data_3NBM # _entry.id 3NBM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3NBM RCSB RCSB059625 WWPDB D_1000059625 # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id apc63979.1 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3NBM _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-06-03 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _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 'Cuff, M.E.' 1 'Chhor, G.' 2 'Clancy, S.' 3 'Joachimiak, A.' 4 'Midwest Center for Structural Genomics (MCSG)' 5 # _citation.id primary _citation.title ;Structure of the lactose-specific IIB component domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) from Streptococcus pneumoniae. ; _citation.journal_abbrev 'TO BE PUBLISHED' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Cuff, M.E.' 1 primary 'Chhor, G.' 2 primary 'Clancy, S.' 3 primary 'Joachimiak, A.' 4 # _cell.length_a 41.372 _cell.length_b 41.372 _cell.length_c 98.527 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3NBM _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 43 21 2' _symmetry.entry_id 3NBM _symmetry.Int_Tables_number 96 _symmetry.pdbx_full_space_group_name_H-M ? _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 'PTS system, lactose-specific IIBC components' 11969.215 1 ? ? 'residues 453-557' ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 water nat water 18.015 150 ? ? ? ? # _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 ;SNASKELKVLVLCAGSGTSAQLANAINEGANLTEVRVIANSGAYGAHYDI(MSE)GVYDLIILAPQVRSYYRE(MSE)KV DAERLGIQIVATRG(MSE)EYIHLTKSPSKALQFVLEHYQ ; _entity_poly.pdbx_seq_one_letter_code_can ;SNASKELKVLVLCAGSGTSAQLANAINEGANLTEVRVIANSGAYGAHYDIMGVYDLIILAPQVRSYYREMKVDAERLGIQ IVATRGMEYIHLTKSPSKALQFVLEHYQ ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier apc63979.1 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 ASN n 1 3 ALA n 1 4 SER n 1 5 LYS n 1 6 GLU n 1 7 LEU n 1 8 LYS n 1 9 VAL n 1 10 LEU n 1 11 VAL n 1 12 LEU n 1 13 CYS n 1 14 ALA n 1 15 GLY n 1 16 SER n 1 17 GLY n 1 18 THR n 1 19 SER n 1 20 ALA n 1 21 GLN n 1 22 LEU n 1 23 ALA n 1 24 ASN n 1 25 ALA n 1 26 ILE n 1 27 ASN n 1 28 GLU n 1 29 GLY n 1 30 ALA n 1 31 ASN n 1 32 LEU n 1 33 THR n 1 34 GLU n 1 35 VAL n 1 36 ARG n 1 37 VAL n 1 38 ILE n 1 39 ALA n 1 40 ASN n 1 41 SER n 1 42 GLY n 1 43 ALA n 1 44 TYR n 1 45 GLY n 1 46 ALA n 1 47 HIS n 1 48 TYR n 1 49 ASP n 1 50 ILE n 1 51 MSE n 1 52 GLY n 1 53 VAL n 1 54 TYR n 1 55 ASP n 1 56 LEU n 1 57 ILE n 1 58 ILE n 1 59 LEU n 1 60 ALA n 1 61 PRO n 1 62 GLN n 1 63 VAL n 1 64 ARG n 1 65 SER n 1 66 TYR n 1 67 TYR n 1 68 ARG n 1 69 GLU n 1 70 MSE n 1 71 LYS n 1 72 VAL n 1 73 ASP n 1 74 ALA n 1 75 GLU n 1 76 ARG n 1 77 LEU n 1 78 GLY n 1 79 ILE n 1 80 GLN n 1 81 ILE n 1 82 VAL n 1 83 ALA n 1 84 THR n 1 85 ARG n 1 86 GLY n 1 87 MSE n 1 88 GLU n 1 89 TYR n 1 90 ILE n 1 91 HIS n 1 92 LEU n 1 93 THR n 1 94 LYS n 1 95 SER n 1 96 PRO n 1 97 SER n 1 98 LYS n 1 99 ALA n 1 100 LEU n 1 101 GLN n 1 102 PHE n 1 103 VAL n 1 104 LEU n 1 105 GLU n 1 106 HIS n 1 107 TYR n 1 108 GLN 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 'lacE-1, SP_0478' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain TIGR4 _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 'Streptococcus pneumoniae' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 170187 _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 'modified 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 pMCSG19 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q97SA8_STRPN _struct_ref.pdbx_db_accession Q97SA8 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SKELKVLVLCAGSGTSAQLANAINEGANLTEVRVIANSGAYGAHYDIMGVYDLIILAPQVRSYYREMKVDAERLGIQIVA TRGMEYIHLTKSPSKALQFVLEHYQ ; _struct_ref.pdbx_align_begin 453 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3NBM _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 4 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 108 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q97SA8 _struct_ref_seq.db_align_beg 453 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 557 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 453 _struct_ref_seq.pdbx_auth_seq_align_end 557 # 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 3NBM SER A 1 ? UNP Q97SA8 ? ? 'expression tag' 450 1 1 3NBM ASN A 2 ? UNP Q97SA8 ? ? 'expression tag' 451 2 1 3NBM ALA A 3 ? UNP Q97SA8 ? ? 'expression tag' 452 3 # 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 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 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 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.crystals_number 1 _exptl.entry_id 3NBM _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.76 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 30.16 _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.pH 7.5 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details '0.2M Ammonium Acetate, 0.1M HEPES pH 7.5, 25% PEG 3350, 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 'ADSC QUANTUM 210r' _diffrn_detector.pdbx_collection_date 2009-12-20 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'SAGITALLY FOCUSED Si(111)' _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 0.97934 _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 0.97934 _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-BM # _reflns.entry_id 3NBM _reflns.d_resolution_high 1.300 _reflns.d_resolution_low 50.000 _reflns.number_obs 21377 _reflns.pdbx_Rmerge_I_obs 0.072 _reflns.pdbx_netI_over_sigmaI 11.400 _reflns.pdbx_chi_squared 2.148 _reflns.pdbx_redundancy 13.300 _reflns.percent_possible_obs 97.300 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3 _reflns.number_all 21377 _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate 10.6 _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 1.30 _reflns_shell.d_res_low 1.32 _reflns_shell.number_measured_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_unique_obs ? _reflns_shell.Rmerge_I_obs 0.370 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 0.956 _reflns_shell.pdbx_redundancy 6.30 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 856 _reflns_shell.percent_possible_all 81.30 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3NBM _refine.ls_d_res_high 1.300 _refine.ls_d_res_low 25.150 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 96.950 _refine.ls_number_reflns_obs 21193 _refine.ls_number_reflns_all 21193 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _refine.ls_R_factor_all 0.134 _refine.ls_R_factor_obs 0.134 _refine.ls_R_factor_R_work 0.132 _refine.ls_wR_factor_R_work 0.131 _refine.ls_R_factor_R_free 0.167 _refine.ls_wR_factor_R_free 0.167 _refine.ls_percent_reflns_R_free 5.200 _refine.ls_number_reflns_R_free 1096 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 13.685 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.330 _refine.aniso_B[2][2] -0.330 _refine.aniso_B[3][3] 0.650 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.975 _refine.correlation_coeff_Fo_to_Fc_free 0.969 _refine.overall_SU_R_Cruickshank_DPI 0.054 _refine.overall_SU_R_free 0.050 _refine.pdbx_overall_ESU_R_Free 0.050 _refine.overall_SU_ML 0.026 _refine.overall_SU_B 1.321 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.400 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.933 _refine.B_iso_max 83.89 _refine.B_iso_min 4.87 _refine.occupancy_max 1.00 _refine.occupancy_min 0.30 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _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 789 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 150 _refine_hist.number_atoms_total 945 _refine_hist.d_res_high 1.300 _refine_hist.d_res_low 25.150 # 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 r_bond_refined_d 883 0.015 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 575 0.009 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1212 1.443 1.975 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1429 0.990 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 123 5.180 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 38 37.284 24.737 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 158 12.160 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 4 20.659 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 142 0.100 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1006 0.007 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 170 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 550 1.505 1.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 225 0.475 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 892 2.338 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 333 3.408 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 310 4.944 4.500 ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 1458 1.307 3.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.300 _refine_ls_shell.d_res_low 1.334 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 80.790 _refine_ls_shell.number_reflns_R_work 1198 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.199 _refine_ls_shell.R_factor_R_free 0.245 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 72 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1270 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3NBM _struct.title ;The lactose-specific IIB component domain structure of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) from Streptococcus pneumoniae. ; _struct.pdbx_descriptor 'PTS system, lactose-specific IIBC components' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag Y _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3NBM _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.text ;PTS_IIB_lactose, phosphoenolpyruvate:carbohydrate system, P-loop, phosphorylation, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TRANSFERASE ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 GLY A 17 ? GLU A 34 ? GLY A 466 GLU A 483 1 ? 18 HELX_P HELX_P2 2 ILE A 50 ? TYR A 54 ? ILE A 499 TYR A 503 5 ? 5 HELX_P HELX_P3 3 PRO A 61 ? SER A 65 ? PRO A 510 SER A 514 5 ? 5 HELX_P HELX_P4 4 TYR A 66 ? GLU A 75 ? TYR A 515 GLU A 524 1 ? 10 HELX_P HELX_P5 5 ARG A 85 ? LYS A 94 ? ARG A 534 LYS A 543 1 ? 10 HELX_P HELX_P6 6 SER A 95 ? HIS A 106 ? SER A 544 HIS A 555 1 ? 12 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale1 covale ? ? A ILE 50 C ? ? ? 1_555 A MSE 51 N ? ? A ILE 499 A MSE 500 1_555 ? ? ? ? ? ? ? 1.327 ? covale2 covale ? ? A MSE 51 C ? ? ? 1_555 A GLY 52 N ? ? A MSE 500 A GLY 501 1_555 ? ? ? ? ? ? ? 1.337 ? covale3 covale ? ? A GLU 69 C ? ? ? 1_555 A MSE 70 N ? ? A GLU 518 A MSE 519 1_555 ? ? ? ? ? ? ? 1.332 ? covale4 covale ? ? A MSE 70 C ? ? ? 1_555 A LYS 71 N ? ? A MSE 519 A LYS 520 1_555 ? ? ? ? ? ? ? 1.337 ? covale5 covale ? ? A GLY 86 C ? ? ? 1_555 A MSE 87 N ? ? A GLY 535 A MSE 536 1_555 ? ? ? ? ? ? ? 1.330 ? covale6 covale ? ? A MSE 87 C ? ? ? 1_555 A GLU 88 N ? ? A MSE 536 A GLU 537 1_555 ? ? ? ? ? ? ? 1.327 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 4 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? parallel A 2 3 ? parallel A 3 4 ? 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 VAL A 37 ? ALA A 43 ? VAL A 486 ALA A 492 A 2 LEU A 7 ? CYS A 13 ? LEU A 456 CYS A 462 A 3 LEU A 56 ? LEU A 59 ? LEU A 505 LEU A 508 A 4 GLN A 80 ? ALA A 83 ? GLN A 529 ALA A 532 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O ILE A 38 ? O ILE A 487 N VAL A 9 ? N VAL A 458 A 2 3 N LEU A 10 ? N LEU A 459 O ILE A 58 ? O ILE A 507 A 3 4 N LEU A 59 ? N LEU A 508 O VAL A 82 ? O VAL A 531 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _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 9 _struct_site.details 'BINDING SITE FOR RESIDUE GOL A 1' # 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 9 HOH C . ? HOH A 58 . ? 3_544 ? 2 AC1 9 HOH C . ? HOH A 99 . ? 1_555 ? 3 AC1 9 HOH C . ? HOH A 122 . ? 1_555 ? 4 AC1 9 ALA A 30 ? ALA A 479 . ? 1_555 ? 5 AC1 9 ASN A 31 ? ASN A 480 . ? 1_555 ? 6 AC1 9 GLU A 34 ? GLU A 483 . ? 1_555 ? 7 AC1 9 VAL A 35 ? VAL A 484 . ? 1_555 ? 8 AC1 9 ALA A 83 ? ALA A 532 . ? 3_544 ? 9 AC1 9 ARG A 85 ? ARG A 534 . ? 3_544 ? # _atom_sites.entry_id 3NBM _atom_sites.fract_transf_matrix[1][1] 0.024171 _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] 0.024171 _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] 0.010150 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O S SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 SER 1 450 ? ? ? A . n A 1 2 ASN 2 451 ? ? ? A . n A 1 3 ALA 3 452 ? ? ? A . n A 1 4 SER 4 453 ? ? ? A . n A 1 5 LYS 5 454 454 LYS LYS A . n A 1 6 GLU 6 455 455 GLU GLU A . n A 1 7 LEU 7 456 456 LEU LEU A . n A 1 8 LYS 8 457 457 LYS LYS A . n A 1 9 VAL 9 458 458 VAL VAL A . n A 1 10 LEU 10 459 459 LEU LEU A . n A 1 11 VAL 11 460 460 VAL VAL A . n A 1 12 LEU 12 461 461 LEU LEU A . n A 1 13 CYS 13 462 462 CYS CYS A . n A 1 14 ALA 14 463 463 ALA ALA A . n A 1 15 GLY 15 464 464 GLY GLY A . n A 1 16 SER 16 465 465 SER SER A . n A 1 17 GLY 17 466 466 GLY GLY A . n A 1 18 THR 18 467 467 THR THR A . n A 1 19 SER 19 468 468 SER SER A . n A 1 20 ALA 20 469 469 ALA ALA A . n A 1 21 GLN 21 470 470 GLN GLN A . n A 1 22 LEU 22 471 471 LEU LEU A . n A 1 23 ALA 23 472 472 ALA ALA A . n A 1 24 ASN 24 473 473 ASN ASN A . n A 1 25 ALA 25 474 474 ALA ALA A . n A 1 26 ILE 26 475 475 ILE ILE A . n A 1 27 ASN 27 476 476 ASN ASN A . n A 1 28 GLU 28 477 477 GLU GLU A . n A 1 29 GLY 29 478 478 GLY GLY A . n A 1 30 ALA 30 479 479 ALA ALA A . n A 1 31 ASN 31 480 480 ASN ASN A . n A 1 32 LEU 32 481 481 LEU LEU A . n A 1 33 THR 33 482 482 THR THR A . n A 1 34 GLU 34 483 483 GLU GLU A . n A 1 35 VAL 35 484 484 VAL VAL A . n A 1 36 ARG 36 485 485 ARG ARG A . n A 1 37 VAL 37 486 486 VAL VAL A . n A 1 38 ILE 38 487 487 ILE ILE A . n A 1 39 ALA 39 488 488 ALA ALA A . n A 1 40 ASN 40 489 489 ASN ASN A . n A 1 41 SER 41 490 490 SER SER A . n A 1 42 GLY 42 491 491 GLY GLY A . n A 1 43 ALA 43 492 492 ALA ALA A . n A 1 44 TYR 44 493 493 TYR TYR A . n A 1 45 GLY 45 494 494 GLY GLY A . n A 1 46 ALA 46 495 495 ALA ALA A . n A 1 47 HIS 47 496 496 HIS HIS A . n A 1 48 TYR 48 497 497 TYR TYR A . n A 1 49 ASP 49 498 498 ASP ASP A . n A 1 50 ILE 50 499 499 ILE ILE A . n A 1 51 MSE 51 500 500 MSE MSE A . n A 1 52 GLY 52 501 501 GLY GLY A . n A 1 53 VAL 53 502 502 VAL VAL A . n A 1 54 TYR 54 503 503 TYR TYR A . n A 1 55 ASP 55 504 504 ASP ASP A . n A 1 56 LEU 56 505 505 LEU LEU A . n A 1 57 ILE 57 506 506 ILE ILE A . n A 1 58 ILE 58 507 507 ILE ILE A . n A 1 59 LEU 59 508 508 LEU LEU A . n A 1 60 ALA 60 509 509 ALA ALA A . n A 1 61 PRO 61 510 510 PRO PRO A . n A 1 62 GLN 62 511 511 GLN GLN A . n A 1 63 VAL 63 512 512 VAL VAL A . n A 1 64 ARG 64 513 513 ARG ARG A . n A 1 65 SER 65 514 514 SER SER A . n A 1 66 TYR 66 515 515 TYR TYR A . n A 1 67 TYR 67 516 516 TYR TYR A . n A 1 68 ARG 68 517 517 ARG ARG A . n A 1 69 GLU 69 518 518 GLU GLU A . n A 1 70 MSE 70 519 519 MSE MSE A . n A 1 71 LYS 71 520 520 LYS LYS A . n A 1 72 VAL 72 521 521 VAL VAL A . n A 1 73 ASP 73 522 522 ASP ASP A . n A 1 74 ALA 74 523 523 ALA ALA A . n A 1 75 GLU 75 524 524 GLU GLU A . n A 1 76 ARG 76 525 525 ARG ARG A . n A 1 77 LEU 77 526 526 LEU LEU A . n A 1 78 GLY 78 527 527 GLY GLY A . n A 1 79 ILE 79 528 528 ILE ILE A . n A 1 80 GLN 80 529 529 GLN GLN A . n A 1 81 ILE 81 530 530 ILE ILE A . n A 1 82 VAL 82 531 531 VAL VAL A . n A 1 83 ALA 83 532 532 ALA ALA A . n A 1 84 THR 84 533 533 THR THR A . n A 1 85 ARG 85 534 534 ARG ARG A . n A 1 86 GLY 86 535 535 GLY GLY A . n A 1 87 MSE 87 536 536 MSE MSE A . n A 1 88 GLU 88 537 537 GLU GLU A . n A 1 89 TYR 89 538 538 TYR TYR A . n A 1 90 ILE 90 539 539 ILE ILE A . n A 1 91 HIS 91 540 540 HIS HIS A . n A 1 92 LEU 92 541 541 LEU LEU A . n A 1 93 THR 93 542 542 THR THR A . n A 1 94 LYS 94 543 543 LYS LYS A . n A 1 95 SER 95 544 544 SER SER A . n A 1 96 PRO 96 545 545 PRO PRO A . n A 1 97 SER 97 546 546 SER SER A . n A 1 98 LYS 98 547 547 LYS LYS A . n A 1 99 ALA 99 548 548 ALA ALA A . n A 1 100 LEU 100 549 549 LEU LEU A . n A 1 101 GLN 101 550 550 GLN GLN A . n A 1 102 PHE 102 551 551 PHE PHE A . n A 1 103 VAL 103 552 552 VAL VAL A . n A 1 104 LEU 104 553 553 LEU LEU A . n A 1 105 GLU 105 554 554 GLU GLU A . n A 1 106 HIS 106 555 555 HIS HIS A . n A 1 107 TYR 107 556 556 TYR TYR A . n A 1 108 GLN 108 557 557 GLN GLN A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Midwest Center for Structural Genomics' _pdbx_SG_project.initial_of_center MCSG # 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 GOL 1 1 1 GOL GOL A . C 3 HOH 1 2 2 HOH HOH A . C 3 HOH 2 3 3 HOH HOH A . C 3 HOH 3 4 4 HOH HOH A . C 3 HOH 4 5 5 HOH HOH A . C 3 HOH 5 6 6 HOH HOH A . C 3 HOH 6 7 7 HOH HOH A . C 3 HOH 7 8 8 HOH HOH A . C 3 HOH 8 9 9 HOH HOH A . C 3 HOH 9 10 10 HOH HOH A . C 3 HOH 10 11 11 HOH HOH A . C 3 HOH 11 12 12 HOH HOH A . C 3 HOH 12 13 13 HOH HOH A . C 3 HOH 13 14 14 HOH HOH A . C 3 HOH 14 15 15 HOH HOH A . C 3 HOH 15 16 16 HOH HOH A . C 3 HOH 16 17 17 HOH HOH A . C 3 HOH 17 18 18 HOH HOH A . C 3 HOH 18 19 19 HOH HOH A . C 3 HOH 19 20 20 HOH HOH A . C 3 HOH 20 21 21 HOH HOH A . C 3 HOH 21 22 22 HOH HOH A . C 3 HOH 22 23 23 HOH HOH A . C 3 HOH 23 24 24 HOH HOH A . C 3 HOH 24 25 25 HOH HOH A . C 3 HOH 25 26 26 HOH HOH A . C 3 HOH 26 27 27 HOH HOH A . C 3 HOH 27 28 28 HOH HOH A . C 3 HOH 28 29 29 HOH HOH A . C 3 HOH 29 30 30 HOH HOH A . C 3 HOH 30 31 31 HOH HOH A . C 3 HOH 31 32 32 HOH HOH A . C 3 HOH 32 33 33 HOH HOH A . C 3 HOH 33 34 34 HOH HOH A . C 3 HOH 34 35 35 HOH HOH A . C 3 HOH 35 36 36 HOH HOH A . C 3 HOH 36 37 37 HOH HOH A . C 3 HOH 37 38 38 HOH HOH A . C 3 HOH 38 39 39 HOH HOH A . C 3 HOH 39 40 40 HOH HOH A . C 3 HOH 40 41 41 HOH HOH A . C 3 HOH 41 42 42 HOH HOH A . C 3 HOH 42 43 43 HOH HOH A . C 3 HOH 43 44 44 HOH HOH A . C 3 HOH 44 45 45 HOH HOH A . C 3 HOH 45 46 46 HOH HOH A . C 3 HOH 46 47 47 HOH HOH A . C 3 HOH 47 48 48 HOH HOH A . C 3 HOH 48 49 49 HOH HOH A . C 3 HOH 49 50 50 HOH HOH A . C 3 HOH 50 51 51 HOH HOH A . C 3 HOH 51 52 52 HOH HOH A . C 3 HOH 52 53 53 HOH HOH A . C 3 HOH 53 54 54 HOH HOH A . C 3 HOH 54 55 55 HOH HOH A . C 3 HOH 55 56 56 HOH HOH A . C 3 HOH 56 57 57 HOH HOH A . C 3 HOH 57 58 58 HOH HOH A . C 3 HOH 58 59 59 HOH HOH A . C 3 HOH 59 60 60 HOH HOH A . C 3 HOH 60 61 61 HOH HOH A . C 3 HOH 61 62 62 HOH HOH A . C 3 HOH 62 63 63 HOH HOH A . C 3 HOH 63 64 64 HOH HOH A . C 3 HOH 64 65 65 HOH HOH A . C 3 HOH 65 66 66 HOH HOH A . C 3 HOH 66 67 67 HOH HOH A . C 3 HOH 67 68 68 HOH HOH A . C 3 HOH 68 69 69 HOH HOH A . C 3 HOH 69 70 70 HOH HOH A . C 3 HOH 70 71 71 HOH HOH A . C 3 HOH 71 72 72 HOH HOH A . C 3 HOH 72 73 73 HOH HOH A . C 3 HOH 73 74 74 HOH HOH A . C 3 HOH 74 75 75 HOH HOH A . C 3 HOH 75 76 76 HOH HOH A . C 3 HOH 76 77 77 HOH HOH A . C 3 HOH 77 78 78 HOH HOH A . C 3 HOH 78 79 79 HOH HOH A . C 3 HOH 79 80 80 HOH HOH A . C 3 HOH 80 81 81 HOH HOH A . C 3 HOH 81 82 82 HOH HOH A . C 3 HOH 82 83 83 HOH HOH A . C 3 HOH 83 84 84 HOH HOH A . C 3 HOH 84 85 85 HOH HOH A . C 3 HOH 85 86 86 HOH HOH A . C 3 HOH 86 87 87 HOH HOH A . C 3 HOH 87 88 88 HOH HOH A . C 3 HOH 88 89 89 HOH HOH A . C 3 HOH 89 90 90 HOH HOH A . C 3 HOH 90 91 91 HOH HOH A . C 3 HOH 91 92 92 HOH HOH A . C 3 HOH 92 93 93 HOH HOH A . C 3 HOH 93 94 94 HOH HOH A . C 3 HOH 94 95 95 HOH HOH A . C 3 HOH 95 96 96 HOH HOH A . C 3 HOH 96 97 97 HOH HOH A . C 3 HOH 97 98 98 HOH HOH A . C 3 HOH 98 99 99 HOH HOH A . C 3 HOH 99 100 100 HOH HOH A . C 3 HOH 100 101 101 HOH HOH A . C 3 HOH 101 102 102 HOH HOH A . C 3 HOH 102 103 103 HOH HOH A . C 3 HOH 103 104 104 HOH HOH A . C 3 HOH 104 105 105 HOH HOH A . C 3 HOH 105 106 106 HOH HOH A . C 3 HOH 106 107 107 HOH HOH A . C 3 HOH 107 108 108 HOH HOH A . C 3 HOH 108 109 109 HOH HOH A . C 3 HOH 109 110 110 HOH HOH A . C 3 HOH 110 111 111 HOH HOH A . C 3 HOH 111 112 112 HOH HOH A . C 3 HOH 112 113 113 HOH HOH A . C 3 HOH 113 114 114 HOH HOH A . C 3 HOH 114 115 115 HOH HOH A . C 3 HOH 115 116 116 HOH HOH A . C 3 HOH 116 117 117 HOH HOH A . C 3 HOH 117 118 118 HOH HOH A . C 3 HOH 118 119 119 HOH HOH A . C 3 HOH 119 120 120 HOH HOH A . C 3 HOH 120 121 121 HOH HOH A . C 3 HOH 121 122 122 HOH HOH A . C 3 HOH 122 123 123 HOH HOH A . C 3 HOH 123 124 124 HOH HOH A . C 3 HOH 124 125 125 HOH HOH A . C 3 HOH 125 126 126 HOH HOH A . C 3 HOH 126 127 127 HOH HOH A . C 3 HOH 127 128 128 HOH HOH A . C 3 HOH 128 129 129 HOH HOH A . C 3 HOH 129 130 130 HOH HOH A . C 3 HOH 130 131 131 HOH HOH A . C 3 HOH 131 132 132 HOH HOH A . C 3 HOH 132 133 133 HOH HOH A . C 3 HOH 133 134 134 HOH HOH A . C 3 HOH 134 135 135 HOH HOH A . C 3 HOH 135 136 136 HOH HOH A . C 3 HOH 136 137 137 HOH HOH A . C 3 HOH 137 138 138 HOH HOH A . C 3 HOH 138 139 139 HOH HOH A . C 3 HOH 139 140 140 HOH HOH A . C 3 HOH 140 141 141 HOH HOH A . C 3 HOH 141 142 142 HOH HOH A . C 3 HOH 142 143 143 HOH HOH A . C 3 HOH 143 144 144 HOH HOH A . C 3 HOH 144 145 145 HOH HOH A . C 3 HOH 145 146 146 HOH HOH A . C 3 HOH 146 147 147 HOH HOH A . C 3 HOH 147 148 148 HOH HOH A . C 3 HOH 148 149 149 HOH HOH A . C 3 HOH 149 150 150 HOH HOH A . C 3 HOH 150 558 1 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 51 A MSE 500 ? MET SELENOMETHIONINE 2 A MSE 70 A MSE 519 ? MET SELENOMETHIONINE 3 A MSE 87 A MSE 536 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details 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 # _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 2010-09-08 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-08 # _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' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # _diffrn_reflns.diffrn_id 1 _diffrn_reflns.pdbx_d_res_high 1.300 _diffrn_reflns.pdbx_d_res_low 50.000 _diffrn_reflns.pdbx_number_obs 21377 _diffrn_reflns.pdbx_Rmerge_I_obs 0.072 _diffrn_reflns.pdbx_Rsym_value ? _diffrn_reflns.pdbx_chi_squared 2.15 _diffrn_reflns.av_sigmaI_over_netI 55.24 _diffrn_reflns.pdbx_redundancy 13.30 _diffrn_reflns.pdbx_percent_possible_obs 97.30 _diffrn_reflns.number 284542 _diffrn_reflns.pdbx_observed_criterion ? _diffrn_reflns.limit_h_max ? _diffrn_reflns.limit_h_min ? _diffrn_reflns.limit_k_max ? _diffrn_reflns.limit_k_min ? _diffrn_reflns.limit_l_max ? _diffrn_reflns.limit_l_min ? # loop_ _pdbx_diffrn_reflns_shell.diffrn_id _pdbx_diffrn_reflns_shell.d_res_high _pdbx_diffrn_reflns_shell.d_res_low _pdbx_diffrn_reflns_shell.number_obs _pdbx_diffrn_reflns_shell.rejects _pdbx_diffrn_reflns_shell.Rmerge_I_obs _pdbx_diffrn_reflns_shell.Rsym_value _pdbx_diffrn_reflns_shell.chi_squared _pdbx_diffrn_reflns_shell.redundancy _pdbx_diffrn_reflns_shell.percent_possible_obs 1 3.53 50.00 ? ? 0.052 ? 5.062 13.20 98.70 1 2.80 3.53 ? ? 0.053 ? 3.603 14.90 100.00 1 2.45 2.80 ? ? 0.065 ? 3.595 15.20 100.00 1 2.22 2.45 ? ? 0.067 ? 3.051 15.10 100.00 1 2.06 2.22 ? ? 0.070 ? 2.510 15.30 100.00 1 1.94 2.06 ? ? 0.078 ? 2.424 15.10 100.00 1 1.84 1.94 ? ? 0.091 ? 2.264 14.90 100.00 1 1.76 1.84 ? ? 0.112 ? 2.177 14.80 100.00 1 1.70 1.76 ? ? 0.121 ? 1.736 15.00 100.00 1 1.64 1.70 ? ? 0.131 ? 1.581 14.90 100.00 1 1.59 1.64 ? ? 0.152 ? 1.427 14.90 100.00 1 1.54 1.59 ? ? 0.165 ? 1.387 14.90 100.00 1 1.50 1.54 ? ? 0.188 ? 1.330 14.60 100.00 1 1.46 1.50 ? ? 0.223 ? 1.247 14.70 99.80 1 1.43 1.46 ? ? 0.254 ? 1.109 13.30 100.00 1 1.40 1.43 ? ? 0.270 ? 1.034 10.90 97.50 1 1.37 1.40 ? ? 0.292 ? 1.000 9.30 94.30 1 1.35 1.37 ? ? 0.310 ? 0.982 8.20 88.90 1 1.32 1.35 ? ? 0.327 ? 0.934 7.20 84.70 1 1.30 1.32 ? ? 0.370 ? 0.956 6.30 81.30 # _pdbx_phasing_MAD_set.id 1 _pdbx_phasing_MAD_set.d_res_high 1.30 _pdbx_phasing_MAD_set.d_res_low 38.15 _pdbx_phasing_MAD_set.reflns_acentric 17906 _pdbx_phasing_MAD_set.loc_acentric 0.100 _pdbx_phasing_MAD_set.power_acentric 0.000 _pdbx_phasing_MAD_set.R_cullis_acentric 1.680 _pdbx_phasing_MAD_set.reflns_centric 3370 _pdbx_phasing_MAD_set.loc_centric 0.100 _pdbx_phasing_MAD_set.power_centric 0.000 _pdbx_phasing_MAD_set.R_cullis_centric 1.000 # loop_ _pdbx_phasing_MAD_set_shell.id _pdbx_phasing_MAD_set_shell.d_res_high _pdbx_phasing_MAD_set_shell.d_res_low _pdbx_phasing_MAD_set_shell.reflns_acentric _pdbx_phasing_MAD_set_shell.loc_acentric _pdbx_phasing_MAD_set_shell.power_acentric _pdbx_phasing_MAD_set_shell.R_cullis_acentric _pdbx_phasing_MAD_set_shell.reflns_centric _pdbx_phasing_MAD_set_shell.loc_centric _pdbx_phasing_MAD_set_shell.power_centric _pdbx_phasing_MAD_set_shell.R_cullis_centric 1 8.40 38.15 35 0.300 0.000 1.310 61 0.200 0.000 1.000 1 4.72 8.40 262 0.300 0.000 1.750 182 0.200 0.000 1.000 1 3.28 4.72 683 0.200 0.000 1.140 283 0.200 0.000 1.000 1 2.51 3.28 1335 0.200 0.000 1.440 397 0.100 0.000 1.000 1 2.04 2.51 2188 0.100 0.000 1.470 501 0.100 0.000 1.000 1 1.71 2.04 3239 0.100 0.000 1.870 598 0.000 0.000 1.000 1 1.48 1.71 4539 0.000 0.000 2.400 702 0.000 0.000 1.000 1 1.30 1.48 5625 0.000 0.000 4.080 646 0.000 0.000 1.000 # loop_ _pdbx_phasing_MAD_set_site.id _pdbx_phasing_MAD_set_site.atom_type_symbol _pdbx_phasing_MAD_set_site.fract_x _pdbx_phasing_MAD_set_site.fract_y _pdbx_phasing_MAD_set_site.fract_z _pdbx_phasing_MAD_set_site.b_iso _pdbx_phasing_MAD_set_site.occupancy_iso _pdbx_phasing_MAD_set_site.occupancy 1 Se -0.681 -0.913 -0.045 19.4581 0.000 3.970 2 Se -0.937 -1.043 -0.096 20.3965 0.000 3.929 3 Se -0.917 -0.921 -0.130 20.2329 0.000 3.204 4 Se -1.153 -0.904 -0.047 12.481 0.000 0.143 # loop_ _pdbx_phasing_MAD_shell.d_res_high _pdbx_phasing_MAD_shell.d_res_low _pdbx_phasing_MAD_shell.reflns _pdbx_phasing_MAD_shell.fom _pdbx_phasing_MAD_shell.reflns_centric _pdbx_phasing_MAD_shell.fom_centric _pdbx_phasing_MAD_shell.reflns_acentric _pdbx_phasing_MAD_shell.fom_acentric 8.40 38.15 96 0.191 61 0.000 35 0.525 4.72 8.40 444 0.346 182 0.000 262 0.586 3.28 4.72 966 0.338 283 0.000 683 0.478 2.51 3.28 1732 0.393 397 0.000 1335 0.510 2.04 2.51 2689 0.313 501 0.000 2188 0.384 1.71 2.04 3837 0.285 598 0.000 3239 0.338 1.48 1.71 5241 0.220 702 0.000 4539 0.254 1.30 1.48 6271 0.120 646 0.000 5625 0.134 # _pdbx_phasing_dm.entry_id 3NBM _pdbx_phasing_dm.method 'Solvent flattening and Histogram matching' _pdbx_phasing_dm.reflns 21276 # loop_ _pdbx_phasing_dm_shell.d_res_high _pdbx_phasing_dm_shell.d_res_low _pdbx_phasing_dm_shell.delta_phi_final _pdbx_phasing_dm_shell.delta_phi_initial _pdbx_phasing_dm_shell.fom_acentric _pdbx_phasing_dm_shell.fom_centric _pdbx_phasing_dm_shell.fom _pdbx_phasing_dm_shell.reflns_acentric _pdbx_phasing_dm_shell.reflns_centric _pdbx_phasing_dm_shell.reflns 4.810 100.000 69.600 ? ? ? 0.769 ? ? 508 3.770 4.810 65.700 ? ? ? 0.874 ? ? 509 3.270 3.770 67.200 ? ? ? 0.860 ? ? 508 2.960 3.270 62.900 ? ? ? 0.866 ? ? 503 2.730 2.960 69.400 ? ? ? 0.843 ? ? 530 2.540 2.730 64.100 ? ? ? 0.828 ? ? 570 2.390 2.540 66.400 ? ? ? 0.830 ? ? 608 2.270 2.390 63.800 ? ? ? 0.804 ? ? 625 2.160 2.270 68.100 ? ? ? 0.815 ? ? 668 2.060 2.160 66.900 ? ? ? 0.788 ? ? 690 1.980 2.060 62.000 ? ? ? 0.819 ? ? 714 1.910 1.980 69.500 ? ? ? 0.799 ? ? 761 1.840 1.910 67.300 ? ? ? 0.789 ? ? 771 1.780 1.840 67.200 ? ? ? 0.779 ? ? 788 1.730 1.780 69.400 ? ? ? 0.754 ? ? 818 1.680 1.730 73.100 ? ? ? 0.754 ? ? 852 1.630 1.680 71.800 ? ? ? 0.746 ? ? 881 1.590 1.630 72.800 ? ? ? 0.715 ? ? 860 1.550 1.590 71.900 ? ? ? 0.700 ? ? 927 1.510 1.550 75.400 ? ? ? 0.704 ? ? 941 1.480 1.510 77.100 ? ? ? 0.689 ? ? 934 1.450 1.480 73.900 ? ? ? 0.680 ? ? 981 1.420 1.450 80.100 ? ? ? 0.685 ? ? 987 1.390 1.420 77.200 ? ? ? 0.657 ? ? 979 1.360 1.390 84.600 ? ? ? 0.657 ? ? 948 1.340 1.360 81.800 ? ? ? 0.650 ? ? 930 1.300 1.340 84.900 ? ? ? 0.621 ? ? 1485 # _phasing.method SAD # _phasing_MAD.entry_id 3NBM _phasing_MAD.pdbx_d_res_high 1.30 _phasing_MAD.pdbx_d_res_low 38.15 _phasing_MAD.pdbx_reflns 21276 _phasing_MAD.pdbx_fom 0.236 _phasing_MAD.pdbx_reflns_centric 3370 _phasing_MAD.pdbx_fom_centric 0.000 _phasing_MAD.pdbx_reflns_acentric 17906 _phasing_MAD.pdbx_fom_acentric 0.280 # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 MLPHARE . ? other 'Eleanor J. Dodson' ccp4@ccp4.ac.uk phasing http://www.ccp4.ac.uk/dist/html/mlphare.html Fortran_77 ? 4 DM 6.0 ? program 'Kevin Cowtan' kowtan@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/dm.html Fortran_77 ? 5 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 6 PDB_EXTRACT 3.100 'May. 21, 2010' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 7 SBC-Collect . ? ? ? ? 'data collection' ? ? ? 8 HKL-3000 . ? ? ? ? 'data reduction' ? ? ? 9 HKL-3000 . ? ? ? ? 'data scaling' ? ? ? 10 HKL-3000 . ? ? ? ? phasing ? ? ? 11 SHELXD . ? ? ? ? phasing ? ? ? 12 SHELXE . ? ? ? ? 'model building' ? ? ? 13 SOLVE . ? ? ? ? phasing ? ? ? 14 RESOLVE . ? ? ? ? phasing ? ? ? 15 ARP/wARP . ? ? ? ? 'model building' ? ? ? 16 CCP4 . ? ? ? ? phasing ? ? ? 17 O . ? ? ? ? 'model building' ? ? ? 18 Coot . ? ? ? ? 'model building' ? ? ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 47 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 101 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 3_544 _pdbx_validate_symm_contact.dist 2.15 # 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 1 A LYS 454 ? CG ? A LYS 5 CG 2 1 Y 1 A LYS 454 ? CD ? A LYS 5 CD 3 1 Y 1 A LYS 454 ? CE ? A LYS 5 CE 4 1 Y 1 A LYS 454 ? NZ ? A LYS 5 NZ 5 1 Y 1 A ARG 517 ? CG ? A ARG 68 CG 6 1 Y 1 A ARG 517 ? CD ? A ARG 68 CD 7 1 Y 1 A ARG 517 ? NE ? A ARG 68 NE 8 1 Y 1 A ARG 517 ? CZ ? A ARG 68 CZ 9 1 Y 1 A ARG 517 ? NH1 ? A ARG 68 NH1 10 1 Y 1 A ARG 517 ? NH2 ? A ARG 68 NH2 11 1 Y 1 A ARG 525 ? CG ? A ARG 76 CG 12 1 Y 1 A ARG 525 ? CD ? A ARG 76 CD 13 1 Y 1 A ARG 525 ? NE ? A ARG 76 NE 14 1 Y 1 A ARG 525 ? CZ ? A ARG 76 CZ 15 1 Y 1 A ARG 525 ? NH1 ? A ARG 76 NH1 16 1 Y 1 A ARG 525 ? NH2 ? A ARG 76 NH2 # 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 SER 450 ? A SER 1 2 1 Y 1 A ASN 451 ? A ASN 2 3 1 Y 1 A ALA 452 ? A ALA 3 4 1 Y 1 A SER 453 ? A SER 4 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 water HOH #