH 84 203 84 HOH WAT A . B 2 HOH 85 204 85 HOH WAT A . B 2 HOH 86 205 86 HOH WAT A . B 2 HOH 87 206 87 HOH WAT A . B 2 HOH 88 207 88 HOH WAT A . B 2 HOH 89 208 89 HOH WAT A . B 2 HOH 90 209 90 HOH WAT A . B 2 HOH 91 210 91 HOH WAT A . B 2 HOH 92 211 92 HOH WAT A . B 2 HOH 93 212 93 HOH WAT A . B 2 HOH 94 213 94 HOH WAT A . B 2 HOH 95 214 95 HOH WAT A . B 2 HOH 96 215 96 HOH WAT A . B 2 HOH 97 216 97 HOH WAT A . B 2 HOH 98 217 98 HOH WAT A . B 2 HOH 99 218 99 HOH WAT A . B 2 HOH 100 219 100 HOH WAT A . B 2 HOH 101 220 101 HOH WAT A . B 2 HOH 102 221 102 HOH WAT A . B 2 HOH 103 222 103 HOH WAT A . B 2 HOH 104 223 104 HOH WAT A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_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 2007-04-10 2 'Structure model' 1 1 2008-12-02 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 2 'Structure model' repository Obsolete ? # 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 HKL . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data processing' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 2 PDB_EXTRACT 1.701 'Nov. 1, 2005' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 3 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 4 HKL . ? ? ? ? 'data scaling' ? ? ? 5 PHASER . ? ? ? ? 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 LEU A 7 ? ? -68.11 1.26 2 1 TYR A 69 ? ? -96.71 41.98 # 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 ALA 1 ? A ALA 1 2 1 Y 1 A THR 2 ? A THR 2 3 1 Y 1 A ASP 3 ? A ASP 3 4 1 Y 1 A LEU 112 ? A LEU 112 5 1 Y 1 A GLU 113 ? A GLU 113 6 1 Y 1 A HIS 114 ? A HIS 114 7 1 Y 1 A HIS 115 ? A HIS 115 8 1 Y 1 A HIS 116 ? A HIS 116 9 1 Y 1 A HIS 117 ? A HIS 117 10 1 Y 1 A HIS 118 ? A HIS 118 11 1 Y 1 A HIS 119 ? A HIS 119 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #