data_4HLB # _entry.id 4HLB # _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 4HLB pdb_00004hlb 10.2210/pdb4hlb/pdb RCSB RCSB075608 ? ? WWPDB D_1000075608 ? ? # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id JCSG-420603 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 4HLB _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-10-16 _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 CASP _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 hypothetical protein (DESPIG_01740) from Desulfovibrio piger ATCC 29098 at 1.80 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 4HLB _cell.length_a 57.821 _cell.length_b 57.821 _cell.length_c 63.890 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _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.entry_id 4HLB _symmetry.Int_Tables_number 154 _symmetry.space_group_name_H-M 'P 32 2 1' _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' 12955.291 1 ? ? 'UNP residues 25-138' ? 2 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 3 water nat water 18.015 72 ? ? ? ? # _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 ;GAEQQADTVTENSDSEVFVDDSDRFTAFEEELLARYADKGIRSVDVAAYAKGIDIVFVAADRK(MSE)TRAEFSAIASRS IRELKERFGFDKDVPIGAVLDYKKDAATDTRTRFVLKLR ; _entity_poly.pdbx_seq_one_letter_code_can ;GAEQQADTVTENSDSEVFVDDSDRFTAFEEELLARYADKGIRSVDVAAYAKGIDIVFVAADRKMTRAEFSAIASRSIREL KERFGFDKDVPIGAVLDYKKDAATDTRTRFVLKLR ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier JCSG-420603 # 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 ALA n 1 3 GLU n 1 4 GLN n 1 5 GLN n 1 6 ALA n 1 7 ASP n 1 8 THR n 1 9 VAL n 1 10 THR n 1 11 GLU n 1 12 ASN n 1 13 SER n 1 14 ASP n 1 15 SER n 1 16 GLU n 1 17 VAL n 1 18 PHE n 1 19 VAL n 1 20 ASP n 1 21 ASP n 1 22 SER n 1 23 ASP n 1 24 ARG n 1 25 PHE n 1 26 THR n 1 27 ALA n 1 28 PHE n 1 29 GLU n 1 30 GLU n 1 31 GLU n 1 32 LEU n 1 33 LEU n 1 34 ALA n 1 35 ARG n 1 36 TYR n 1 37 ALA n 1 38 ASP n 1 39 LYS n 1 40 GLY n 1 41 ILE n 1 42 ARG n 1 43 SER n 1 44 VAL n 1 45 ASP n 1 46 VAL n 1 47 ALA n 1 48 ALA n 1 49 TYR n 1 50 ALA n 1 51 LYS n 1 52 GLY n 1 53 ILE n 1 54 ASP n 1 55 ILE n 1 56 VAL n 1 57 PHE n 1 58 VAL n 1 59 ALA n 1 60 ALA n 1 61 ASP n 1 62 ARG n 1 63 LYS n 1 64 MSE n 1 65 THR n 1 66 ARG n 1 67 ALA n 1 68 GLU n 1 69 PHE n 1 70 SER n 1 71 ALA n 1 72 ILE n 1 73 ALA n 1 74 SER n 1 75 ARG n 1 76 SER n 1 77 ILE n 1 78 ARG n 1 79 GLU n 1 80 LEU n 1 81 LYS n 1 82 GLU n 1 83 ARG n 1 84 PHE n 1 85 GLY n 1 86 PHE n 1 87 ASP n 1 88 LYS n 1 89 ASP n 1 90 VAL n 1 91 PRO n 1 92 ILE n 1 93 GLY n 1 94 ALA n 1 95 VAL n 1 96 LEU n 1 97 ASP n 1 98 TYR n 1 99 LYS n 1 100 LYS n 1 101 ASP n 1 102 ALA n 1 103 ALA n 1 104 THR n 1 105 ASP n 1 106 THR n 1 107 ARG n 1 108 THR n 1 109 ARG n 1 110 PHE n 1 111 VAL n 1 112 LEU n 1 113 LYS n 1 114 LEU n 1 115 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 ZP_03311821.1 _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 'Desulfovibrio piger' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 411464 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc 29098 _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 B6WUJ7_9DELT _struct_ref.pdbx_db_accession B6WUJ7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;AEQQADTVTENSDSEVFVDDSDRFTAFEEELLARYADKGIRSVDVAAYAKGIDIVFVAADRKMTRAEFSAIASRSIRELK ERFGFDKDVPIGAVLDYKKDAATDTRTRFVLKLR ; _struct_ref.pdbx_align_begin 25 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4HLB _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 115 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession B6WUJ7 _struct_ref_seq.db_align_beg 25 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 138 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 25 _struct_ref_seq.pdbx_auth_seq_align_end 138 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 4HLB _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 B6WUJ7 _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 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 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.method 'X-RAY DIFFRACTION' _exptl.entry_id 4HLB # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.38 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 48.31 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.pdbx_details ;0.20M sodium acetate, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K ; _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.pH 8.5 # _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.details 'KOHZU: Double Crystal Si(111)' _diffrn_detector.type 'ADSC QUANTUM 315' _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 MAD _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.979095 1.0 2 0.979338 1.0 3 0.953725 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_list 0.979095,0.979338,0.953725 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ALS # _reflns.entry_id 4HLB _reflns.d_resolution_high 1.80 _reflns.d_resolution_low 28.910 _reflns.number_all 11856 _reflns.number_obs 11856 _reflns.pdbx_netI_over_sigmaI 16.300 _reflns.pdbx_Rsym_value 0.103 _reflns.pdbx_redundancy 13.300 _reflns.percent_possible_obs 100.000 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.pdbx_Rmerge_I_obs ? _reflns.B_iso_Wilson_estimate 26.120 _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 1.800 1.850 ? 6715 ? 0.014 0.6 1.374 ? 8.000 ? 843 100.000 1 1 1.850 1.900 ? 11915 ? 0.014 0.7 1.152 ? 14.100 ? 846 100.000 2 1 1.900 1.950 ? 11514 ? 0.014 0.8 0.910 ? 14.100 ? 815 100.000 3 1 1.950 2.010 ? 11138 ? 0.014 1.2 0.649 ? 14.100 ? 791 100.000 4 1 2.010 2.080 ? 10834 ? 0.014 1.7 0.444 ? 14.000 ? 775 100.000 5 1 2.080 2.150 ? 10552 ? 0.014 2.4 0.315 ? 14.000 ? 755 100.000 6 1 2.150 2.230 ? 9844 ? 0.014 2.7 0.284 ? 14.000 ? 701 100.000 7 1 2.230 2.320 ? 9949 ? 0.014 3.0 0.253 ? 13.900 ? 714 100.000 8 1 2.320 2.430 ? 9227 ? 0.014 4.1 0.189 ? 13.900 ? 663 100.000 9 1 2.430 2.550 ? 8909 ? 0.014 4.8 0.153 ? 13.700 ? 648 100.000 10 1 2.550 2.680 ? 8395 ? 0.014 5.7 0.130 ? 13.900 ? 605 100.000 11 1 2.680 2.850 ? 7807 ? 0.014 6.8 0.102 ? 13.600 ? 576 100.000 12 1 2.850 3.040 ? 7533 ? 0.014 8.8 0.082 ? 13.500 ? 558 100.000 13 1 3.040 3.290 ? 6659 ? 0.014 10.4 0.064 ? 13.100 ? 509 100.000 14 1 3.290 3.600 ? 6127 ? 0.014 12.0 0.053 ? 12.600 ? 485 100.000 15 1 3.600 4.020 ? 5124 ? 0.014 12.2 0.054 ? 12.100 ? 422 100.000 16 1 4.020 4.650 ? 5359 ? 0.014 10.3 0.058 ? 13.800 ? 387 100.000 17 1 4.650 5.690 ? 4672 ? 0.014 10.3 0.057 ? 13.800 ? 339 100.000 18 1 5.690 8.050 ? 3509 ? 0.014 14.8 0.044 ? 13.300 ? 264 100.000 19 1 8.050 28.911 ? 1903 ? 0.014 17.4 0.035 ? 11.900 ? 160 98.300 20 1 # _refine.ls_percent_reflns_R_free 4.7000 _refine.overall_SU_B 5.8030 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_R_Free_selection_details RANDOM _refine.overall_FOM_free_R_set ? _refine.pdbx_data_cutoff_low_absF ? _refine.entry_id 4HLB _refine.aniso_B[2][3] 0.0000 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_ML 0.0900 _refine.pdbx_ls_sigma_I ? _refine.aniso_B[1][3] 0.0000 _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.aniso_B[3][3] -1.6100 _refine.occupancy_max 1.000 _refine.ls_number_restraints ? _refine.aniso_B[1][1] 0.4900 _refine.pdbx_overall_ESU_R 0.1170 _refine.ls_R_factor_obs 0.1966 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_starting_model ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_method_to_determine_struct MAD _refine.solvent_model_param_ksol ? _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.correlation_coeff_Fo_to_Fc 0.9580 _refine.ls_number_reflns_R_free 562 _refine.correlation_coeff_Fo_to_Fc_free 0.9490 _refine.pdbx_ls_sigma_F 0.000 _refine.ls_percent_reflns_obs 99.9700 _refine.ls_R_factor_R_work 0.1953 _refine.overall_SU_R_free ? _refine.ls_d_res_high 1.8000 _refine.pdbx_overall_ESU_R_Free 0.1120 _refine.B_iso_min 16.980 _refine.occupancy_min 0.500 _refine.B_iso_mean 33.7023 _refine.pdbx_stereochem_target_val_spec_case ? _refine.ls_R_factor_all ? _refine.aniso_B[2][2] 0.4900 _refine.B_iso_max 118.950 _refine.ls_d_res_low 28.910 _refine.pdbx_overall_phase_error ? _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.aniso_B[1][2] 0.4900 _refine.ls_R_factor_R_free 0.2228 _refine.ls_R_factor_R_free_error ? _refine.ls_number_reflns_obs 11834 _refine.overall_FOM_work_R_set ? _refine.ls_number_parameters ? _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.SODIUM (NA) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO THE STRUCTURE ; _refine.ls_number_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.solvent_model_param_bsol ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _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 751 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 72 _refine_hist.number_atoms_total 824 _refine_hist.d_res_high 1.8000 _refine_hist.d_res_low 28.910 # 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 785 0.010 0.019 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 760 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1059 1.361 1.973 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 1736 0.732 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 98 5.462 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 41 30.821 21.707 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 137 13.990 15.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg 12 18.443 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 118 0.078 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 893 0.005 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 191 0.001 0.020 ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.d_res_high 1.8000 _refine_ls_shell.d_res_low 1.8470 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 100.0000 _refine_ls_shell.number_reflns_R_work 814 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.3110 _refine_ls_shell.R_factor_R_free 0.3570 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 32 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 846 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.title ;Crystal structure of an alpha-lytic protease prodomain-like protein (DESPIG_01740) from Desulfovibrio piger ATCC 29098 at 1.80 A resolution ; _struct.entry_id 4HLB _struct.pdbx_model_type_details ? _struct.pdbx_model_details ? _struct.pdbx_CASP_flag Y # _struct_keywords.pdbx_keywords 'STRUCTURAL GENOMICS, UNKNOWN FUNCTION' _struct_keywords.text ;Alpha-lytic protease prodomain-like fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION ; _struct_keywords.entry_id 4HLB # 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 PHE A 25 ? ALA A 37 ? PHE A 48 ALA A 60 1 ? 13 HELX_P HELX_P2 2 THR A 65 ? GLY A 85 ? THR A 88 GLY A 108 1 ? 21 # _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 covale1 covale both ? A LYS 63 C ? ? ? 1_555 A MSE 64 N ? ? A LYS 86 A MSE 87 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale2 covale both ? A MSE 64 C ? ? ? 1_555 A THR 65 N ? ? A MSE 87 A THR 88 1_555 ? ? ? ? ? ? ? 1.337 ? ? metalc1 metalc ? ? A VAL 44 O ? ? ? 1_555 B NA . NA ? ? A VAL 67 A NA 201 1_555 ? ? ? ? ? ? ? 2.428 ? ? metalc2 metalc ? ? B NA . NA ? ? ? 1_555 C HOH . O ? ? A NA 201 A HOH 304 1_555 ? ? ? ? ? ? ? 2.568 ? ? metalc3 metalc ? ? B NA . NA ? ? ? 1_555 C HOH . O ? ? A NA 201 A HOH 311 1_555 ? ? ? ? ? ? ? 2.664 ? ? metalc4 metalc ? ? B NA . NA ? ? ? 1_555 C HOH . O ? ? A NA 201 A HOH 313 1_555 ? ? ? ? ? ? ? 2.314 ? ? metalc5 metalc ? ? B NA . NA ? ? ? 1_555 C HOH . O ? ? A NA 201 A HOH 346 1_555 ? ? ? ? ? ? ? 2.386 ? ? metalc6 metalc ? ? B NA . NA ? ? ? 1_555 C HOH . O ? ? A NA 201 A HOH 365 1_555 ? ? ? ? ? ? ? 2.548 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? # _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 ? anti-parallel A 2 3 ? parallel A 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ILE A 41 ? ALA A 48 ? ILE A 64 ALA A 71 A 2 ILE A 53 ? ALA A 59 ? ILE A 76 ALA A 82 A 3 ILE A 92 ? TYR A 98 ? ILE A 115 TYR A 121 A 4 ARG A 107 ? ARG A 115 ? ARG A 130 ARG A 138 # 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 ARG A 42 ? N ARG A 65 O VAL A 58 ? O VAL A 81 A 2 3 N PHE A 57 ? N PHE A 80 O VAL A 95 ? O VAL A 118 A 3 4 N TYR A 98 ? N TYR A 121 O ARG A 107 ? O ARG A 130 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id NA _struct_site.pdbx_auth_seq_id 201 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE NA A 201' # 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 6 VAL A 44 ? VAL A 67 . ? 1_555 ? 2 AC1 6 HOH C . ? HOH A 304 . ? 1_555 ? 3 AC1 6 HOH C . ? HOH A 311 . ? 1_555 ? 4 AC1 6 HOH C . ? HOH A 313 . ? 1_555 ? 5 AC1 6 HOH C . ? HOH A 346 . ? 1_555 ? 6 AC1 6 HOH C . ? HOH A 365 . ? 1_555 ? # _atom_sites.entry_id 4HLB _atom_sites.fract_transf_matrix[1][1] 0.017295 _atom_sites.fract_transf_matrix[1][2] 0.009985 _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] 0.019970 _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] 0.015652 _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 NA O SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 ? ? ? A . n A 1 2 ALA 2 25 ? ? ? A . n A 1 3 GLU 3 26 ? ? ? A . n A 1 4 GLN 4 27 ? ? ? A . n A 1 5 GLN 5 28 ? ? ? A . n A 1 6 ALA 6 29 ? ? ? A . n A 1 7 ASP 7 30 ? ? ? A . n A 1 8 THR 8 31 ? ? ? A . n A 1 9 VAL 9 32 ? ? ? A . n A 1 10 THR 10 33 ? ? ? A . n A 1 11 GLU 11 34 ? ? ? A . n A 1 12 ASN 12 35 ? ? ? A . n A 1 13 SER 13 36 ? ? ? A . n A 1 14 ASP 14 37 ? ? ? A . n A 1 15 SER 15 38 ? ? ? A . n A 1 16 GLU 16 39 ? ? ? A . n A 1 17 VAL 17 40 ? ? ? A . n A 1 18 PHE 18 41 ? ? ? A . n A 1 19 VAL 19 42 ? ? ? A . n A 1 20 ASP 20 43 ? ? ? A . n A 1 21 ASP 21 44 44 ASP ASP A . n A 1 22 SER 22 45 45 SER SER A . n A 1 23 ASP 23 46 46 ASP ASP A . n A 1 24 ARG 24 47 47 ARG ARG A . n A 1 25 PHE 25 48 48 PHE PHE A . n A 1 26 THR 26 49 49 THR THR A . n A 1 27 ALA 27 50 50 ALA ALA A . n A 1 28 PHE 28 51 51 PHE PHE A . n A 1 29 GLU 29 52 52 GLU GLU A . n A 1 30 GLU 30 53 53 GLU GLU A . n A 1 31 GLU 31 54 54 GLU GLU A . n A 1 32 LEU 32 55 55 LEU LEU A . n A 1 33 LEU 33 56 56 LEU LEU A . n A 1 34 ALA 34 57 57 ALA ALA A . n A 1 35 ARG 35 58 58 ARG ARG A . n A 1 36 TYR 36 59 59 TYR TYR A . n A 1 37 ALA 37 60 60 ALA ALA A . n A 1 38 ASP 38 61 61 ASP ASP A . n A 1 39 LYS 39 62 62 LYS LYS A . n A 1 40 GLY 40 63 63 GLY GLY A . n A 1 41 ILE 41 64 64 ILE ILE A . n A 1 42 ARG 42 65 65 ARG ARG A . n A 1 43 SER 43 66 66 SER SER A . n A 1 44 VAL 44 67 67 VAL VAL A . n A 1 45 ASP 45 68 68 ASP ASP A . n A 1 46 VAL 46 69 69 VAL VAL A . n A 1 47 ALA 47 70 70 ALA ALA A . n A 1 48 ALA 48 71 71 ALA ALA A . n A 1 49 TYR 49 72 72 TYR TYR A . n A 1 50 ALA 50 73 73 ALA ALA A . n A 1 51 LYS 51 74 74 LYS LYS A . n A 1 52 GLY 52 75 75 GLY GLY A . n A 1 53 ILE 53 76 76 ILE ILE A . n A 1 54 ASP 54 77 77 ASP ASP A . n A 1 55 ILE 55 78 78 ILE ILE A . n A 1 56 VAL 56 79 79 VAL VAL A . n A 1 57 PHE 57 80 80 PHE PHE A . n A 1 58 VAL 58 81 81 VAL VAL A . n A 1 59 ALA 59 82 82 ALA ALA A . n A 1 60 ALA 60 83 83 ALA ALA A . n A 1 61 ASP 61 84 84 ASP ASP A . n A 1 62 ARG 62 85 85 ARG ARG A . n A 1 63 LYS 63 86 86 LYS LYS A . n A 1 64 MSE 64 87 87 MSE MSE A . n A 1 65 THR 65 88 88 THR THR A . n A 1 66 ARG 66 89 89 ARG ARG A . n A 1 67 ALA 67 90 90 ALA ALA A . n A 1 68 GLU 68 91 91 GLU GLU A . n A 1 69 PHE 69 92 92 PHE PHE A . n A 1 70 SER 70 93 93 SER SER A . n A 1 71 ALA 71 94 94 ALA ALA A . n A 1 72 ILE 72 95 95 ILE ILE A . n A 1 73 ALA 73 96 96 ALA ALA A . n A 1 74 SER 74 97 97 SER SER A . n A 1 75 ARG 75 98 98 ARG ARG A . n A 1 76 SER 76 99 99 SER SER A . n A 1 77 ILE 77 100 100 ILE ILE A . n A 1 78 ARG 78 101 101 ARG ARG A . n A 1 79 GLU 79 102 102 GLU GLU A . n A 1 80 LEU 80 103 103 LEU LEU A . n A 1 81 LYS 81 104 104 LYS LYS A . n A 1 82 GLU 82 105 105 GLU GLU A . n A 1 83 ARG 83 106 106 ARG ARG A . n A 1 84 PHE 84 107 107 PHE PHE A . n A 1 85 GLY 85 108 108 GLY GLY A . n A 1 86 PHE 86 109 109 PHE PHE A . n A 1 87 ASP 87 110 110 ASP ASP A . n A 1 88 LYS 88 111 111 LYS LYS A . n A 1 89 ASP 89 112 112 ASP ASP A . n A 1 90 VAL 90 113 113 VAL VAL A . n A 1 91 PRO 91 114 114 PRO PRO A . n A 1 92 ILE 92 115 115 ILE ILE A . n A 1 93 GLY 93 116 116 GLY GLY A . n A 1 94 ALA 94 117 117 ALA ALA A . n A 1 95 VAL 95 118 118 VAL VAL A . n A 1 96 LEU 96 119 119 LEU LEU A . n A 1 97 ASP 97 120 120 ASP ASP A . n A 1 98 TYR 98 121 121 TYR TYR A . n A 1 99 LYS 99 122 122 LYS LYS A . n A 1 100 LYS 100 123 123 LYS LYS A . n A 1 101 ASP 101 124 124 ASP ASP A . n A 1 102 ALA 102 125 125 ALA ALA A . n A 1 103 ALA 103 126 126 ALA ALA A . n A 1 104 THR 104 127 127 THR THR A . n A 1 105 ASP 105 128 128 ASP ASP A . n A 1 106 THR 106 129 129 THR THR A . n A 1 107 ARG 107 130 130 ARG ARG A . n A 1 108 THR 108 131 131 THR THR A . n A 1 109 ARG 109 132 132 ARG ARG A . n A 1 110 PHE 110 133 133 PHE PHE A . n A 1 111 VAL 111 134 134 VAL VAL A . n A 1 112 LEU 112 135 135 LEU LEU A . n A 1 113 LYS 113 136 136 LYS LYS A . n A 1 114 LEU 114 137 137 LEU LEU A . n A 1 115 ARG 115 138 138 ARG ARG A . n # _pdbx_SG_project.project_name PSI:Biology _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.initial_of_center JCSG _pdbx_SG_project.id 1 # 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 NA 1 201 139 NA NA A . C 3 HOH 1 301 140 HOH HOH A . C 3 HOH 2 302 141 HOH HOH A . C 3 HOH 3 303 142 HOH HOH A . C 3 HOH 4 304 143 HOH HOH A . C 3 HOH 5 305 144 HOH HOH A . C 3 HOH 6 306 145 HOH HOH A . C 3 HOH 7 307 146 HOH HOH A . C 3 HOH 8 308 147 HOH HOH A . C 3 HOH 9 309 148 HOH HOH A . C 3 HOH 10 310 149 HOH HOH A . C 3 HOH 11 311 150 HOH HOH A . C 3 HOH 12 312 151 HOH HOH A . C 3 HOH 13 313 152 HOH HOH A . C 3 HOH 14 314 153 HOH HOH A . C 3 HOH 15 315 154 HOH HOH A . C 3 HOH 16 316 155 HOH HOH A . C 3 HOH 17 317 156 HOH HOH A . C 3 HOH 18 318 157 HOH HOH A . C 3 HOH 19 319 158 HOH HOH A . C 3 HOH 20 320 159 HOH HOH A . C 3 HOH 21 321 160 HOH HOH A . C 3 HOH 22 322 161 HOH HOH A . C 3 HOH 23 323 162 HOH HOH A . C 3 HOH 24 324 163 HOH HOH A . C 3 HOH 25 325 164 HOH HOH A . C 3 HOH 26 326 165 HOH HOH A . C 3 HOH 27 327 166 HOH HOH A . C 3 HOH 28 328 167 HOH HOH A . C 3 HOH 29 329 168 HOH HOH A . C 3 HOH 30 330 169 HOH HOH A . C 3 HOH 31 331 170 HOH HOH A . C 3 HOH 32 332 171 HOH HOH A . C 3 HOH 33 333 172 HOH HOH A . C 3 HOH 34 334 173 HOH HOH A . C 3 HOH 35 335 174 HOH HOH A . C 3 HOH 36 336 175 HOH HOH A . C 3 HOH 37 337 176 HOH HOH A . C 3 HOH 38 338 177 HOH HOH A . C 3 HOH 39 339 178 HOH HOH A . C 3 HOH 40 340 179 HOH HOH A . C 3 HOH 41 341 180 HOH HOH A . C 3 HOH 42 342 181 HOH HOH A . C 3 HOH 43 343 182 HOH HOH A . C 3 HOH 44 344 183 HOH HOH A . C 3 HOH 45 345 184 HOH HOH A . C 3 HOH 46 346 185 HOH HOH A . C 3 HOH 47 347 186 HOH HOH A . C 3 HOH 48 348 187 HOH HOH A . C 3 HOH 49 349 188 HOH HOH A . C 3 HOH 50 350 189 HOH HOH A . C 3 HOH 51 351 190 HOH HOH A . C 3 HOH 52 352 191 HOH HOH A . C 3 HOH 53 353 192 HOH HOH A . C 3 HOH 54 354 193 HOH HOH A . C 3 HOH 55 355 194 HOH HOH A . C 3 HOH 56 356 195 HOH HOH A . C 3 HOH 57 357 196 HOH HOH A . C 3 HOH 58 358 197 HOH HOH A . C 3 HOH 59 359 198 HOH HOH A . C 3 HOH 60 360 199 HOH HOH A . C 3 HOH 61 361 200 HOH HOH A . C 3 HOH 62 362 201 HOH HOH A . C 3 HOH 63 363 202 HOH HOH A . C 3 HOH 64 364 203 HOH HOH A . C 3 HOH 65 365 204 HOH HOH A . C 3 HOH 66 366 205 HOH HOH A . C 3 HOH 67 367 206 HOH HOH A . C 3 HOH 68 368 207 HOH HOH A . C 3 HOH 69 369 208 HOH HOH A . C 3 HOH 70 370 209 HOH HOH A . C 3 HOH 71 371 210 HOH HOH A . C 3 HOH 72 372 211 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id MSE _pdbx_struct_mod_residue.label_seq_id 64 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id MSE _pdbx_struct_mod_residue.auth_seq_id 87 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id MET _pdbx_struct_mod_residue.details 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,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_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? A VAL 44 ? A VAL 67 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 304 ? 1_555 92.8 ? 2 O ? A VAL 44 ? A VAL 67 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 311 ? 1_555 79.3 ? 3 O ? C HOH . ? A HOH 304 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 311 ? 1_555 87.9 ? 4 O ? A VAL 44 ? A VAL 67 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 313 ? 1_555 81.9 ? 5 O ? C HOH . ? A HOH 304 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 313 ? 1_555 169.9 ? 6 O ? C HOH . ? A HOH 311 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 313 ? 1_555 99.5 ? 7 O ? A VAL 44 ? A VAL 67 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 346 ? 1_555 95.2 ? 8 O ? C HOH . ? A HOH 304 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 346 ? 1_555 81.6 ? 9 O ? C HOH . ? A HOH 311 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 346 ? 1_555 167.9 ? 10 O ? C HOH . ? A HOH 313 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 346 ? 1_555 90.3 ? 11 O ? A VAL 44 ? A VAL 67 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 365 ? 1_555 171.1 ? 12 O ? C HOH . ? A HOH 304 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 365 ? 1_555 92.5 ? 13 O ? C HOH . ? A HOH 311 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 365 ? 1_555 93.8 ? 14 O ? C HOH . ? A HOH 313 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 365 ? 1_555 93.8 ? 15 O ? C HOH . ? A HOH 346 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 365 ? 1_555 92.6 ? # 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 2012-12-12 2 'Structure model' 1 1 2014-12-24 3 'Structure model' 1 2 2017-11-15 4 'Structure model' 1 3 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' 'Structure summary' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' software 2 4 'Structure model' database_2 3 4 'Structure model' pdbx_struct_conn_angle 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_ref_seq_dif 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.value' 16 4 'Structure model' '_struct_conn.pdbx_dist_value' 17 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 18 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 19 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 24 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 29 4 'Structure model' '_struct_ref_seq_dif.details' 30 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 31 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 32 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 28.0085 _pdbx_refine_tls.origin_y 20.3541 _pdbx_refine_tls.origin_z 2.1180 _pdbx_refine_tls.T[1][1] 0.1133 _pdbx_refine_tls.T[2][2] 0.1001 _pdbx_refine_tls.T[3][3] 0.0368 _pdbx_refine_tls.T[1][2] 0.0115 _pdbx_refine_tls.T[1][3] -0.0115 _pdbx_refine_tls.T[2][3] -0.0067 _pdbx_refine_tls.L[1][1] 2.2336 _pdbx_refine_tls.L[2][2] 2.0216 _pdbx_refine_tls.L[3][3] 2.8619 _pdbx_refine_tls.L[1][2] 0.1440 _pdbx_refine_tls.L[1][3] -0.2320 _pdbx_refine_tls.L[2][3] -0.5632 _pdbx_refine_tls.S[1][1] -0.0516 _pdbx_refine_tls.S[2][2] -0.0044 _pdbx_refine_tls.S[3][3] 0.0560 _pdbx_refine_tls.S[1][2] 0.0049 _pdbx_refine_tls.S[1][3] 0.0109 _pdbx_refine_tls.S[2][3] -0.1521 _pdbx_refine_tls.S[2][1] -0.0463 _pdbx_refine_tls.S[3][1] -0.0792 _pdbx_refine_tls.S[3][2] -0.0399 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 44 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 138 _pdbx_refine_tls_group.selection_details ? _pdbx_refine_tls_group.beg_label_asym_id . _pdbx_refine_tls_group.beg_label_seq_id . _pdbx_refine_tls_group.end_label_asym_id . _pdbx_refine_tls_group.end_label_seq_id . _pdbx_refine_tls_group.selection ? # _phasing.method MAD # 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 SOLVE . ? program 'Tom Terwilliger' terwilliger@LANL.gov phasing http://www.solve.lanl.gov/ ? ? 4 SCALA 3.3.20 ? package 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' ? ? ? 5 REFMAC 5.7.0029 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 6 MOSFLM . ? ? ? ? 'data reduction' ? ? ? # _pdbx_entry_details.compound_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 25-138 OF THE TARGET SEQUENCE. ; _pdbx_entry_details.entry_id 4HLB _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ASP _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 124 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -173.51 _pdbx_validate_torsion.psi -178.34 # 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 SER 45 ? OG ? A SER 22 OG 2 1 Y 1 A LYS 74 ? CG ? A LYS 51 CG 3 1 Y 1 A LYS 74 ? CD ? A LYS 51 CD 4 1 Y 1 A LYS 74 ? CE ? A LYS 51 CE 5 1 Y 1 A LYS 74 ? NZ ? A LYS 51 NZ 6 1 Y 1 A LYS 136 ? CG ? A LYS 113 CG 7 1 Y 1 A LYS 136 ? CD ? A LYS 113 CD 8 1 Y 1 A LYS 136 ? CE ? A LYS 113 CE 9 1 Y 1 A LYS 136 ? NZ ? A LYS 113 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 ALA 25 ? A ALA 2 3 1 Y 1 A GLU 26 ? A GLU 3 4 1 Y 1 A GLN 27 ? A GLN 4 5 1 Y 1 A GLN 28 ? A GLN 5 6 1 Y 1 A ALA 29 ? A ALA 6 7 1 Y 1 A ASP 30 ? A ASP 7 8 1 Y 1 A THR 31 ? A THR 8 9 1 Y 1 A VAL 32 ? A VAL 9 10 1 Y 1 A THR 33 ? A THR 10 11 1 Y 1 A GLU 34 ? A GLU 11 12 1 Y 1 A ASN 35 ? A ASN 12 13 1 Y 1 A SER 36 ? A SER 13 14 1 Y 1 A ASP 37 ? A ASP 14 15 1 Y 1 A SER 38 ? A SER 15 16 1 Y 1 A GLU 39 ? A GLU 16 17 1 Y 1 A VAL 40 ? A VAL 17 18 1 Y 1 A PHE 41 ? A PHE 18 19 1 Y 1 A VAL 42 ? A VAL 19 20 1 Y 1 A ASP 43 ? A ASP 20 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 water HOH #