data_4HWM # _entry.id 4HWM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4HWM pdb_00004hwm 10.2210/pdb4hwm/pdb RCSB RCSB076011 ? ? WWPDB D_1000076011 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-386122 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4HWM _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-11-08 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of a lipoprotein YedD (KPN_02420) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.38 A resolution' _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 ? # _citation_author.citation_id primary _citation_author.name 'Joint Center for Structural Genomics (JCSG)' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # _cell.entry_id 4HWM _cell.length_a 39.810 _cell.length_b 51.067 _cell.length_c 52.436 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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 4HWM _symmetry.Int_Tables_number 19 _symmetry.space_group_name_H-M 'P 21 21 21' _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 'Uncharacterized protein yedD' 14453.691 1 ? ? 'UNP residues 16-144' ? 2 water nat water 18.015 154 ? ? ? ? # _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 ;GGCVQVDRYEDVVKAPAPAGLAGFWQTKGPQSA(MSE)(MSE)SPDAIASLIVTKEGDTFDCRQWQRVIAQPGKL(MSE) NRDSEIYNVTASLDIYPVEREGNTISYDR(MSE)TLSRVERLTPECEKAWAKARATGPVSAPASTR ; _entity_poly.pdbx_seq_one_letter_code_can ;GGCVQVDRYEDVVKAPAPAGLAGFWQTKGPQSAMMSPDAIASLIVTKEGDTFDCRQWQRVIAQPGKLMNRDSEIYNVTAS LDIYPVEREGNTISYDRMTLSRVERLTPECEKAWAKARATGPVSAPASTR ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier JCSG-386122 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 GLY n 1 3 CYS n 1 4 VAL n 1 5 GLN n 1 6 VAL n 1 7 ASP n 1 8 ARG n 1 9 TYR n 1 10 GLU n 1 11 ASP n 1 12 VAL n 1 13 VAL n 1 14 LYS n 1 15 ALA n 1 16 PRO n 1 17 ALA n 1 18 PRO n 1 19 ALA n 1 20 GLY n 1 21 LEU n 1 22 ALA n 1 23 GLY n 1 24 PHE n 1 25 TRP n 1 26 GLN n 1 27 THR n 1 28 LYS n 1 29 GLY n 1 30 PRO n 1 31 GLN n 1 32 SER n 1 33 ALA n 1 34 MSE n 1 35 MSE n 1 36 SER n 1 37 PRO n 1 38 ASP n 1 39 ALA n 1 40 ILE n 1 41 ALA n 1 42 SER n 1 43 LEU n 1 44 ILE n 1 45 VAL n 1 46 THR n 1 47 LYS n 1 48 GLU n 1 49 GLY n 1 50 ASP n 1 51 THR n 1 52 PHE n 1 53 ASP n 1 54 CYS n 1 55 ARG n 1 56 GLN n 1 57 TRP n 1 58 GLN n 1 59 ARG n 1 60 VAL n 1 61 ILE n 1 62 ALA n 1 63 GLN n 1 64 PRO n 1 65 GLY n 1 66 LYS n 1 67 LEU n 1 68 MSE n 1 69 ASN n 1 70 ARG n 1 71 ASP n 1 72 SER n 1 73 GLU n 1 74 ILE n 1 75 TYR n 1 76 ASN n 1 77 VAL n 1 78 THR n 1 79 ALA n 1 80 SER n 1 81 LEU n 1 82 ASP n 1 83 ILE n 1 84 TYR n 1 85 PRO n 1 86 VAL n 1 87 GLU n 1 88 ARG n 1 89 GLU n 1 90 GLY n 1 91 ASN n 1 92 THR n 1 93 ILE n 1 94 SER n 1 95 TYR n 1 96 ASP n 1 97 ARG n 1 98 MSE n 1 99 THR n 1 100 LEU n 1 101 SER n 1 102 ARG n 1 103 VAL n 1 104 GLU n 1 105 ARG n 1 106 LEU n 1 107 THR n 1 108 PRO n 1 109 GLU n 1 110 CYS n 1 111 GLU n 1 112 LYS n 1 113 ALA n 1 114 TRP n 1 115 ALA n 1 116 LYS n 1 117 ALA n 1 118 ARG n 1 119 ALA n 1 120 THR n 1 121 GLY n 1 122 PRO n 1 123 VAL n 1 124 SER n 1 125 ALA n 1 126 PRO n 1 127 ALA n 1 128 SER n 1 129 THR n 1 130 ARG 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 'yedD, KPN78578_23820, KPN_02420' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 700721 / MGH 78578' _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 'Klebsiella pneumoniae subsp. pneumoniae' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 272620 _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 PB1 _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 SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A6TB72_KLEP7 _struct_ref.pdbx_db_accession A6TB72 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;GCVQVDRYEDVVKAPAPAGLAGFWQTKGPQSAMMSPDAIASLIVTKEGDTFDCRQWQRVIAQPGKLMNRDSEIYNVTASL DIYPVEREGNTISYDRMTLSRVERLTPECEKAWAKARATGPVSAPASTR ; _struct_ref.pdbx_align_begin 16 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4HWM _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 130 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A6TB72 _struct_ref_seq.db_align_beg 16 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 144 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 16 _struct_ref_seq.pdbx_auth_seq_align_end 144 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4HWM _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code A6TB72 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 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 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 4HWM # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.84 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 33.29 _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 9.5 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details '30.00% polyethylene glycol 3000, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K' _exptl_crystal_grow.temp_details ? _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 315' _diffrn_detector.details 'KOHZU: Double Crystal Si(111)' _diffrn_detector.pdbx_collection_date 2012-09-19 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Double Crystal Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.979133 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.pdbx_wavelength 0.979133 _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site ALS # _reflns.entry_id 4HWM _reflns.d_resolution_high 1.38 _reflns.d_resolution_low 39.810 _reflns.number_obs 22613 _reflns.pdbx_Rmerge_I_obs 0.045 _reflns.pdbx_netI_over_sigmaI 15.440 _reflns.percent_possible_obs 99.800 _reflns.B_iso_Wilson_estimate 16.745 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy 7.00 _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 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.380 1.430 15472 ? 4254 0.841 1.5 ? ? ? ? ? 99.600 1 1 1.430 1.490 16489 ? 4425 0.574 2.3 ? ? ? ? ? 100.000 2 1 1.490 1.550 14024 ? 3761 0.371 3.5 ? ? ? ? ? 100.000 3 1 1.550 1.640 17556 ? 4681 0.249 5.4 ? ? ? ? ? 99.900 4 1 1.640 1.740 15583 ? 4131 0.163 8.1 ? ? ? ? ? 100.000 5 1 1.740 1.870 15515 ? 4108 0.094 12.8 ? ? ? ? ? 100.000 6 1 1.870 2.060 16212 ? 4288 0.056 20.1 ? ? ? ? ? 99.900 7 1 2.060 2.360 16112 ? 4282 0.042 26.6 ? ? ? ? ? 99.800 8 1 2.360 2.970 15573 ? 4230 0.033 33.2 ? ? ? ? ? 99.900 9 1 2.970 39.810 15822 ? 4258 0.027 40.7 ? ? ? ? ? 99.300 10 1 # _refine.entry_id 4HWM _refine.ls_d_res_high 1.3800 _refine.ls_d_res_low 39.810 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.8900 _refine.ls_number_reflns_obs 22564 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1509 _refine.ls_R_factor_R_work 0.1494 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.1795 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.1000 _refine.ls_number_reflns_R_free 1152 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 21.1093 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.1500 _refine.aniso_B[2][2] 0.0800 _refine.aniso_B[3][3] -0.2300 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9740 _refine.correlation_coeff_Fo_to_Fc_free 0.9690 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.0680 _refine.pdbx_overall_ESU_R_Free 0.0590 _refine.overall_SU_ML 0.0380 _refine.overall_SU_B 2.1450 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _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 ? _refine.B_iso_max 64.570 _refine.B_iso_min 9.320 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 0.150 _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 910 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 154 _refine_hist.number_atoms_total 1064 _refine_hist.d_res_high 1.3800 _refine_hist.d_res_low 39.810 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 1037 0.013 0.022 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 741 0.002 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1431 1.567 1.971 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 1820 1.025 3.002 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 145 6.041 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 49 41.573 24.082 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 192 13.045 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 10 16.273 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 156 0.103 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 1192 0.007 0.021 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 207 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_mcbond_it 639 2.601 3.000 ? ? 'X-RAY DIFFRACTION' r_mcbond_other 250 1.851 3.000 ? ? 'X-RAY DIFFRACTION' r_mcangle_it 1052 4.030 5.000 ? ? 'X-RAY DIFFRACTION' r_scbond_it 398 4.694 8.000 ? ? 'X-RAY DIFFRACTION' r_scangle_it 363 6.592 11.000 ? ? 'X-RAY DIFFRACTION' r_rigid_bond_restr 1778 1.912 3.000 ? ? 'X-RAY DIFFRACTION' r_sphericity_free 156 7.608 3.000 ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded 1741 4.468 3.000 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 1.3800 _refine_ls_shell.d_res_low 1.4160 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.8800 _refine_ls_shell.number_reflns_R_work 1556 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2530 _refine_ls_shell.R_factor_R_free 0.2920 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 66 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1622 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 4HWM _struct.title 'Crystal structure of a lipoprotein YedD (KPN_02420) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.38 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag Y _struct.pdbx_model_type_details ? # _struct_keywords.text ;YedD-like protein, PF13987 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION ; _struct_keywords.pdbx_keywords 'STRUCTURAL GENOMICS, UNKNOWN FUNCTION' _struct_keywords.entry_id 4HWM # 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 ARG A 8 ? VAL A 12 ? ARG A 22 VAL A 26 5 ? 5 HELX_P HELX_P2 2 THR A 107 ? ALA A 119 ? THR A 121 ALA A 133 1 ? 13 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 54 SG ? ? ? 1_555 A CYS 110 SG B ? A CYS 68 A CYS 124 1_555 ? ? ? ? ? ? ? 2.081 ? ? covale1 covale both ? A ALA 33 C ? ? ? 1_555 A MSE 34 N A ? A ALA 47 A MSE 48 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale2 covale both ? A ALA 33 C ? ? ? 1_555 A MSE 34 N B ? A ALA 47 A MSE 48 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale3 covale both ? A MSE 34 C A ? ? 1_555 A MSE 35 N ? ? A MSE 48 A MSE 49 1_555 ? ? ? ? ? ? ? 1.321 ? ? covale4 covale both ? A MSE 34 C B ? ? 1_555 A MSE 35 N ? ? A MSE 48 A MSE 49 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale5 covale both ? A MSE 35 C ? ? ? 1_555 A SER 36 N ? ? A MSE 49 A SER 50 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale6 covale both ? A LEU 67 C ? ? ? 1_555 A MSE 68 N ? ? A LEU 81 A MSE 82 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale7 covale both ? A MSE 68 C ? ? ? 1_555 A ASN 69 N ? ? A MSE 82 A ASN 83 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale8 covale both ? A ARG 97 C ? ? ? 1_555 A MSE 98 N ? ? A ARG 111 A MSE 112 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale9 covale both ? A MSE 98 C ? ? ? 1_555 A THR 99 N ? ? A MSE 112 A THR 113 1_555 ? ? ? ? ? ? ? 1.318 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 9 _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 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? anti-parallel A 6 7 ? anti-parallel A 7 8 ? anti-parallel A 8 9 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 GLY A 23 ? GLN A 26 ? GLY A 37 GLN A 40 A 2 ILE A 40 ? VAL A 45 ? ILE A 54 VAL A 59 A 3 ASP A 50 ? GLN A 56 ? ASP A 64 GLN A 70 A 4 VAL A 60 ? ARG A 70 ? VAL A 74 ARG A 84 A 5 GLU A 73 ? THR A 78 ? GLU A 87 THR A 92 A 6 ILE A 83 ? GLU A 89 ? ILE A 97 GLU A 103 A 7 THR A 92 ? TYR A 95 ? THR A 106 TYR A 109 A 8 MSE A 98 ? VAL A 103 ? MSE A 112 VAL A 117 A 9 GLY A 23 ? GLN A 26 ? GLY A 37 GLN A 40 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N GLY A 23 ? N GLY A 37 O VAL A 45 ? O VAL A 59 A 2 3 N ILE A 40 ? N ILE A 54 O GLN A 56 ? O GLN A 70 A 3 4 N ARG A 55 ? N ARG A 69 O ILE A 61 ? O ILE A 75 A 4 5 N LYS A 66 ? N LYS A 80 O VAL A 77 ? O VAL A 91 A 5 6 N ASN A 76 ? N ASN A 90 O TYR A 84 ? O TYR A 98 A 6 7 N GLU A 89 ? N GLU A 103 O THR A 92 ? O THR A 106 A 7 8 N ILE A 93 ? N ILE A 107 O LEU A 100 ? O LEU A 114 A 8 9 O SER A 101 ? O SER A 115 N GLN A 26 ? N GLN A 40 # _atom_sites.entry_id 4HWM _atom_sites.fract_transf_matrix[1][1] 0.025119 _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] 0.019582 _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] 0.019071 _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 GLY 1 0 ? ? ? A . n A 1 2 GLY 2 16 ? ? ? A . n A 1 3 CYS 3 17 ? ? ? A . n A 1 4 VAL 4 18 ? ? ? A . n A 1 5 GLN 5 19 ? ? ? A . n A 1 6 VAL 6 20 ? ? ? A . n A 1 7 ASP 7 21 21 ASP ASP A . n A 1 8 ARG 8 22 22 ARG ARG A . n A 1 9 TYR 9 23 23 TYR TYR A . n A 1 10 GLU 10 24 24 GLU GLU A . n A 1 11 ASP 11 25 25 ASP ASP A . n A 1 12 VAL 12 26 26 VAL VAL A . n A 1 13 VAL 13 27 27 VAL VAL A . n A 1 14 LYS 14 28 28 LYS LYS A . n A 1 15 ALA 15 29 29 ALA ALA A . n A 1 16 PRO 16 30 30 PRO PRO A . n A 1 17 ALA 17 31 31 ALA ALA A . n A 1 18 PRO 18 32 32 PRO PRO A . n A 1 19 ALA 19 33 33 ALA ALA A . n A 1 20 GLY 20 34 34 GLY GLY A . n A 1 21 LEU 21 35 35 LEU LEU A . n A 1 22 ALA 22 36 36 ALA ALA A . n A 1 23 GLY 23 37 37 GLY GLY A . n A 1 24 PHE 24 38 38 PHE PHE A . n A 1 25 TRP 25 39 39 TRP TRP A . n A 1 26 GLN 26 40 40 GLN GLN A . n A 1 27 THR 27 41 41 THR THR A . n A 1 28 LYS 28 42 42 LYS LYS A . n A 1 29 GLY 29 43 43 GLY GLY A . n A 1 30 PRO 30 44 44 PRO PRO A . n A 1 31 GLN 31 45 45 GLN GLN A . n A 1 32 SER 32 46 46 SER SER A . n A 1 33 ALA 33 47 47 ALA ALA A . n A 1 34 MSE 34 48 48 MSE MSE A . n A 1 35 MSE 35 49 49 MSE MSE A . n A 1 36 SER 36 50 50 SER SER A . n A 1 37 PRO 37 51 51 PRO PRO A . n A 1 38 ASP 38 52 52 ASP ASP A . n A 1 39 ALA 39 53 53 ALA ALA A . n A 1 40 ILE 40 54 54 ILE ILE A . n A 1 41 ALA 41 55 55 ALA ALA A . n A 1 42 SER 42 56 56 SER SER A . n A 1 43 LEU 43 57 57 LEU LEU A . n A 1 44 ILE 44 58 58 ILE ILE A . n A 1 45 VAL 45 59 59 VAL VAL A . n A 1 46 THR 46 60 60 THR THR A . n A 1 47 LYS 47 61 61 LYS LYS A . n A 1 48 GLU 48 62 62 GLU GLU A . n A 1 49 GLY 49 63 63 GLY GLY A . n A 1 50 ASP 50 64 64 ASP ASP A . n A 1 51 THR 51 65 65 THR THR A . n A 1 52 PHE 52 66 66 PHE PHE A . n A 1 53 ASP 53 67 67 ASP ASP A . n A 1 54 CYS 54 68 68 CYS CYS A . n A 1 55 ARG 55 69 69 ARG ARG A . n A 1 56 GLN 56 70 70 GLN GLN A . n A 1 57 TRP 57 71 71 TRP TRP A . n A 1 58 GLN 58 72 72 GLN GLN A . n A 1 59 ARG 59 73 73 ARG ARG A . n A 1 60 VAL 60 74 74 VAL VAL A . n A 1 61 ILE 61 75 75 ILE ILE A . n A 1 62 ALA 62 76 76 ALA ALA A . n A 1 63 GLN 63 77 77 GLN GLN A . n A 1 64 PRO 64 78 78 PRO PRO A . n A 1 65 GLY 65 79 79 GLY GLY A . n A 1 66 LYS 66 80 80 LYS LYS A . n A 1 67 LEU 67 81 81 LEU LEU A . n A 1 68 MSE 68 82 82 MSE MSE A . n A 1 69 ASN 69 83 83 ASN ASN A . n A 1 70 ARG 70 84 84 ARG ARG A . n A 1 71 ASP 71 85 85 ASP ASP A . n A 1 72 SER 72 86 86 SER SER A . n A 1 73 GLU 73 87 87 GLU GLU A . n A 1 74 ILE 74 88 88 ILE ILE A . n A 1 75 TYR 75 89 89 TYR TYR A . n A 1 76 ASN 76 90 90 ASN ASN A . n A 1 77 VAL 77 91 91 VAL VAL A . n A 1 78 THR 78 92 92 THR THR A . n A 1 79 ALA 79 93 93 ALA ALA A . n A 1 80 SER 80 94 94 SER SER A . n A 1 81 LEU 81 95 95 LEU LEU A . n A 1 82 ASP 82 96 96 ASP ASP A . n A 1 83 ILE 83 97 97 ILE ILE A . n A 1 84 TYR 84 98 98 TYR TYR A . n A 1 85 PRO 85 99 99 PRO PRO A . n A 1 86 VAL 86 100 100 VAL VAL A . n A 1 87 GLU 87 101 101 GLU GLU A . n A 1 88 ARG 88 102 102 ARG ARG A . n A 1 89 GLU 89 103 103 GLU GLU A . n A 1 90 GLY 90 104 104 GLY GLY A . n A 1 91 ASN 91 105 105 ASN ASN A . n A 1 92 THR 92 106 106 THR THR A . n A 1 93 ILE 93 107 107 ILE ILE A . n A 1 94 SER 94 108 108 SER SER A . n A 1 95 TYR 95 109 109 TYR TYR A . n A 1 96 ASP 96 110 110 ASP ASP A . n A 1 97 ARG 97 111 111 ARG ARG A . n A 1 98 MSE 98 112 112 MSE MSE A . n A 1 99 THR 99 113 113 THR THR A . n A 1 100 LEU 100 114 114 LEU LEU A . n A 1 101 SER 101 115 115 SER SER A . n A 1 102 ARG 102 116 116 ARG ARG A . n A 1 103 VAL 103 117 117 VAL VAL A . n A 1 104 GLU 104 118 118 GLU GLU A . n A 1 105 ARG 105 119 119 ARG ARG A . n A 1 106 LEU 106 120 120 LEU LEU A . n A 1 107 THR 107 121 121 THR THR A . n A 1 108 PRO 108 122 122 PRO PRO A . n A 1 109 GLU 109 123 123 GLU GLU A . n A 1 110 CYS 110 124 124 CYS CYS A . n A 1 111 GLU 111 125 125 GLU GLU A . n A 1 112 LYS 112 126 126 LYS LYS A . n A 1 113 ALA 113 127 127 ALA ALA A . n A 1 114 TRP 114 128 128 TRP TRP A . n A 1 115 ALA 115 129 129 ALA ALA A . n A 1 116 LYS 116 130 130 LYS LYS A . n A 1 117 ALA 117 131 131 ALA ALA A . n A 1 118 ARG 118 132 132 ARG ARG A . n A 1 119 ALA 119 133 133 ALA ALA A . n A 1 120 THR 120 134 134 THR THR A . n A 1 121 GLY 121 135 135 GLY GLY A . n A 1 122 PRO 122 136 136 PRO PRO A . n A 1 123 VAL 123 137 137 VAL VAL A . n A 1 124 SER 124 138 ? ? ? A . n A 1 125 ALA 125 139 ? ? ? A . n A 1 126 PRO 126 140 ? ? ? A . n A 1 127 ALA 127 141 ? ? ? A . n A 1 128 SER 128 142 ? ? ? A . n A 1 129 THR 129 143 ? ? ? A . n A 1 130 ARG 130 144 ? ? ? A . n # _pdbx_SG_project.project_name PSI:Biology _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # 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 1 201 245 HOH HOH A . B 2 HOH 2 202 246 HOH HOH A . B 2 HOH 3 203 247 HOH HOH A . B 2 HOH 4 204 248 HOH HOH A . B 2 HOH 5 205 249 HOH HOH A . B 2 HOH 6 206 250 HOH HOH A . B 2 HOH 7 207 251 HOH HOH A . B 2 HOH 8 208 252 HOH HOH A . B 2 HOH 9 209 253 HOH HOH A . B 2 HOH 10 210 254 HOH HOH A . B 2 HOH 11 211 255 HOH HOH A . B 2 HOH 12 212 256 HOH HOH A . B 2 HOH 13 213 257 HOH HOH A . B 2 HOH 14 214 258 HOH HOH A . B 2 HOH 15 215 259 HOH HOH A . B 2 HOH 16 216 260 HOH HOH A . B 2 HOH 17 217 261 HOH HOH A . B 2 HOH 18 218 262 HOH HOH A . B 2 HOH 19 219 263 HOH HOH A . B 2 HOH 20 220 264 HOH HOH A . B 2 HOH 21 221 265 HOH HOH A . B 2 HOH 22 222 266 HOH HOH A . B 2 HOH 23 223 267 HOH HOH A . B 2 HOH 24 224 268 HOH HOH A . B 2 HOH 25 225 269 HOH HOH A . B 2 HOH 26 226 270 HOH HOH A . B 2 HOH 27 227 271 HOH HOH A . B 2 HOH 28 228 272 HOH HOH A . B 2 HOH 29 229 273 HOH HOH A . B 2 HOH 30 230 274 HOH HOH A . B 2 HOH 31 231 275 HOH HOH A . B 2 HOH 32 232 276 HOH HOH A . B 2 HOH 33 233 277 HOH HOH A . B 2 HOH 34 234 278 HOH HOH A . B 2 HOH 35 235 279 HOH HOH A . B 2 HOH 36 236 280 HOH HOH A . B 2 HOH 37 237 281 HOH HOH A . B 2 HOH 38 238 282 HOH HOH A . B 2 HOH 39 239 283 HOH HOH A . B 2 HOH 40 240 284 HOH HOH A . B 2 HOH 41 241 285 HOH HOH A . B 2 HOH 42 242 286 HOH HOH A . B 2 HOH 43 243 287 HOH HOH A . B 2 HOH 44 244 288 HOH HOH A . B 2 HOH 45 245 289 HOH HOH A . B 2 HOH 46 246 290 HOH HOH A . B 2 HOH 47 247 291 HOH HOH A . B 2 HOH 48 248 292 HOH HOH A . B 2 HOH 49 249 293 HOH HOH A . B 2 HOH 50 250 294 HOH HOH A . B 2 HOH 51 251 295 HOH HOH A . B 2 HOH 52 252 296 HOH HOH A . B 2 HOH 53 253 297 HOH HOH A . B 2 HOH 54 254 298 HOH HOH A . B 2 HOH 55 255 299 HOH HOH A . B 2 HOH 56 256 300 HOH HOH A . B 2 HOH 57 257 301 HOH HOH A . B 2 HOH 58 258 302 HOH HOH A . B 2 HOH 59 259 303 HOH HOH A . B 2 HOH 60 260 304 HOH HOH A . B 2 HOH 61 261 305 HOH HOH A . B 2 HOH 62 262 306 HOH HOH A . B 2 HOH 63 263 307 HOH HOH A . B 2 HOH 64 264 308 HOH HOH A . B 2 HOH 65 265 309 HOH HOH A . B 2 HOH 66 266 310 HOH HOH A . B 2 HOH 67 267 311 HOH HOH A . B 2 HOH 68 268 312 HOH HOH A . B 2 HOH 69 269 313 HOH HOH A . B 2 HOH 70 270 314 HOH HOH A . B 2 HOH 71 271 315 HOH HOH A . B 2 HOH 72 272 316 HOH HOH A . B 2 HOH 73 273 317 HOH HOH A . B 2 HOH 74 274 318 HOH HOH A . B 2 HOH 75 275 319 HOH HOH A . B 2 HOH 76 276 320 HOH HOH A . B 2 HOH 77 277 321 HOH HOH A . B 2 HOH 78 278 322 HOH HOH A . B 2 HOH 79 279 323 HOH HOH A . B 2 HOH 80 280 324 HOH HOH A . B 2 HOH 81 281 325 HOH HOH A . B 2 HOH 82 282 326 HOH HOH A . B 2 HOH 83 283 327 HOH HOH A . B 2 HOH 84 284 328 HOH HOH A . B 2 HOH 85 285 329 HOH HOH A . B 2 HOH 86 286 330 HOH HOH A . B 2 HOH 87 287 331 HOH HOH A . B 2 HOH 88 288 332 HOH HOH A . B 2 HOH 89 289 333 HOH HOH A . B 2 HOH 90 290 334 HOH HOH A . B 2 HOH 91 291 335 HOH HOH A . B 2 HOH 92 292 336 HOH HOH A . B 2 HOH 93 293 337 HOH HOH A . B 2 HOH 94 294 338 HOH HOH A . B 2 HOH 95 295 339 HOH HOH A . B 2 HOH 96 296 340 HOH HOH A . B 2 HOH 97 297 341 HOH HOH A . B 2 HOH 98 298 342 HOH HOH A . B 2 HOH 99 299 343 HOH HOH A . B 2 HOH 100 300 344 HOH HOH A . B 2 HOH 101 301 345 HOH HOH A . B 2 HOH 102 302 346 HOH HOH A . B 2 HOH 103 303 347 HOH HOH A . B 2 HOH 104 304 348 HOH HOH A . B 2 HOH 105 305 349 HOH HOH A . B 2 HOH 106 306 350 HOH HOH A . B 2 HOH 107 307 351 HOH HOH A . B 2 HOH 108 308 352 HOH HOH A . B 2 HOH 109 309 353 HOH HOH A . B 2 HOH 110 310 354 HOH HOH A . B 2 HOH 111 311 355 HOH HOH A . B 2 HOH 112 312 356 HOH HOH A . B 2 HOH 113 313 357 HOH HOH A . B 2 HOH 114 314 358 HOH HOH A . B 2 HOH 115 315 359 HOH HOH A . B 2 HOH 116 316 360 HOH HOH A . B 2 HOH 117 317 361 HOH HOH A . B 2 HOH 118 318 362 HOH HOH A . B 2 HOH 119 319 363 HOH HOH A . B 2 HOH 120 320 364 HOH HOH A . B 2 HOH 121 321 365 HOH HOH A . B 2 HOH 122 322 366 HOH HOH A . B 2 HOH 123 323 367 HOH HOH A . B 2 HOH 124 324 368 HOH HOH A . B 2 HOH 125 325 369 HOH HOH A . B 2 HOH 126 326 370 HOH HOH A . B 2 HOH 127 327 371 HOH HOH A . B 2 HOH 128 328 372 HOH HOH A . B 2 HOH 129 329 373 HOH HOH A . B 2 HOH 130 330 374 HOH HOH A . B 2 HOH 131 331 375 HOH HOH A . B 2 HOH 132 332 376 HOH HOH A . B 2 HOH 133 333 377 HOH HOH A . B 2 HOH 134 334 378 HOH HOH A . B 2 HOH 135 335 379 HOH HOH A . B 2 HOH 136 336 380 HOH HOH A . B 2 HOH 137 337 381 HOH HOH A . B 2 HOH 138 338 382 HOH HOH A . B 2 HOH 139 339 383 HOH HOH A . B 2 HOH 140 340 384 HOH HOH A . B 2 HOH 141 341 385 HOH HOH A . B 2 HOH 142 342 386 HOH HOH A . B 2 HOH 143 343 387 HOH HOH A . B 2 HOH 144 344 388 HOH HOH A . B 2 HOH 145 345 389 HOH HOH A . B 2 HOH 146 346 390 HOH HOH A . B 2 HOH 147 347 391 HOH HOH A . B 2 HOH 148 348 392 HOH HOH A . B 2 HOH 149 349 393 HOH HOH A . B 2 HOH 150 350 394 HOH HOH A . B 2 HOH 151 351 395 HOH HOH A . B 2 HOH 152 352 396 HOH HOH A . B 2 HOH 153 353 397 HOH HOH A . B 2 HOH 154 354 398 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 34 A MSE 48 ? MET SELENOMETHIONINE 2 A MSE 35 A MSE 49 ? MET SELENOMETHIONINE 3 A MSE 68 A MSE 82 ? MET SELENOMETHIONINE 4 A MSE 98 A MSE 112 ? 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 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 2013-01-02 2 'Structure model' 1 1 2017-11-15 3 'Structure model' 1 2 2023-02-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Refinement description' 2 3 'Structure model' 'Database references' 3 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' software 2 3 'Structure model' database_2 3 3 'Structure model' struct_conn 4 3 'Structure model' struct_ref_seq_dif # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_software.classification' 2 2 'Structure model' '_software.name' 3 3 'Structure model' '_database_2.pdbx_DOI' 4 3 'Structure model' '_database_2.pdbx_database_accession' 5 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 3 'Structure model' '_struct_ref_seq_dif.details' # _phasing.method SAD # 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 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 2 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 3 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 4 SHARP . ? package 'Eric de La Fortelle' sharp-develop@globalphasing.com phasing http://www.globalphasing.com/sharp/ ? ? 5 XSCALE 'March 15, 2012' ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 6 REFMAC 5.5.0110 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 7 XDS . ? ? ? ? 'data reduction' ? ? ? 8 SHELXD . ? ? ? ? phasing ? ? ? # _pdbx_entry_details.entry_id 4HWM _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT (16-144) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 NH1 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 ARG _pdbx_validate_close_contact.auth_seq_id_1 111 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 352 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.19 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE A ARG 132 ? ? CZ A ARG 132 ? ? NH1 A ARG 132 ? ? 125.45 120.30 5.15 0.50 N 2 1 NE A ARG 132 ? ? CZ A ARG 132 ? ? NH2 A ARG 132 ? ? 116.84 120.30 -3.46 0.50 N # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id TRP _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 71 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -151.88 _pdbx_validate_torsion.psi -98.13 # 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 42 ? CD ? A LYS 28 CD 2 1 Y 1 A LYS 42 ? CE ? A LYS 28 CE 3 1 Y 1 A LYS 42 ? NZ ? A LYS 28 NZ # 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 GLY 0 ? A GLY 1 2 1 Y 1 A GLY 16 ? A GLY 2 3 1 Y 1 A CYS 17 ? A CYS 3 4 1 Y 1 A VAL 18 ? A VAL 4 5 1 Y 1 A GLN 19 ? A GLN 5 6 1 Y 1 A VAL 20 ? A VAL 6 7 1 Y 1 A SER 138 ? A SER 124 8 1 Y 1 A ALA 139 ? A ALA 125 9 1 Y 1 A PRO 140 ? A PRO 126 10 1 Y 1 A ALA 141 ? A ALA 127 11 1 Y 1 A SER 142 ? A SER 128 12 1 Y 1 A THR 143 ? A THR 129 13 1 Y 1 A ARG 144 ? A ARG 130 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #