data_3LWC # _entry.id 3LWC # _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 3LWC pdb_00003lwc 10.2210/pdb3lwc/pdb RCSB RCSB057811 ? ? WWPDB D_1000057811 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 403814 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3LWC _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-02-23 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _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 Structural Genomics, unknown function (YP_766765.1) from Rhizobium leguminosarum BV. viciae 3841 at 1.40 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 3LWC _cell.length_a 90.663 _cell.length_b 90.663 _cell.length_c 45.129 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 12 _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 3LWC _symmetry.Int_Tables_number 179 _symmetry.space_group_name_H-M 'P 65 2 2' _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' 13053.868 1 ? ? 'sequence database residues 14-131' ? 2 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 3 non-polymer syn 1,2-ETHANEDIOL 62.068 1 ? ? ? ? 4 water nat water 18.015 59 ? ? ? ? # _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 ;GKT(MSE)K(MSE)RKFTIADASLERSPGQEADISVGNLVDERHGGPITIGYGRYAPGQSLTET(MSE)AVDDV(MSE)I VLEGRLSVSTDGETVTAGPGEIVY(MSE)PKGETVTIRSHEEGALTAYVTYPHWRPAHA ; _entity_poly.pdbx_seq_one_letter_code_can ;GKTMKMRKFTIADASLERSPGQEADISVGNLVDERHGGPITIGYGRYAPGQSLTETMAVDDVMIVLEGRLSVSTDGETVT AGPGEIVYMPKGETVTIRSHEEGALTAYVTYPHWRPAHA ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 403814 # 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 LYS n 1 3 THR n 1 4 MSE n 1 5 LYS n 1 6 MSE n 1 7 ARG n 1 8 LYS n 1 9 PHE n 1 10 THR n 1 11 ILE n 1 12 ALA n 1 13 ASP n 1 14 ALA n 1 15 SER n 1 16 LEU n 1 17 GLU n 1 18 ARG n 1 19 SER n 1 20 PRO n 1 21 GLY n 1 22 GLN n 1 23 GLU n 1 24 ALA n 1 25 ASP n 1 26 ILE n 1 27 SER n 1 28 VAL n 1 29 GLY n 1 30 ASN n 1 31 LEU n 1 32 VAL n 1 33 ASP n 1 34 GLU n 1 35 ARG n 1 36 HIS n 1 37 GLY n 1 38 GLY n 1 39 PRO n 1 40 ILE n 1 41 THR n 1 42 ILE n 1 43 GLY n 1 44 TYR n 1 45 GLY n 1 46 ARG n 1 47 TYR n 1 48 ALA n 1 49 PRO n 1 50 GLY n 1 51 GLN n 1 52 SER n 1 53 LEU n 1 54 THR n 1 55 GLU n 1 56 THR n 1 57 MSE n 1 58 ALA n 1 59 VAL n 1 60 ASP n 1 61 ASP n 1 62 VAL n 1 63 MSE n 1 64 ILE n 1 65 VAL n 1 66 LEU n 1 67 GLU n 1 68 GLY n 1 69 ARG n 1 70 LEU n 1 71 SER n 1 72 VAL n 1 73 SER n 1 74 THR n 1 75 ASP n 1 76 GLY n 1 77 GLU n 1 78 THR n 1 79 VAL n 1 80 THR n 1 81 ALA n 1 82 GLY n 1 83 PRO n 1 84 GLY n 1 85 GLU n 1 86 ILE n 1 87 VAL n 1 88 TYR n 1 89 MSE n 1 90 PRO n 1 91 LYS n 1 92 GLY n 1 93 GLU n 1 94 THR n 1 95 VAL n 1 96 THR n 1 97 ILE n 1 98 ARG n 1 99 SER n 1 100 HIS n 1 101 GLU n 1 102 GLU n 1 103 GLY n 1 104 ALA n 1 105 LEU n 1 106 THR n 1 107 ALA n 1 108 TYR n 1 109 VAL n 1 110 THR n 1 111 TYR n 1 112 PRO n 1 113 HIS n 1 114 TRP n 1 115 ARG n 1 116 PRO n 1 117 ALA n 1 118 HIS n 1 119 ALA 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 RL1159 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'bv. viciae str. 3841' _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 'Rhizobium leguminosarum' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 216596 _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 HK100 _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 Q1MK54_RHIL3 _struct_ref.pdbx_db_accession Q1MK54 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;KTMKMRKFTIADASLERSPGQEADISVGNLVDERHGGPITIGYGRYAPGQSLTETMAVDDVMIVLEGRLSVSTDGETVTA GPGEIVYMPKGETVTIRSHEEGALTAYVTYPHWRPAHA ; _struct_ref.pdbx_align_begin 14 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3LWC _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 119 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q1MK54 _struct_ref_seq.db_align_beg 14 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 131 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 14 _struct_ref_seq.pdbx_auth_seq_align_end 131 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3LWC _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 Q1MK54 _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 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 3LWC # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.05 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 40.02 _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 4.6 _exptl_crystal_grow.temp 293 _exptl_crystal_grow.pdbx_details '2.0000M ammonium sulfate, 0.1M sodium acetate pH 4.6, 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 'MARMOSAIC 325 mm CCD' _diffrn_detector.details 'Flat collimating mirror, toroid focusing mirror' _diffrn_detector.pdbx_collection_date 2009-11-06 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Double crystal monochromator' _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 0.91162 1.0 2 0.97944 1.0 3 0.97932 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL9-2 _diffrn_source.type 'SSRL BEAMLINE BL9-2' _diffrn_source.pdbx_wavelength_list 0.91162,0.97944,0.97932 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3LWC _reflns.d_resolution_high 1.40 _reflns.d_resolution_low 29.676 _reflns.number_obs 21970 _reflns.pdbx_Rmerge_I_obs 0.083 _reflns.pdbx_netI_over_sigmaI 16.370 _reflns.percent_possible_obs 99.500 _reflns.B_iso_Wilson_estimate 15.910 _reflns.observed_criterion_sigma_I -3.00 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? _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 1.40 1.45 42745 ? 3934 0.011 2.4 ? ? ? ? ? 95.90 1 1 1.45 1.51 46998 ? 4239 0.011 3.6 ? ? ? ? ? 100.00 2 1 1.51 1.58 45920 ? 4109 0.011 4.8 ? ? ? ? ? 100.00 3 1 1.58 1.66 44638 ? 3949 0.011 6.5 ? ? ? ? ? 100.00 4 1 1.66 1.76 44457 ? 3902 0.011 9.1 ? ? ? ? ? 99.90 5 1 1.76 1.90 48630 ? 4250 0.011 13.6 ? ? ? ? ? 100.00 6 1 1.90 2.09 46472 ? 4056 0.011 20.8 ? ? ? ? ? 100.00 7 1 2.09 2.39 46936 ? 4088 0.011 27.2 ? ? ? ? ? 100.00 8 1 2.39 3.01 47081 ? 4107 0.011 32.5 ? ? ? ? ? 99.90 9 1 3.01 29.676 46383 ? 4130 0.011 42.4 ? ? ? ? ? 99.70 10 1 # _refine.entry_id 3LWC _refine.ls_d_res_high 1.400 _refine.ls_d_res_low 29.676 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.860 _refine.ls_number_reflns_obs 21944 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.SULFATE IONS AND ETHYLENE GLYCOL FROM CRYSTALLIZATION/ CRYOPROTECTANT ARE MODELED IN THE STRUCTURE. ; _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.181 _refine.ls_R_factor_R_work 0.181 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.189 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.100 _refine.ls_number_reflns_R_free 1126 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 14.381 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.250 _refine.aniso_B[2][2] -0.250 _refine.aniso_B[3][3] 0.370 _refine.aniso_B[1][2] -0.120 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.961 _refine.correlation_coeff_Fo_to_Fc_free 0.960 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R 0.064 _refine.pdbx_overall_ESU_R_Free 0.060 _refine.overall_SU_ML 0.034 _refine.overall_SU_B 1.876 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _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_method_to_determine_struct MAD _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 53.83 _refine.B_iso_min 5.63 _refine.occupancy_max 1.00 _refine.occupancy_min 0.15 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _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_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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 755 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 59 _refine_hist.number_atoms_total 828 _refine_hist.d_res_high 1.400 _refine_hist.d_res_low 29.676 # loop_ _refine_ls_restr.type _refine_ls_restr.pdbx_refine_id _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 r_bond_refined_d 'X-RAY DIFFRACTION' 989 0.017 0.021 ? ? r_bond_other_d 'X-RAY DIFFRACTION' 644 0.001 0.020 ? ? r_angle_refined_deg 'X-RAY DIFFRACTION' 1361 1.687 1.992 ? ? r_angle_other_deg 'X-RAY DIFFRACTION' 1582 0.882 3.000 ? ? r_dihedral_angle_1_deg 'X-RAY DIFFRACTION' 141 8.089 5.000 ? ? r_dihedral_angle_2_deg 'X-RAY DIFFRACTION' 35 39.982 23.714 ? ? r_dihedral_angle_3_deg 'X-RAY DIFFRACTION' 156 12.860 15.000 ? ? r_dihedral_angle_4_deg 'X-RAY DIFFRACTION' 7 15.753 15.000 ? ? r_chiral_restr 'X-RAY DIFFRACTION' 154 0.100 0.200 ? ? r_gen_planes_refined 'X-RAY DIFFRACTION' 1173 0.007 0.021 ? ? r_gen_planes_other 'X-RAY DIFFRACTION' 190 0.003 0.020 ? ? r_mcbond_it 'X-RAY DIFFRACTION' 659 1.104 1.500 ? ? r_mcbond_other 'X-RAY DIFFRACTION' 268 0.289 1.500 ? ? r_mcangle_it 'X-RAY DIFFRACTION' 1073 2.026 2.000 ? ? r_scbond_it 'X-RAY DIFFRACTION' 330 3.056 3.000 ? ? r_scangle_it 'X-RAY DIFFRACTION' 288 4.828 4.500 ? ? # _refine_ls_shell.d_res_high 1.402 _refine_ls_shell.d_res_low 1.438 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 99.000 _refine_ls_shell.number_reflns_R_work 1495 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.230 _refine_ls_shell.R_factor_R_free 0.203 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 89 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1584 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3LWC _struct.title ;Crystal structure of Structural Genomics, unknown function (YP_766765.1) from Rhizobium leguminosarum BV. viciae 3841 at 1.40 A resolution ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;STRUCTURAL GENOMICS, UNKNOWN FUNCTION, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Cupin domain, ethanolamine utilization ; _struct_keywords.pdbx_keywords 'STRUCTURAL GENOMICS, UNKNOWN FUNCTION' _struct_keywords.entry_id 3LWC # 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 2 ? D N N 3 ? E N N 4 ? # _struct_biol.id 1 _struct_biol.details ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id THR _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 10 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id SER _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 19 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id THR _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 22 _struct_conf.end_auth_comp_id SER _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 31 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 10 # _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 MSE 4 C ? ? ? 1_555 A LYS 5 N ? ? A MSE 16 A LYS 17 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale2 covale both ? A LYS 5 C ? ? ? 1_555 A MSE 6 N A ? A LYS 17 A MSE 18 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale3 covale both ? A LYS 5 C ? ? ? 1_555 A MSE 6 N B ? A LYS 17 A MSE 18 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale4 covale both ? A MSE 6 C A ? ? 1_555 A ARG 7 N ? ? A MSE 18 A ARG 19 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale5 covale both ? A MSE 6 C B ? ? 1_555 A ARG 7 N ? ? A MSE 18 A ARG 19 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale6 covale both ? A THR 56 C ? ? ? 1_555 A MSE 57 N ? ? A THR 68 A MSE 69 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale7 covale both ? A MSE 57 C ? ? ? 1_555 A ALA 58 N ? ? A MSE 69 A ALA 70 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale8 covale both ? A VAL 62 C ? ? ? 1_555 A MSE 63 N A ? A VAL 74 A MSE 75 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale9 covale both ? A VAL 62 C ? ? ? 1_555 A MSE 63 N B ? A VAL 74 A MSE 75 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale10 covale both ? A MSE 63 C A ? ? 1_555 A ILE 64 N ? ? A MSE 75 A ILE 76 1_555 ? ? ? ? ? ? ? 1.319 ? ? covale11 covale both ? A MSE 63 C B ? ? 1_555 A ILE 64 N ? ? A MSE 75 A ILE 76 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale12 covale both ? A TYR 88 C ? ? ? 1_555 A MSE 89 N A ? A TYR 100 A MSE 101 1_555 ? ? ? ? ? ? ? 1.317 ? ? covale13 covale both ? A TYR 88 C ? ? ? 1_555 A MSE 89 N B ? A TYR 100 A MSE 101 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale14 covale both ? A MSE 89 C A ? ? 1_555 A PRO 90 N ? ? A MSE 101 A PRO 102 1_555 ? ? ? ? ? ? ? 1.342 ? ? covale15 covale both ? A MSE 89 C B ? ? 1_555 A PRO 90 N ? ? A MSE 101 A PRO 102 1_555 ? ? ? ? ? ? ? 1.340 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id GLY _struct_mon_prot_cis.label_seq_id 38 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id GLY _struct_mon_prot_cis.auth_seq_id 50 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 39 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 51 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -4.01 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 4 ? # 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 B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 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 GLU A 23 ? LEU A 31 ? GLU A 35 LEU A 43 A 2 ILE A 40 ? TYR A 47 ? ILE A 52 TYR A 59 A 3 THR A 94 ? TYR A 111 ? THR A 106 TYR A 123 A 4 ASP A 60 ? THR A 74 ? ASP A 72 THR A 86 A 5 GLU A 77 ? ALA A 81 ? GLU A 89 ALA A 93 B 1 SER A 52 ? THR A 56 ? SER A 64 THR A 68 B 2 THR A 94 ? TYR A 111 ? THR A 106 TYR A 123 B 3 ASP A 60 ? THR A 74 ? ASP A 72 THR A 86 B 4 ILE A 86 ? MSE A 89 ? ILE A 98 MSE A 101 # 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 LEU A 31 ? N LEU A 43 O ILE A 40 ? O ILE A 52 A 2 3 N TYR A 47 ? N TYR A 59 O ALA A 104 ? O ALA A 116 A 3 4 O LEU A 105 ? O LEU A 117 N LEU A 66 ? N LEU A 78 A 4 5 N LEU A 70 ? N LEU A 82 O ALA A 81 ? O ALA A 93 B 1 2 N LEU A 53 ? N LEU A 65 O ILE A 97 ? O ILE A 109 B 2 3 O LEU A 105 ? O LEU A 117 N LEU A 66 ? N LEU A 78 B 3 4 N ASP A 61 ? N ASP A 73 O MSE A 89 ? O MSE A 101 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _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 _struct_site.details AC1 Software A SO4 1 ? 7 'BINDING SITE FOR RESIDUE SO4 A 1' AC2 Software A SO4 2 ? 3 'BINDING SITE FOR RESIDUE SO4 A 2' AC3 Software A EDO 3 ? 4 'BINDING SITE FOR RESIDUE EDO A 3' # 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 7 LYS A 8 ? LYS A 20 . ? 4_664 ? 2 AC1 7 ARG A 69 ? ARG A 81 . ? 1_555 ? 3 AC1 7 VAL A 79 ? VAL A 91 . ? 10_665 ? 4 AC1 7 THR A 80 ? THR A 92 . ? 10_665 ? 5 AC1 7 HOH E . ? HOH A 135 . ? 1_555 ? 6 AC1 7 HOH E . ? HOH A 159 . ? 10_665 ? 7 AC1 7 HOH E . ? HOH A 180 . ? 1_555 ? 8 AC2 3 ARG A 7 ? ARG A 19 . ? 1_555 ? 9 AC2 3 GLY A 29 ? GLY A 41 . ? 1_555 ? 10 AC2 3 ASN A 30 ? ASN A 42 . ? 1_555 ? 11 AC3 4 PRO A 83 ? PRO A 95 . ? 4_665 ? 12 AC3 4 GLY A 84 ? GLY A 96 . ? 4_665 ? 13 AC3 4 HOH E . ? HOH A 132 . ? 1_555 ? 14 AC3 4 HOH E . ? HOH A 136 . ? 4_665 ? # _atom_sites.entry_id 3LWC _atom_sites.fract_transf_matrix[1][1] 0.011030 _atom_sites.fract_transf_matrix[1][2] 0.006368 _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] 0.012736 _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] 0.022159 _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 LYS 2 14 ? ? ? A . n A 1 3 THR 3 15 ? ? ? A . n A 1 4 MSE 4 16 16 MSE MSE A . n A 1 5 LYS 5 17 17 LYS LYS A . n A 1 6 MSE 6 18 18 MSE MSE A . n A 1 7 ARG 7 19 19 ARG ARG A . n A 1 8 LYS 8 20 20 LYS LYS A . n A 1 9 PHE 9 21 21 PHE PHE A . n A 1 10 THR 10 22 22 THR THR A . n A 1 11 ILE 11 23 23 ILE ILE A . n A 1 12 ALA 12 24 24 ALA ALA A . n A 1 13 ASP 13 25 25 ASP ASP A . n A 1 14 ALA 14 26 26 ALA ALA A . n A 1 15 SER 15 27 27 SER SER A . n A 1 16 LEU 16 28 28 LEU LEU A . n A 1 17 GLU 17 29 29 GLU GLU A . n A 1 18 ARG 18 30 30 ARG ARG A . n A 1 19 SER 19 31 31 SER SER A . n A 1 20 PRO 20 32 32 PRO PRO A . n A 1 21 GLY 21 33 33 GLY GLY A . n A 1 22 GLN 22 34 34 GLN GLN A . n A 1 23 GLU 23 35 35 GLU GLU A . n A 1 24 ALA 24 36 36 ALA ALA A . n A 1 25 ASP 25 37 37 ASP ASP A . n A 1 26 ILE 26 38 38 ILE ILE A . n A 1 27 SER 27 39 39 SER SER A . n A 1 28 VAL 28 40 40 VAL VAL A . n A 1 29 GLY 29 41 41 GLY GLY A . n A 1 30 ASN 30 42 42 ASN ASN A . n A 1 31 LEU 31 43 43 LEU LEU A . n A 1 32 VAL 32 44 ? ? ? A . n A 1 33 ASP 33 45 ? ? ? A . n A 1 34 GLU 34 46 ? ? ? A . n A 1 35 ARG 35 47 ? ? ? A . n A 1 36 HIS 36 48 ? ? ? A . n A 1 37 GLY 37 49 ? ? ? A . n A 1 38 GLY 38 50 50 GLY GLY A . n A 1 39 PRO 39 51 51 PRO PRO A . n A 1 40 ILE 40 52 52 ILE ILE A . n A 1 41 THR 41 53 53 THR THR A . n A 1 42 ILE 42 54 54 ILE ILE A . n A 1 43 GLY 43 55 55 GLY GLY A . n A 1 44 TYR 44 56 56 TYR TYR A . n A 1 45 GLY 45 57 57 GLY GLY A . n A 1 46 ARG 46 58 58 ARG ARG A . n A 1 47 TYR 47 59 59 TYR TYR A . n A 1 48 ALA 48 60 60 ALA ALA A . n A 1 49 PRO 49 61 61 PRO PRO A . n A 1 50 GLY 50 62 62 GLY GLY A . n A 1 51 GLN 51 63 63 GLN GLN A . n A 1 52 SER 52 64 64 SER SER A . n A 1 53 LEU 53 65 65 LEU LEU A . n A 1 54 THR 54 66 66 THR THR A . n A 1 55 GLU 55 67 67 GLU GLU A . n A 1 56 THR 56 68 68 THR THR A . n A 1 57 MSE 57 69 69 MSE MSE A . n A 1 58 ALA 58 70 70 ALA ALA A . n A 1 59 VAL 59 71 71 VAL VAL A . n A 1 60 ASP 60 72 72 ASP ASP A . n A 1 61 ASP 61 73 73 ASP ASP A . n A 1 62 VAL 62 74 74 VAL VAL A . n A 1 63 MSE 63 75 75 MSE MSE A . n A 1 64 ILE 64 76 76 ILE ILE A . n A 1 65 VAL 65 77 77 VAL VAL A . n A 1 66 LEU 66 78 78 LEU LEU A . n A 1 67 GLU 67 79 79 GLU GLU A . n A 1 68 GLY 68 80 80 GLY GLY A . n A 1 69 ARG 69 81 81 ARG ARG A . n A 1 70 LEU 70 82 82 LEU LEU A . n A 1 71 SER 71 83 83 SER SER A . n A 1 72 VAL 72 84 84 VAL VAL A . n A 1 73 SER 73 85 85 SER SER A . n A 1 74 THR 74 86 86 THR THR A . n A 1 75 ASP 75 87 87 ASP ASP A . n A 1 76 GLY 76 88 88 GLY GLY A . n A 1 77 GLU 77 89 89 GLU GLU A . n A 1 78 THR 78 90 90 THR THR A . n A 1 79 VAL 79 91 91 VAL VAL A . n A 1 80 THR 80 92 92 THR THR A . n A 1 81 ALA 81 93 93 ALA ALA A . n A 1 82 GLY 82 94 94 GLY GLY A . n A 1 83 PRO 83 95 95 PRO PRO A . n A 1 84 GLY 84 96 96 GLY GLY A . n A 1 85 GLU 85 97 97 GLU GLU A . n A 1 86 ILE 86 98 98 ILE ILE A . n A 1 87 VAL 87 99 99 VAL VAL A . n A 1 88 TYR 88 100 100 TYR TYR A . n A 1 89 MSE 89 101 101 MSE MSE A . n A 1 90 PRO 90 102 102 PRO PRO A . n A 1 91 LYS 91 103 103 LYS LYS A . n A 1 92 GLY 92 104 104 GLY GLY A . n A 1 93 GLU 93 105 105 GLU GLU A . n A 1 94 THR 94 106 106 THR THR A . n A 1 95 VAL 95 107 107 VAL VAL A . n A 1 96 THR 96 108 108 THR THR A . n A 1 97 ILE 97 109 109 ILE ILE A . n A 1 98 ARG 98 110 110 ARG ARG A . n A 1 99 SER 99 111 111 SER SER A . n A 1 100 HIS 100 112 112 HIS HIS A . n A 1 101 GLU 101 113 113 GLU GLU A . n A 1 102 GLU 102 114 114 GLU GLU A . n A 1 103 GLY 103 115 115 GLY GLY A . n A 1 104 ALA 104 116 116 ALA ALA A . n A 1 105 LEU 105 117 117 LEU LEU A . n A 1 106 THR 106 118 118 THR THR A . n A 1 107 ALA 107 119 119 ALA ALA A . n A 1 108 TYR 108 120 120 TYR TYR A . n A 1 109 VAL 109 121 121 VAL VAL A . n A 1 110 THR 110 122 122 THR THR A . n A 1 111 TYR 111 123 123 TYR TYR A . n A 1 112 PRO 112 124 124 PRO PRO A . n A 1 113 HIS 113 125 125 HIS HIS A . n A 1 114 TRP 114 126 ? ? ? A . n A 1 115 ARG 115 127 ? ? ? A . n A 1 116 PRO 116 128 ? ? ? A . n A 1 117 ALA 117 129 ? ? ? A . n A 1 118 HIS 118 130 ? ? ? A . n A 1 119 ALA 119 131 ? ? ? A . n # _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _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 SO4 1 1 1 SO4 SO4 A . C 2 SO4 1 2 2 SO4 SO4 A . D 3 EDO 1 3 3 EDO EDO A . E 4 HOH 1 4 4 HOH HOH A . E 4 HOH 2 5 5 HOH HOH A . E 4 HOH 3 6 6 HOH HOH A . E 4 HOH 4 7 7 HOH HOH A . E 4 HOH 5 8 8 HOH HOH A . E 4 HOH 6 9 9 HOH HOH A . E 4 HOH 7 10 10 HOH HOH A . E 4 HOH 8 11 11 HOH HOH A . E 4 HOH 9 12 12 HOH HOH A . E 4 HOH 10 132 13 HOH HOH A . E 4 HOH 11 133 14 HOH HOH A . E 4 HOH 12 134 15 HOH HOH A . E 4 HOH 13 135 16 HOH HOH A . E 4 HOH 14 136 17 HOH HOH A . E 4 HOH 15 137 18 HOH HOH A . E 4 HOH 16 138 19 HOH HOH A . E 4 HOH 17 139 20 HOH HOH A . E 4 HOH 18 140 21 HOH HOH A . E 4 HOH 19 141 22 HOH HOH A . E 4 HOH 20 142 23 HOH HOH A . E 4 HOH 21 143 24 HOH HOH A . E 4 HOH 22 144 25 HOH HOH A . E 4 HOH 23 145 26 HOH HOH A . E 4 HOH 24 146 27 HOH HOH A . E 4 HOH 25 147 28 HOH HOH A . E 4 HOH 26 148 29 HOH HOH A . E 4 HOH 27 149 30 HOH HOH A . E 4 HOH 28 150 31 HOH HOH A . E 4 HOH 29 151 32 HOH HOH A . E 4 HOH 30 152 33 HOH HOH A . E 4 HOH 31 153 34 HOH HOH A . E 4 HOH 32 154 35 HOH HOH A . E 4 HOH 33 155 36 HOH HOH A . E 4 HOH 34 156 37 HOH HOH A . E 4 HOH 35 157 38 HOH HOH A . E 4 HOH 36 158 39 HOH HOH A . E 4 HOH 37 159 40 HOH HOH A . E 4 HOH 38 160 41 HOH HOH A . E 4 HOH 39 161 42 HOH HOH A . E 4 HOH 40 162 43 HOH HOH A . E 4 HOH 41 163 44 HOH HOH A . E 4 HOH 42 164 45 HOH HOH A . E 4 HOH 43 165 46 HOH HOH A . E 4 HOH 44 166 47 HOH HOH A . E 4 HOH 45 167 48 HOH HOH A . E 4 HOH 46 168 49 HOH HOH A . E 4 HOH 47 169 50 HOH HOH A . E 4 HOH 48 170 51 HOH HOH A . E 4 HOH 49 171 52 HOH HOH A . E 4 HOH 50 172 53 HOH HOH A . E 4 HOH 51 173 54 HOH HOH A . E 4 HOH 52 174 55 HOH HOH A . E 4 HOH 53 175 56 HOH HOH A . E 4 HOH 54 176 57 HOH HOH A . E 4 HOH 55 177 58 HOH HOH A . E 4 HOH 56 178 59 HOH HOH A . E 4 HOH 57 179 60 HOH HOH A . E 4 HOH 58 180 61 HOH HOH A . E 4 HOH 59 181 62 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 4 A MSE 16 ? MET SELENOMETHIONINE 2 A MSE 6 A MSE 18 ? MET SELENOMETHIONINE 3 A MSE 57 A MSE 69 ? MET SELENOMETHIONINE 4 A MSE 63 A MSE 75 ? MET SELENOMETHIONINE 5 A MSE 89 A MSE 101 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3770 ? 1 MORE -65 ? 1 'SSA (A^2)' 9450 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 7_555 y,x,-z+2/3 -0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 30.0860000000 # 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 2010-04-07 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-08 4 'Structure model' 1 3 2019-07-17 5 'Structure model' 1 4 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' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Refinement description' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' 'Database references' 8 5 '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' software 3 4 'Structure model' struct_conn 4 5 'Structure model' database_2 5 5 'Structure model' struct_ref_seq_dif 6 5 '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' '_software.classification' 4 4 'Structure model' '_software.contact_author' 5 4 'Structure model' '_software.contact_author_email' 6 4 'Structure model' '_software.language' 7 4 'Structure model' '_software.location' 8 4 'Structure model' '_software.name' 9 4 'Structure model' '_software.type' 10 4 'Structure model' '_software.version' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 5 'Structure model' '_database_2.pdbx_DOI' 13 5 'Structure model' '_database_2.pdbx_database_accession' 14 5 'Structure model' '_struct_ref_seq_dif.details' 15 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 5 '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 19.7004 _pdbx_refine_tls.origin_y 52.9889 _pdbx_refine_tls.origin_z 16.5822 _pdbx_refine_tls.T[1][1] 0.0366 _pdbx_refine_tls.T[2][2] 0.0222 _pdbx_refine_tls.T[3][3] 0.0320 _pdbx_refine_tls.T[1][2] -0.0044 _pdbx_refine_tls.T[1][3] 0.0074 _pdbx_refine_tls.T[2][3] -0.0161 _pdbx_refine_tls.L[1][1] 0.8250 _pdbx_refine_tls.L[2][2] 0.6112 _pdbx_refine_tls.L[3][3] 0.5996 _pdbx_refine_tls.L[1][2] -0.4665 _pdbx_refine_tls.L[1][3] -0.0150 _pdbx_refine_tls.L[2][3] -0.1995 _pdbx_refine_tls.S[1][1] 0.0244 _pdbx_refine_tls.S[2][2] -0.0216 _pdbx_refine_tls.S[3][3] -0.0028 _pdbx_refine_tls.S[1][2] -0.0642 _pdbx_refine_tls.S[1][3] 0.0456 _pdbx_refine_tls.S[2][3] -0.0388 _pdbx_refine_tls.S[2][1] -0.0107 _pdbx_refine_tls.S[3][1] -0.0521 _pdbx_refine_tls.S[3][2] 0.0322 # _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 16 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 125 _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.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal REFMAC 5.5.0053 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SHELX . ? package 'George M. Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 3 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 4 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? ? 5 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 XDS . ? ? ? ? 'data reduction' ? ? ? 7 SHELXD . ? ? ? ? phasing ? ? ? 8 autoSHARP . ? ? ? ? phasing ? ? ? 9 # _pdbx_entry_details.entry_id 3LWC _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 14-131 OF THE FULL LENGTH PROTEIN. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CD _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 GLU _pdbx_validate_rmsd_bond.auth_seq_id_1 29 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 A _pdbx_validate_rmsd_bond.auth_atom_id_2 OE1 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 GLU _pdbx_validate_rmsd_bond.auth_seq_id_2 29 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 A _pdbx_validate_rmsd_bond.bond_value 1.327 _pdbx_validate_rmsd_bond.bond_target_value 1.252 _pdbx_validate_rmsd_bond.bond_deviation 0.075 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.011 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 SER A 27 ? A 37.55 51.61 2 1 SER A 27 ? B 71.18 44.73 3 1 LEU A 28 ? B -53.65 28.26 4 1 GLU A 29 ? B -141.38 -24.58 5 1 ARG A 30 ? B -55.04 -1.09 6 1 GLU A 35 ? A -170.26 132.55 7 1 ALA A 36 ? B -164.46 118.68 8 1 SER A 64 ? B -173.85 149.21 9 1 ASP A 87 ? A 49.59 -121.02 # 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 MSE 16 ? CG ? A MSE 4 CG 2 1 Y 1 A MSE 16 ? SE ? A MSE 4 SE 3 1 Y 1 A MSE 16 ? CE ? A MSE 4 CE 4 1 Y 1 A LYS 17 ? CG ? A LYS 5 CG 5 1 Y 1 A LYS 17 ? CD ? A LYS 5 CD 6 1 Y 1 A LYS 17 ? CE ? A LYS 5 CE 7 1 Y 1 A LYS 17 ? NZ ? A LYS 5 NZ 8 1 Y 1 A GLU 67 ? CG ? A GLU 55 CG 9 1 Y 1 A GLU 67 ? CD ? A GLU 55 CD 10 1 Y 1 A GLU 67 ? OE1 ? A GLU 55 OE1 11 1 Y 1 A GLU 67 ? OE2 ? A GLU 55 OE2 12 1 Y 1 A ASP 87 ? CG ? A ASP 75 CG 13 1 Y 1 A ASP 87 ? OD1 ? A ASP 75 OD1 14 1 Y 1 A ASP 87 ? OD2 ? A ASP 75 OD2 15 1 Y 1 A GLU 89 ? CG ? A GLU 77 CG 16 1 Y 1 A GLU 89 ? CD ? A GLU 77 CD 17 1 Y 1 A GLU 89 ? OE1 ? A GLU 77 OE1 18 1 Y 1 A GLU 89 ? OE2 ? A GLU 77 OE2 19 1 Y 1 A GLU 114 ? CD ? A GLU 102 CD 20 1 Y 1 A GLU 114 ? OE1 ? A GLU 102 OE1 21 1 Y 1 A GLU 114 ? OE2 ? A GLU 102 OE2 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLY 0 ? A GLY 1 2 1 Y 1 A LYS 14 ? A LYS 2 3 1 Y 1 A THR 15 ? A THR 3 4 1 Y 1 A VAL 44 ? A VAL 32 5 1 Y 1 A ASP 45 ? A ASP 33 6 1 Y 1 A GLU 46 ? A GLU 34 7 1 Y 1 A ARG 47 ? A ARG 35 8 1 Y 1 A HIS 48 ? A HIS 36 9 1 Y 1 A GLY 49 ? A GLY 37 10 1 Y 1 A TRP 126 ? A TRP 114 11 1 Y 1 A ARG 127 ? A ARG 115 12 1 Y 1 A PRO 128 ? A PRO 116 13 1 Y 1 A ALA 129 ? A ALA 117 14 1 Y 1 A HIS 130 ? A HIS 118 15 1 Y 1 A ALA 131 ? A ALA 119 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 1,2-ETHANEDIOL EDO 4 water HOH #